data_50242 ####################### # Entry information # ####################### save_entry_information_1 _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information_1 _Entry.ID 50242 _Entry.Title ; Chemical shifts for [r(UGGUGG)d(U)]4 G-quadruplex ; _Entry.Type macromolecule _Entry.Version_type original _Entry.Submission_date 2020-04-22 _Entry.Accession_date 2020-04-22 _Entry.Last_release_date 2020-04-22 _Entry.Original_release_date 2020-04-22 _Entry.Origination author _Entry.Format_name . _Entry.NMR_STAR_version 3.2.6.0 _Entry.NMR_STAR_dict_location . _Entry.Original_NMR_STAR_version 3.1 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype solution _Entry.Source_data_format . _Entry.Source_data_format_version . _Entry.Generated_software_name . _Entry.Generated_software_version . _Entry.Generated_software_ID . _Entry.Generated_software_label . _Entry.Generated_date . _Entry.DOI . _Entry.UUID . _Entry.Related_coordinate_file_name . _Entry.Details . _Entry.BMRB_internal_directory_name . loop_ _Entry_author.Ordinal _Entry_author.Given_name _Entry_author.Family_name _Entry_author.First_initial _Entry_author.Middle_initials _Entry_author.Family_title _Entry_author.ORCID _Entry_author.Entry_ID 1 Witold Andralojc . . . . 50242 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID assigned_chemical_shifts 1 50242 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID '1H chemical shifts' 52 50242 '31P chemical shifts' 6 50242 stop_ loop_ _Release.Release_number _Release.Format_type _Release.Format_version _Release.Date _Release.Submission_date _Release.Type _Release.Author _Release.Detail _Release.Entry_ID 1 . . 2020-05-20 . original BMRB . 50242 stop_ loop_ _Related_entries.Database_name _Related_entries.Database_accession_code _Related_entries.Relationship _Related_entries.Entry_ID BMRB 50244 "[r(UGGUGG)(2'OMeU)]4 G-quadruplex" 50242 BMRB 50245 '[r(UGGUGGC)]4 G-quadruplex' 50242 BMRB 50246 '[r(UGGUGGT)]4 G-quadruplex' 50242 BMRB 50247 '[r(UGGUGG)d(T)]4 G-quadruplex' 50242 BMRB 50248 '[r(UGGUGG)(LNA-T)]4 G-quadruplex' 50242 BMRB 50249 '[r(UGGUGGPs)]4 G-quadruplex' 50242 stop_ save_ ############### # Citations # ############### save_citations_1 _Citation.Sf_category citations _Citation.Sf_framecode citations_1 _Citation.Entry_ID 50242 _Citation.ID 1 _Citation.Name . _Citation.Class 'entry citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.PubMed_ID . _Citation.DOI . _Citation.Full_citation . _Citation.Title ; The origin of the high stability of 3'-terminal uridine tetrads. The contributions of hydrogen bonding, stacking interactions and steric factors evaluated using modified oligonucleotide analogs. ; _Citation.Status 'in preparation' _Citation.Type journal _Citation.Journal_abbrev 'Not known' _Citation.Journal_name_full . _Citation.Journal_volume . _Citation.Journal_issue . _Citation.Journal_ASTM . _Citation.Journal_ISSN . _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first . _Citation.Page_last . _Citation.Year . _Citation.Details . loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.ORCID _Citation_author.Entry_ID _Citation_author.Citation_ID 1 Witold Andralojc . . . . 50242 1 2 Karol Pasternak . . . . 50242 1 3 Joanna Sarzynska . . . . 50242 1 4 Karolina Zielinska . . . . 50242 1 5 Ryszard Kierzek . . . . 50242 1 6 Zofia Gdaniec . . . . 50242 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly_1 _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly_1 _Assembly.Entry_ID 50242 _Assembly.ID 1 _Assembly.Name '[r(UGGUGG)d(U)]4 G-quadruplex' _Assembly.BMRB_code . _Assembly.Number_of_components 1 _Assembly.Organic_ligands 0 _Assembly.Metal_ions 0 _Assembly.Non_standard_bonds no _Assembly.Ambiguous_conformational_states no _Assembly.Ambiguous_chem_comp_sites . _Assembly.Molecules_in_chemical_exchange no _Assembly.Paramagnetic no _Assembly.Thiol_state . _Assembly.Molecular_mass . _Assembly.Enzyme_commission_number . _Assembly.Details . _Assembly.DB_query_date . _Assembly.DB_query_revised_last_date . loop_ _Entity_assembly.ID _Entity_assembly.Entity_assembly_name _Entity_assembly.Entity_ID _Entity_assembly.Entity_label _Entity_assembly.Asym_ID _Entity_assembly.PDB_chain_ID _Entity_assembly.Experimental_data_reported _Entity_assembly.Physical_state _Entity_assembly.Conformational_isomer _Entity_assembly.Chemical_exchange_state _Entity_assembly.Magnetic_equivalence_group_code _Entity_assembly.Role _Entity_assembly.Details _Entity_assembly.Entry_ID _Entity_assembly.Assembly_ID 1 '[r(UGGUGG)d(U)]4 G-quadruplex' 1 $entity_1 . . yes native no no . . . 50242 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_entity_1 _Entity.Sf_category entity _Entity.Sf_framecode entity_1 _Entity.Entry_ID 50242 _Entity.ID 1 _Entity.BMRB_code . _Entity.Name entity_1 _Entity.Type polymer _Entity.Polymer_common_type . _Entity.Polymer_type polyribonucleotide _Entity.Polymer_type_details . _Entity.Polymer_strand_ID . _Entity.Polymer_seq_one_letter_code_can . _Entity.Polymer_seq_one_letter_code ; UGGUGGX ; _Entity.Target_identifier . _Entity.Polymer_author_defined_seq . _Entity.Polymer_author_seq_details . _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_monomer yes _Entity.Nstd_chirality no _Entity.Nstd_linkage no _Entity.Nonpolymer_comp_ID . _Entity.Nonpolymer_comp_label . _Entity.Number_of_monomers 7 _Entity.Number_of_nonpolymer_components . _Entity.Paramagnetic no _Entity.Thiol_state 'not present' _Entity.Src_method . _Entity.Parent_entity_ID 1 _Entity.Fragment . _Entity.Mutation . _Entity.EC_number . _Entity.Calc_isoelectric_point . _Entity.Formula_weight . _Entity.Formula_weight_exptl . _Entity.Formula_weight_exptl_meth . _Entity.Details . _Entity.DB_query_date . _Entity.DB_query_revised_last_date . loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 . U . 50242 1 2 . G . 50242 1 3 . G . 50242 1 4 . U . 50242 1 5 . G . 50242 1 6 . G . 50242 1 7 . DU . 50242 1 stop_ loop_ _Entity_poly_seq.Hetero _Entity_poly_seq.Mon_ID _Entity_poly_seq.Num _Entity_poly_seq.Comp_index_ID _Entity_poly_seq.Entry_ID _Entity_poly_seq.Entity_ID . U 1 1 50242 1 . G 2 2 50242 1 . G 3 3 50242 1 . U 4 4 50242 1 . G 5 5 50242 1 . G 6 6 50242 1 . DU 7 7 50242 1 stop_ save_ #################### # Natural source # #################### save_natural_source_1 _Entity_natural_src_list.Sf_category natural_source _Entity_natural_src_list.Sf_framecode natural_source_1 _Entity_natural_src_list.Entry_ID 50242 _Entity_natural_src_list.ID 1 loop_ _Entity_natural_src.ID _Entity_natural_src.Entity_ID _Entity_natural_src.Entity_label _Entity_natural_src.Entity_chimera_segment_ID _Entity_natural_src.NCBI_taxonomy_ID _Entity_natural_src.Type _Entity_natural_src.Common _Entity_natural_src.Organism_name_scientific _Entity_natural_src.Organism_name_common _Entity_natural_src.Organism_acronym _Entity_natural_src.ICTVdb_decimal_code _Entity_natural_src.Superkingdom _Entity_natural_src.Kingdom _Entity_natural_src.Genus _Entity_natural_src.Species _Entity_natural_src.Strain _Entity_natural_src.Variant _Entity_natural_src.Organ _Entity_natural_src.Tissue _Entity_natural_src.Tissue_fraction _Entity_natural_src.Cell_line _Entity_natural_src.Cell_type _Entity_natural_src.ATCC_number _Entity_natural_src.Organelle _Entity_natural_src.Secretion _Entity_natural_src.Plasmid _Entity_natural_src.Gene_mnemonic _Entity_natural_src.Details _Entity_natural_src.Entry_ID _Entity_natural_src.Entity_natural_src_list_ID 1 1 $entity_1 . . 'no natural source' . . . . . . . . . . . . . . . . . . . . . . 