data_4392
#######################
# Entry information #
#######################
save_entry_information
_Saveframe_category entry_information
_Entry_title
;
Binding of AR-1-144, a tri-imidazole DNA minor groove binder, to CCGG sequence
analyzed by NMR spectroscopy
;
_BMRB_accession_number 4392
_BMRB_flat_file_name bmr4392.str
_Entry_type original
_Submission_date 1999-09-08
_Accession_date 1999-09-09
_Entry_origination author
_NMR_STAR_version 2.1.1
_Experimental_method NMR
_Details .
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Yang X. -L. .
2 Kaenzig C. . .
3 Lee M. . .
4 Wang A. H.-J. .
stop_
loop_
_Saveframe_category_type
_Saveframe_category_type_count
assigned_chemical_shifts 3
stop_
loop_
_Data_type
_Data_type_count
"1H chemical shifts" 104
stop_
loop_
_Revision_date
_Revision_keyword
_Revision_author
_Revision_detail
2013-08-09 update BMRB 'update ligand based PDB entry 1CYZ'
2010-07-19 update BMRB 'update DNA residue label to two-letter code'
2007-07-13 original author 'original release'
stop_
save_
#############################
# Citation for this entry #
#############################
save_entry_citation
_Saveframe_category entry_citation
_Citation_full
;
Yang, X-L., Kaenzig, C., Lee, M., and Wang, A. H.-J., "Binding of AR-1-144, a
tri-imidazole DNA minor groove binder, to CCGG sequence analyzed by NMR spectroscopy,"
Eur. J. Biochem. 263, 646-655 (1999).
;
_Citation_title
;
Binding of AR-1-144, a tri-imidazole DNA minor groove binder, to CCGG sequence
analyzed by NMR spectroscop
;
_Citation_status published
_Citation_type journal
_CAS_abstract_code .
_MEDLINE_UI_code 99398329
_PubMed_ID ?
loop_
_Author_ordinal
_Author_family_name
_Author_given_name
_Author_middle_initials
_Author_family_title
1 Yang X. -L. .
2 Kaenzig C. . .
3 Lee M. . .
4 Wang A. H.-J. .
stop_
_Journal_abbreviation 'Eur. J. Biochem.'
_Journal_name_full 'European Journal of Biochemistry'
_Journal_volume 263
_Journal_issue 3
_Journal_CSD .
_Book_chapter_title .
_Book_volume .
_Book_series .
_Book_ISBN .
_Conference_state_province .
_Conference_abstract_number .
_Page_first 646
_Page_last 655
_Year 1999
_Details .
loop_
_Keyword
'Anticancer drug'
'drug design'
'DNA structure'
'Sequence specific recognition'
stop_
save_
##################################
# Molecular system description #
##################################
save_MGB
_Saveframe_category molecular_system
_Mol_system_name 'DNA minor groove binder'
_Abbreviation_common MGB
_Enzyme_commission_number .
loop_
_Mol_system_component_name
_Mol_label
'DNA strand A' $DNA_strand
'DNA strand B' $DNA_strand
AR-1-144 $entity_AR1
stop_
_System_molecular_weight .
_System_physical_state native
_System_oligomer_state monomer
_System_paramagnetic no
_System_thiol_state 'not present'
_Database_query_date .
_Details .
save_
########################
# Monomeric polymers #
########################
save_DNA_strand
_Saveframe_category monomeric_polymer
_Mol_type polymer
_Mol_polymer_class DNA
_Name_common 'DNA strand'
_Name_variant none
_Abbreviation_common 'DNA strand'
_Molecular_mass .
_Mol_thiol_state 'not present'
_Details .
##############################
# Polymer residue sequence #
##############################
_Residue_count 10
_Mol_residue_sequence GAACCGGTTC
loop_
_Residue_seq_code
_Residue_label
1 DG 2 DA 3 DA 4 DC 5 DC
6 DG 7 DG 8 DT 9 DT 10 DC
stop_
_Sequence_homology_query_date .