50242 1 stop_ save_ ######################### # Experimental source # ######################### save_experimental_source_1 _Entity_experimental_src_list.Sf_category experimental_source _Entity_experimental_src_list.Sf_framecode experimental_source_1 _Entity_experimental_src_list.Entry_ID 50242 _Entity_experimental_src_list.ID 1 loop_ _Entity_experimental_src.ID _Entity_experimental_src.Entity_ID _Entity_experimental_src.Entity_label _Entity_experimental_src.Entity_chimera_segment_ID _Entity_experimental_src.Production_method _Entity_experimental_src.Host_org_scientific_name _Entity_experimental_src.Host_org_name_common _Entity_experimental_src.Host_org_details _Entity_experimental_src.Host_org_NCBI_taxonomy_ID _Entity_experimental_src.Host_org_genus _Entity_experimental_src.Host_org_species _Entity_experimental_src.Host_org_strain _Entity_experimental_src.Host_org_variant _Entity_experimental_src.Host_org_ATCC_number _Entity_experimental_src.Vector_type _Entity_experimental_src.PDBview_host_org_vector_name _Entity_experimental_src.PDBview_plasmid_name _Entity_experimental_src.Vector_name _Entity_experimental_src.Vector_details _Entity_experimental_src.Vendor_name _Entity_experimental_src.Details _Entity_experimental_src.Entry_ID _Entity_experimental_src.Entity_experimental_src_list_ID 1 1 $entity_1 . 'chemical synthesis' . . . . . . . . . . . . . . . . 50242 1 stop_ save_ ################################# # Polymer residues and ligands # ################################# save_chem_comp_DU _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_DU _Chem_comp.Entry_ID 50242 _Chem_comp.ID DU _Chem_comp.Provenance PDB _Chem_comp.Name 2'-DEOXYURIDINE-5'-MONOPHOSPHATE _Chem_comp.Type 'DNA LINKING' _Chem_comp.BMRB_code DU _Chem_comp.PDB_code DU _Chem_comp.Ambiguous_flag no _Chem_comp.Initial_date 2012-11-20 _Chem_comp.Modified_date 2012-11-20 _Chem_comp.Release_status REL _Chem_comp.Replaced_by . _Chem_comp.Replaces . _Chem_comp.One_letter_code U _Chem_comp.Three_letter_code DU _Chem_comp.Number_atoms_all 33 _Chem_comp.Number_atoms_nh 20 _Chem_comp.Atom_nomenclature_source . _Chem_comp.PubChem_code . _Chem_comp.Subcomponent_list . _Chem_comp.InChI_code ; InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1 ; _Chem_comp.Mon_nstd_flag . _Chem_comp.Mon_nstd_class . _Chem_comp.Mon_nstd_details . _Chem_comp.Mon_nstd_parent . _Chem_comp.Mon_nstd_parent_comp_ID . _Chem_comp.Std_deriv_one_letter_code . _Chem_comp.Std_deriv_three_letter_code . _Chem_comp.Std_deriv_BMRB_code . _Chem_comp.Std_deriv_PDB_code . _Chem_comp.Std_deriv_chem_comp_name . _Chem_comp.Synonyms . _Chem_comp.Formal_charge 0 _Chem_comp.Paramagnetic . _Chem_comp.Aromatic no _Chem_comp.Formula 'C9 H13 N2 O8 P' _Chem_comp.Formula_weight 308.182 _Chem_comp.Formula_mono_iso_wt_nat . _Chem_comp.Formula_mono_iso_wt_13C . _Chem_comp.Formula_mono_iso_wt_15N . _Chem_comp.Formula_mono_iso_wt_13C_15N . _Chem_comp.Image_file_name . _Chem_comp.Image_file_format . _Chem_comp.Topo_file_name . _Chem_comp.Topo_file_format . _Chem_comp.Struct_file_name . _Chem_comp.Struct_file_format . _Chem_comp.Stereochem_param_file_name . _Chem_comp.Stereochem_param_file_format . _Chem_comp.Model_details . _Chem_comp.Model_erf . _Chem_comp.Model_source . _Chem_comp.Model_coordinates_details . _Chem_comp.Model_coordinates_missing_flag yes _Chem_comp.Ideal_coordinates_details . _Chem_comp.Ideal_coordinates_missing_flag no _Chem_comp.Model_coordinates_db_code . _Chem_comp.Processing_site PDBJ _Chem_comp.Vendor . _Chem_comp.Vendor_product_code . _Chem_comp.Details . _Chem_comp.DB_query_date . _Chem_comp.DB_last_query_revised_last_date . loop_ _Chem_comp_descriptor.Descriptor _Chem_comp_descriptor.Type _Chem_comp_descriptor.Program _Chem_comp_descriptor.Program_version _Chem_comp_descriptor.Entry_ID _Chem_comp_descriptor.Comp_ID C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O SMILES 'OpenEye OEToolkits' 1.5.0 50242 DU C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 50242 DU ; InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1 ; InChI InChI 1.03 50242 DU JSRLJPSBLDHEIO-SHYZEUOFSA-N InChIKey InChI 1.03 50242 DU O=C1NC(=O)N(C=C1)C2OC(C(O)C2)COP(=O)(O)O SMILES ACDLabs 10.04 50242 DU O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O SMILES_CANONICAL CACTVS 3.341 50242 DU O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O SMILES CACTVS 3.341 50242 DU stop_ loop_ _Chem_comp_identifier.Identifier _Chem_comp_identifier.Type _Chem_comp_identifier.Program _Chem_comp_identifier.Program_version _Chem_comp_identifier.Entry_ID _Chem_comp_identifier.Comp_ID "2'-deoxy-5'-uridylic acid" 'SYSTEMATIC NAME' ACDLabs 10.04 50242 DU '[(2R,3S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate' 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 50242 DU stop_ loop_ _Chem_comp_atom.Atom_ID _Chem_comp_atom.BMRB_code _Chem_comp_atom.PDB_atom_ID _Chem_comp_atom.Alt_atom_ID _Chem_comp_atom.Auth_atom_ID _Chem_comp_atom.Type_symbol _Chem_comp_atom.Isotope_number _Chem_comp_atom.Chirality _Chem_comp_atom.Stereo_config _Chem_comp_atom.Charge _Chem_comp_atom.Partial_charge _Chem_comp_atom.Oxidation_number _Chem_comp_atom.Unpaired_electron_number _Chem_comp_atom.Align _Chem_comp_atom.Aromatic_flag _Chem_comp_atom.Leaving_atom_flag _Chem_comp_atom.Substruct_code _Chem_comp_atom.Ionizable _Chem_comp_atom.Drawing_2D_coord_x _Chem_comp_atom.Drawing_2D_coord_y _Chem_comp_atom.Model_Cartn_x _Chem_comp_atom.Model_Cartn_x_esd _Chem_comp_atom.Model_Cartn_y _Chem_comp_atom.Model_Cartn_y_esd _Chem_comp_atom.Model_Cartn_z _Chem_comp_atom.Model_Cartn_z_esd _Chem_comp_atom.Model_Cartn_x_ideal _Chem_comp_atom.Model_Cartn_y_ideal _Chem_comp_atom.Model_Cartn_z_ideal _Chem_comp_atom.PDBX_ordinal _Chem_comp_atom.Details _Chem_comp_atom.Entry_ID _Chem_comp_atom.Comp_ID OP3 OP3 OP3 O3P . O . . N 0 . . . 1 no yes . . . . . . . . . . -3.912 -2.311 1.636 1 . 50242 DU P P P P . P . . N 0 . . . 1 no no . . . . 12.190 . -12.289 . 0.399 . -3.968 -1.665 3.118 2 . 50242 DU OP1 OP1 OP1 O1P . O . . N 0 . . . 1 no no . . . . 12.477 . -13.576 . -0.294 . -4.406 -2.599 4.208 3 . 50242 DU OP2 OP2 OP2 O2P . O . . N 0 . . . 1 no no . . . . 13.315 . -11.490 . 0.952 . -4.901 -0.360 2.920 4 . 50242 DU O5' O5' O5' O5* . O . . N 0 . . . 1 no no . . . . 11.149 . -12.592 . 1.572 . -2.493 -1.028 3.315 5 . 50242 DU C5' C5' C5' C5* . C . . N 0 . . . 1 no no . . . . 10.832 . -11.580 . 2.548 . -2.005 -0.136 2.327 6 . 50242 DU C4' C4' C4' C4* . C . . R 0 . . . 1 no no . . . . 10.441 . -12.214 . 3.863 . -0.611 0.328 2.728 7 . 50242 DU O4' O4' O4' O4* . O . . N 0 . . . 1 no no . . . . 9.125 . -12.814 . 3.763 . 0.247 -0.829 2.764 8 . 50242 DU C3' C3' C3' C3* . C . . S 0 . . . 1 no no . . . . 11.363 . -13.310 . 4.399 . 0.008 1.286 1.720 9 . 50242 DU O3' O3' O3' O3* . O . . N 0 . . . 1 no no . . . . 11.383 . -13.192 . 5.818 . 0.965 2.121 2.368 10 . 50242 DU C2' C2' C2' C2* . C . . N 0 . . . 1 no no . . . . 10.645 . -14.591 . 3.996 . 0.710 0.360 0.754 11 . 50242 DU C1' C1' C1' C1* . C . . R 0 . . . 1 no no . . . . 9.182 . -14.190 . 4.131 . 1.157 -0.778 1.657 12 . 50242 DU N1 N1 N1 N1 . N . . N 0 . . . 1 no no . . . . 8.265 . -14.921 . 3.249 . 1.164 -2.047 0.989 13 . 50242 DU C2 C2 C2 C2 . C . . N 0 . . . 1 no no . . . . 7.200 . -15.588 . 3.823 . 2.334 -2.545 0.374 14 . 50242 DU O2 O2 O2 O2 . O . . N 0 . . . 1 no no . . . . 7.004 . -15.607 . 5.027 . 3.412 -1.946 0.363 15 . 50242 DU N3 N3 N3 N3 . N . . N 0 . . . 1 no no . . . . 6.374 . -16.236 . 2.929 . 2.195 -3.797 -0.241 16 . 50242 DU C4 C4 C4 C4 . C . . N 0 . . . 1 no no . . . . 6.516 . -16.285 . 1.561 . 1.046 -4.570 -0.300 17 . 50242 DU O4 O4 O4 O4 . O . . N 0 . . . 1 no no . . . . 5.711 . -16.929 . 0.891 . 0.971 -5.663 -0.852 18 . 50242 DU C5 C5 C5 C5 . C . . N 0 . . . 1 no no . . . . 7.641 . -15.573 . 1.051 . -0.130 -3.976 0.367 19 . 50242 DU C6 C6 C6 C6 . C . . N 0 . . . 1 no no . . . . 8.456 . -14.933 . 1.890 . -0.013 -2.784 0.958 20 . 50242 DU HOP3 HOP3 HOP3 3HOP . H . . N 0 . . . 0 no no . . . . -0.183 . 0.821 . 0.442 . -4.684 -2.823 1.313 21 . 50242 DU HOP2 HOP2 HOP2 2HOP . H . . N 0 . . . 0 no no . . . . 13.036 . -10.589 . 1.070 . -5.874 -0.475 2.871 22 . 50242 DU H5' H5' H5' 1H5* . H . . N 0 . . . 1 no no . . . . 9.987 . -10.981 . 2.177 . -1.971 -0.654 1.366 23 . 50242 DU H5'' H5'' H5'' 2H5* . H . . N 0 . . . 0 no no . . . . 11.714 . -10.942 . 2.704 . -2.683 0.718 2.254 24 . 50242 DU H4' H4' H4' H4* . H . . N 0 . . . 1 no no . . . . 10.496 . -11.368 . 4.564 . -0.644 0.753 3.736 25 . 50242 DU H3' H3' H3' H3* . H . . N 0 . . . 1 no no . . . . 12.397 . -13.269 . 4.027 . -0.722 1.941 1.236 26 . 50242 DU HO3' HO3' HO3' H3T . H . . N 0 . . . 0 no yes . . . . 12.283 . -13.166 . 6.121 . 0.743 3.042 2.146 27 . 50242 DU H2' H2' H2' 1H2* . H . . N 0 . . . 1 no no . . . . 10.921 . -15.462 . 4.608 . -0.003 -0.001 0.003 28 . 50242 DU H2'' H2'' H2'' 2H2* . H . . N 0 . . . 0 no no . . . . 10.896 . -14.899 . 2.970 . 1.556 0.818 0.232 29 . 50242 DU H1' H1' H1' H1* . H . . N 0 . . . 1 no no . . . . 8.861 . -14.411 . 5.160 . 2.163 -0.604 2.054 30 . 50242 DU H3 H3 H3 H3 . H . . N 0 . . . 1 no no . . . . 5.590 . -16.721 . 3.315 . 3.023 -4.177 -0.691 31 . 50242 DU H5 H5 H5 H5 . H . . N 0 . . . 1 no no . . . . 7.832 . -15.552 . -0.012 . -1.065 -4.523 0.362 32 . 50242 DU H6 H6 H6 H6 . H . . N 0 . . . 1 no no . . . . 9.303 . -14.401 . 1.483 . -0.864 -2.330 1.454 33 . 50242 DU stop_ loop_ _Chem_comp_bond.ID _Chem_comp_bond.Type _Chem_comp_bond.Value_order _Chem_comp_bond.Atom_ID_1 _Chem_comp_bond.Atom_ID_2 _Chem_comp_bond.Aromatic_flag _Chem_comp_bond.Stereo_config _Chem_comp_bond.Ordinal _Chem_comp_bond.Details _Chem_comp_bond.Entry_ID _Chem_comp_bond.Comp_ID 1 . SING OP3 P no N 1 . 50242 DU 2 . SING OP3 HOP3 no N 2 . 50242 DU 3 . DOUB P OP1 no N 3 . 50242 DU 4 . SING P OP2 no N 4 . 50242 DU 5 . SING P O5' no N 5 . 50242 DU 6 . SING OP2 HOP2 no N 6 . 50242 DU 7 . SING O5' C5' no N 7 . 50242 DU 8 . SING C5' C4' no N 8 . 50242 DU 9 . SING C5' H5' no N 9 . 50242 DU 10 . SING C5' H5'' no N 10 . 50242 DU 11 . SING C4' O4' no N 11 . 50242 DU 12 . SING C4' C3' no N 12 . 50242 DU 13 . SING C4' H4' no N 13 . 50242 DU 14 . SING O4' C1' no N 14 . 50242 DU 15 . SING C3' O3' no N 15 . 50242 DU 16 . SING C3' C2' no N 16 . 50242 DU 17 . SING C3' H3' no N 17 . 50242 DU 18 . SING O3' HO3' no N 18 . 50242 DU 19 . SING C2' C1' no N 19 . 50242 DU 20 . SING C2' H2' no N 20 . 50242 DU 21 . SING C2' H2'' no N 21 . 50242 DU 22 . SING C1' N1 no N 22 . 50242 DU 23 . SING C1' H1' no N 23 . 50242 DU 24 . SING N1 C2 no N 24 . 50242 DU 25 . SING N1 C6 no N 25 . 50242 DU 26 . DOUB C2 O2 no N 26 . 50242 DU 27 . SING C2 N3 no N 27 . 50242 DU 28 . SING N3 C4 no N 28 . 50242 DU 29 . SING N3 H3 no N 29 . 50242 DU 30 . DOUB C4 O4 no N 30 . 50242 DU 31 . SING C4 C5 no N 31 . 50242 DU 32 . DOUB C5 C6 no N 32 . 50242 DU 33 . SING C5 H5 no N 33 . 50242 DU 34 . SING C6 H6 no N 34 . 50242 DU stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID 50242 _Sample.ID 1 _Sample.Name Na _Sample.Type solution _Sample.Sub_type . _Sample.Details . _Sample.Aggregate_sample_number 1 _Sample.Solvent_system '100% D2O' _Sample.Preparation_date . _Sample.Preparation_expiration_date . _Sample.Polycrystallization_protocol . _Sample.Single_crystal_protocol . _Sample.Crystal_grow_apparatus . _Sample.Crystal_grow_atmosphere . _Sample.Crystal_grow_details . _Sample.Crystal_grow_method . _Sample.Crystal_grow_method_cit_ID . _Sample.Crystal_grow_pH . _Sample.Crystal_grow_pH_range . _Sample.Crystal_grow_pressure . _Sample.Crystal_grow_pressure_esd . _Sample.Crystal_grow_seeding . _Sample.Crystal_grow_seeding_cit_ID . _Sample.Crystal_grow_temp . _Sample.Crystal_grow_temp_details . _Sample.Crystal_grow_temp_esd . _Sample.Crystal_grow_time . _Sample.Oriented_sample_prep_protocol . _Sample.Lyophilization_cryo_protectant . _Sample.Storage_protocol . loop_ _Sample_component.ID _Sample_component.Mol_common_name _Sample_component.Isotopic_labeling _Sample_component.Assembly_ID _Sample_component.Assembly_label _Sample_component.Entity_ID _Sample_component.Entity_label _Sample_component.Product_ID _Sample_component.Type _Sample_component.Concentration_val _Sample_component.Concentration_val_min _Sample_component.Concentration_val_max _Sample_component.Concentration_val_units _Sample_component.Concentration_val_err _Sample_component.Vendor _Sample_component.Vendor_product_name _Sample_component.Vendor_product_code _Sample_component.Entry_ID _Sample_component.Sample_ID 1 '[r(UGGUGG)d(U)]4 G-quadruplex' 'natural abundance' . . 1 $entity_1 . . 1 . . mM . . . . 50242 1 2 'sodium phosphate' 'natural abundance' . . . . . . 10 . . mM . . . . 50242 1 3 'sodium chloride' 'natural abundance' . . . . . . 150 . . mM . . . . 50242 1 stop_ save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Sample_condition_list.Sf_category sample_conditions _Sample_condition_list.Sf_framecode sample_conditions_1 _Sample_condition_list.Entry_ID 50242 _Sample_condition_list.ID 1 _Sample_condition_list.Name Na_25C_D2O _Sample_condition_list.Details . loop_ _Sample_condition_variable.Type _Sample_condition_variable.Val _Sample_condition_variable.Val_err _Sample_condition_variable.Val_units _Sample_condition_variable.Entry_ID _Sample_condition_variable.Sample_condition_list_ID 'ionic strength' 150 . mM 50242 1 pH 6.8 . pH 50242 1 pressure 1 . atm 50242 1 temperature 298 . K 50242 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID 50242 _Software.ID 1 _Software.Type . _Software.Name TOPSPIN _Software.Version . _Software.DOI . _Software.Details . loop_ _Task.Software_module _Task.Task _Task.Entry_ID _Task.Software_ID . collection 50242 1 stop_ save_ save_software_2 _Software.Sf_category software _Software.Sf_framecode software_2 _Software.Entry_ID 50242 _Software.ID 2 _Software.Type . _Software.Name SPARKY _Software.Version . _Software.DOI . _Software.Details . loop_ _Task.Software_module _Task.Task _Task.Entry_ID _Task.Software_ID . 'chemical shift assignment' 50242 2 stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _NMR_spectrometer.Sf_category NMR_spectrometer _NMR_spectrometer.Sf_framecode NMR_spectrometer_1 _NMR_spectrometer.Entry_ID 50242 _NMR_spectrometer.ID 1 _NMR_spectrometer.Name '700 MHz' _NMR_spectrometer.Details . _NMR_spectrometer.Manufacturer Bruker _NMR_spectrometer.Model 'Avance III' _NMR_spectrometer.Serial_number . _NMR_spectrometer.Field_strength 700 save_ ############################# # NMR applied experiments # ############################# save_experiment_list_1 _Experiment_list.Sf_category experiment_list _Experiment_list.Sf_framecode experiment_list_1 _Experiment_list.Entry_ID 50242 _Experiment_list.ID 1 _Experiment_list.Details . loop_ _Experiment.ID _Experiment.Name _Experiment.Raw_data_flag _Experiment.NMR_spec_expt_ID _Experiment.NMR_spec_expt_label _Experiment.MS_expt_ID _Experiment.MS_expt_label _Experiment.SAXS_expt_ID _Experiment.SAXS_expt_label _Experiment.FRET_expt_ID _Experiment.FRET_expt_label _Experiment.EMR_expt_ID _Experiment.EMR_expt_label _Experiment.Sample_ID _Experiment.Sample_label _Experiment.Sample_state _Experiment.Sample_volume _Experiment.Sample_volume_units _Experiment.Sample_condition_list_ID _Experiment.Sample_condition_list_label _Experiment.Sample_spinning_rate _Experiment.Sample_angle _Experiment.NMR_tube_type _Experiment.NMR_spectrometer_ID _Experiment.NMR_spectrometer_label _Experiment.NMR_spectrometer_probe_ID _Experiment.NMR_spectrometer_probe_label _Experiment.NMR_spectral_processing_ID _Experiment.NMR_spectral_processing_label _Experiment.Mass_spectrometer_ID _Experiment.Mass_spectrometer_label _Experiment.Xray_instrument_ID _Experiment.Xray_instrument_label _Experiment.Fluorescence_instrument_ID _Experiment.Fluorescence_instrument_label _Experiment.EMR_instrument_ID _Experiment.EMR_instrument_label _Experiment.Chromatographic_system_ID _Experiment.Chromatographic_system_label _Experiment.Chromatographic_column_ID _Experiment.Chromatographic_column_label _Experiment.Entry_ID _Experiment.Experiment_list_ID 1 '2D 1H-1H NOESY' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . 50242 1 2 '2D 1H-13C HSQC' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . 50242 1 3 '2D 1H-31H COSY' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . 50242 1 4 '2D DQF-COSY' no . . . . . . . . . . 1 $sample_1 isotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . 50242 1 stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Chem_shift_reference.Sf_category chem_shift_reference _Chem_shift_reference.Sf_framecode chem_shift_reference_1 _Chem_shift_reference.Entry_ID 50242 _Chem_shift_reference.ID 1 _Chem_shift_reference.Name TSP _Chem_shift_reference.Details . loop_ _Chem_shift_ref.Atom_type _Chem_shift_ref.Atom_isotope_number _Chem_shift_ref.Mol_common_name _Chem_shift_ref.Atom_group _Chem_shift_ref.Concentration_val _Chem_shift_ref.Concentration_units _Chem_shift_ref.Solvent _Chem_shift_ref.Rank _Chem_shift_ref.Chem_shift_units _Chem_shift_ref.Chem_shift_val _Chem_shift_ref.Ref_method _Chem_shift_ref.Ref_type _Chem_shift_ref.Indirect_shift_ratio _Chem_shift_ref.External_ref_loc _Chem_shift_ref.External_ref_sample_geometry _Chem_shift_ref.External_ref_axis _Chem_shift_ref.Ref_correction_type _Chem_shift_ref.Correction_val _Chem_shift_ref.Entry_ID _Chem_shift_ref.Chem_shift_reference_ID H 1 TSP 'methyl protons' . . . . ppm 0.00 internal direct 1 . . . . . 50242 1 P 31 TSP 'methyl protons' . . . . ppm 0.00 internal indirect . . . . . . 50242 1 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chemical_shifts_1 _Assigned_chem_shift_list.Sf_category assigned_chemical_shifts _Assigned_chem_shift_list.Sf_framecode assigned_chemical_shifts_1 _Assigned_chem_shift_list.Entry_ID 50242 _Assigned_chem_shift_list.ID 1 _Assigned_chem_shift_list.Name 'non-exchangeable protons and 31P' _Assigned_chem_shift_list.Sample_condition_list_ID 1 _Assigned_chem_shift_list.Sample_condition_list_label $sample_conditions_1 _Assigned_chem_shift_list.Chem_shift_reference_ID 1 _Assigned_chem_shift_list.Chem_shift_reference_label $chem_shift_reference_1 _Assigned_chem_shift_list.Chem_shift_1H_err . _Assigned_chem_shift_list.Chem_shift_13C_err . _Assigned_chem_shift_list.Chem_shift_15N_err . _Assigned_chem_shift_list.Chem_shift_31P_err . _Assigned_chem_shift_list.Chem_shift_2H_err . _Assigned_chem_shift_list.Chem_shift_19F_err . _Assigned_chem_shift_list.Error_derivation_method . _Assigned_chem_shift_list.Details . _Assigned_chem_shift_list.Text_data_format . _Assigned_chem_shift_list.Text_data . loop_ _Chem_shift_experiment.Experiment_ID _Chem_shift_experiment.Experiment_name _Chem_shift_experiment.Sample_ID _Chem_shift_experiment.Sample_label _Chem_shift_experiment.Sample_state _Chem_shift_experiment.Entry_ID _Chem_shift_experiment.Assigned_chem_shift_list_ID 1 '2D 1H-1H NOESY' . . . 50242 1 2 '2D 1H-13C HSQC' . . . 50242 1 3 '2D 1H-31H COSY' . . . 50242 1 4 '2D DQF-COSY' . . . 50242 1 stop_ loop_ _Chem_shift_software.Software_ID _Chem_shift_software.Software_label _Chem_shift_software.Method_ID _Chem_shift_software.Method_label _Chem_shift_software.Entry_ID _Chem_shift_software.Assigned_chem_shift_list_ID 2 $software_2 . . 50242 1 stop_ loop_ _Atom_chem_shift.ID _Atom_chem_shift.Assembly_atom_ID _Atom_chem_shift.Entity_assembly_ID _Atom_chem_shift.Entity_assembly_asym_ID _Atom_chem_shift.Entity_ID _Atom_chem_shift.Comp_index_ID _Atom_chem_shift.Seq_ID _Atom_chem_shift.Comp_ID _Atom_chem_shift.Atom_ID _Atom_chem_shift.Atom_type _Atom_chem_shift.Atom_isotope_number _Atom_chem_shift.Val _Atom_chem_shift.Val_err _Atom_chem_shift.Assign_fig_of_merit _Atom_chem_shift.Ambiguity_code _Atom_chem_shift.Ambiguity_set_ID _Atom_chem_shift.Occupancy _Atom_chem_shift.Resonance_ID _Atom_chem_shift.Auth_entity_assembly_ID _Atom_chem_shift.Auth_asym_ID _Atom_chem_shift.Auth_seq_ID _Atom_chem_shift.Auth_comp_ID _Atom_chem_shift.Auth_atom_ID _Atom_chem_shift.Details _Atom_chem_shift.Entry_ID _Atom_chem_shift.Assigned_chem_shift_list_ID 1 . 1 . 1 1 1 U H1' H 1 5.329 0.01 . 1 . . . . . 1 U H1' . 50242 1 2 . 1 . 1 1 1 U H2' H 1 3.849 0.01 . 1 . . . . . 1 U H2' . 50242 1 3 . 1 . 1 1 1 U H3' H 1 4.547 0.01 . 1 . . . . . 1 U H3' . 50242 1 4 . 1 . 1 1 1 U H4' H 1 4.317 0.01 . 1 . . . . . 1 U H4' . 50242 1 5 . 1 . 1 1 1 U H5 H 1 5.711 0.01 . 1 . . . . . 1 U H5 . 50242 1 6 . 1 . 1 1 1 U H5' H 1 4.044 0.01 . 2 . . . . . 1 U H5' . 50242 1 7 . 1 . 1 1 1 U H5'' H 1 4.213 0.01 . 2 . . . . . 1 U H5'' . 50242 1 8 . 1 . 1 1 1 U H6 H 1 7.954 0.01 . 1 . . . . . 1 U H6 . 50242 1 9 . 1 . 1 1 1 U P P 31 -0.966 0.05 . 1 . . . . . 1 U P . 50242 1 10 . 1 . 1 2 2 G H1' H 1 5.896 0.01 . 1 . . . . . 2 G H1' . 50242 1 11 . 1 . 1 2 2 G H2' H 1 5.060 0.01 . 1 . . . . . 2 G H2' . 50242 1 12 . 1 . 1 2 2 G H3' H 1 4.933 0.01 . 1 . . . . . 2 G H3' . 50242 1 13 . 1 . 1 2 2 G H4' H 1 4.609 0.01 . 1 . . . . . 2 G H4' . 50242 1 14 . 1 . 1 2 2 G H5' H 1 4.168 0.01 . 2 . . . . . 2 G H5' . 50242 1 15 . 1 . 1 2 2 G H5'' H 1 4.375 0.01 . 2 . . . . . 2 G H5'' . 50242 1 16 . 1 . 1 2 2 G H8 H 1 8.305 0.01 . 1 . . . . . 2 G H8 . 50242 1 17 . 1 . 1 3 3 G H1' H 1 6.239 0.01 . 1 . . . . . 3 G H1' . 50242 1 18 . 1 . 1 3 3 G H2' H 1 4.859 0.01 . 1 . . . . . 3 G H2' . 50242 1 19 . 1 . 1 3 3 G H3' H 1 4.393 0.01 . 1 . . . . . 3 G H3' . 50242 1 20 . 1 . 1 3 3 G H4' H 1 4.722 0.01 . 1 . . . . . 3 G H4' . 50242 1 21 . 1 . 1 3 3 G H5' H 1 4.364 0.01 . 2 . . . . . 3 G H5' . 50242 1 22 . 1 . 1 3 3 G H5'' H 1 4.580 0.01 . 2 . . . . . 3 G H5'' . 50242 1 23 . 1 . 1 3 3 G H8 H 1 8.139 0.01 . 1 . . . . . 3 G H8 . 50242 1 24 . 1 . 1 3 3 G P P 31 -2.098 0.05 . 1 . . . . . 3 G P . 50242 1 25 . 1 . 1 4 4 U H1' H 1 5.436 0.01 . 1 . . . . . 4 U H1' . 50242 1 26 . 1 . 1 4 4 U H2' H 1 4.285 0.01 . 1 . . . . . 4 U H2' . 50242 1 27 . 1 . 1 4 4 U H3' H 1 4.347 0.01 . 1 . . . . . 4 U H3' . 50242 1 28 . 1 . 1 4 4 U H4' H 1 4.537 0.01 . 1 . . . . . 4 U H4' . 50242 1 29 . 1 . 1 4 4 U H5 H 1 4.603 0.01 . 1 . . . . . 4 U H5 . 50242 1 30 . 1 . 1 4 4 U H5' H 1 4.174 0.01 . 2 . . . . . 4 U H5' . 50242 1 31 . 1 . 1 4 4 U H5'' H 1 4.634 0.01 . 2 . . . . . 4 U H5'' . 50242 1 32 . 1 . 1 4 4 U H6 H 1 7.336 0.01 . 1 . . . . . 4 U H6 . 50242 1 33 . 1 . 1 4 4 U P P 31 -2.931 0.05 . 1 . . . . . 4 U P . 50242 1 34 . 1 . 1 5 5 G H1' H 1 5.865 0.01 . 1 . . . . . 5 G H1' . 50242 1 35 . 1 . 1 5 5 G H2' H 1 4.366 0.01 . 1 . . . . . 5 G H2' . 50242 1 36 . 1 . 1 5 5 G H3' H 1 5.004 0.01 . 1 . . . . . 5 G H3' . 50242 1 37 . 1 . 1 5 5 G H4' H 1 4.498 0.01 . 1 . . . . . 5 G H4' . 50242 1 38 . 1 . 1 5 5 G H5' H 1 4.188 0.01 . 2 . . . . . 5 G H5' . 50242 1 39 . 1 . 1 5 5 G H5'' H 1 4.730 0.01 . 2 . . . . . 5 G H5'' . 50242 1 40 . 1 . 1 5 5 G H8 H 1 8.458 0.01 . 1 . . . . . 5 G H8 . 50242 1 41 . 1 . 1 5 5 G P P 31 -5.224 0.05 . 1 . . . . . 5 G P . 50242 1 42 . 1 . 1 6 6 G H1' H 1 6.246 0.01 . 1 . . . . . 6 G H1' . 50242 1 43 . 1 . 1 6 6 G H2' H 1 4.149 0.01 . 1 . . . . . 6 G H2' . 50242 1 44 . 1 . 1 6 6 G H3' H 1 4.604 0.01 . 1 . . . . . 6 G H3' . 50242 1 45 . 1 . 1 6 6 G H4' H 1 4.438 0.01 . 1 . . . . . 6 G H4' . 50242 1 46 . 1 . 1 6 6 G H5' H 1 4.139 0.01 . 2 . . . . . 6 G H5' . 50242 1 47 . 1 . 1 6 6 G H5'' H 1 4.613 0.01 . 2 . . . . . 6 G H5'' . 50242 1 48 . 1 . 1 6 6 G H8 H 1 7.524 0.01 . 1 . . . . . 6 G H8 . 50242 1 49 . 1 . 1 6 6 G P P 31 -4.024 0.05 . 1 . . . . . 6 G P . 50242 1 50 . 1 . 1 7 7 DU H1' H 1 6.188 0.01 . 1 . . . . . 7 DU H1' . 50242 1 51 . 1 . 1 7 7 DU H2' H 1 1.908 0.01 . 1 . . . . . 7 DU H2' . 50242 1 52 . 1 . 1 7 7 DU H2'' H 1 2.573 0.01 . 1 . . . . . 7 DU H2'' . 50242 1 53 . 1 . 1 7 7 DU H3' H 1 4.667 0.01 . 1 . . . . . 7 DU H3' . 50242 1 54 . 1 . 1 7 7 DU H4' H 1 4.128 0.01 . 1 . . . . . 7 DU H4' . 50242 1 55 . 1 . 1 7 7 DU H5 H 1 5.107 0.01 . 1 . . . . . 7 DU H5 . 50242 1 56 . 1 . 1 7 7 DU H5' H 1 4.120 0.01 . 2 . . . . . 7 DU H5' . 50242 1 57 . 1 . 1 7 7 DU H6 H 1 7.830 0.01 . 1 . . . . . 7 DU H6 . 50242 1 58 . 1 . 1 7 7 DU P P 31 -3.247 0.05 . 1 . . . . . 7 DU P . 50242 1 stop_ save_