_Sequence_homology_query_revised_last_date .
save_
#############
# Ligands #
#############
save_AR1
_Saveframe_category ligand
_Mol_type "non-polymer (NON-POLYMER)"
_Name_common (2-{[4-({4-[(4-FORMYLAMINO-1-METHYL-1H-IMIDAZOLE-2-CARBONYL)-AMINO]-1-METHYL-1H-IMIDAZOLE-2-CARBONYL}-AMINO)-1-METHYL-1H-IMIDAZOLE-2-CARBONYL]-AMINO}-ETHYL)-DIMETHYL-AMMONIUM
_BMRB_code AR1
_PDB_code AR1
_Molecular_mass 486.508
_Mol_charge 1
_Mol_paramagnetic .
_Mol_aromatic yes
_Details .
loop_
_Atom_name
_PDB_atom_name
_Atom_type
_Atom_chirality
_Atom_charge
_Atom_oxidation_number
_Atom_unpaired_electrons
C1 C1 C . 0 . ?
C11 C11 C . 0 . ?
C12 C12 C . 0 . ?
C13 C13 C . 0 . ?
C1T C1T C . 0 . ?
C2 C2 C . 0 . ?
C2T C2T C . 0 . ?
C3 C3 C . 0 . ?
C31 C31 C . 0 . ?
C32 C32 C . 0 . ?
C33 C33 C . 0 . ?
C51 C51 C . 0 . ?
C52 C52 C . 0 . ?
C53 C53 C . 0 . ?
CA CA C . 0 . ?
CMT CMT C . 0 . ?
CN1 CN1 C . 0 . ?
CN2 CN2 C . 0 . ?
CN3 CN3 C . 0 . ?
CNT CNT C . 0 . ?
H1T1 H1T1 H . 0 . ?
H1T2 H1T2 H . 0 . ?
H2T1 H2T1 H . 0 . ?
H2T2 H2T2 H . 0 . ?
H51 H51 H . 0 . ?
H52 H52 H . 0 . ?
H53 H53 H . 0 . ?
HA HA H . 0 . ?
HMT1 HMT1 H . 0 . ?
HMT2 HMT2 H . 0 . ?
HMT3 HMT3 H . 0 . ?
HN1 HN1 H . 0 . ?
HN11 HN11 H . 0 . ?
HN12 HN12 H . 0 . ?
HN13 HN13 H . 0 . ?
HN2 HN2 H . 0 . ?
HN21 HN21 H . 0 . ?
HN22 HN22 H . 0 . ?
HN23 HN23 H . 0 . ?
HN3 HN3 H . 0 . ?
HN31 HN31 H . 0 . ?
HN32 HN32 H . 0 . ?
HN33 HN33 H . 0 . ?
HNT HNT H . 0 . ?
HNT1 HNT1 H . 0 . ?
HNT2 HNT2 H . 0 . ?
HNT3 HNT3 H . 0 . ?
HT HT H . 0 . ?
N1 N1 N . 0 . ?
N2 N2 N . 0 . ?
N21 N21 N . 0 . ?
N22 N22 N . 0 . ?
N23 N23 N . 0 . ?
N3 N3 N . 0 . ?
N3T N3T N . 1 . ?
N41 N41 N . 0 . ?
N42 N42 N . 0 . ?
N43 N43 N . 0 . ?
NT NT N . 0 . ?
O1 O1 O . 0 . ?
O2 O2 O . 0 . ?
O3 O3 O . 0 . ?
OA OA O . 0 . ?
stop_
loop_
_Bond_order
_Bond_atom_one_atom_name
_Bond_atom_two_atom_name
_PDB_bond_atom_one_atom_name
_PDB_bond_atom_two_atom_name
DOUB CA OA ? ?
SING CA N1 ? ?
SING CA HA ? ?
SING N1 C11 ? ?
SING N1 HN1 ? ?
SING C11 N21 ? ?
DOUB C11 C51 ? ?
DOUB N21 C31 ? ?
SING C31 N41 ? ?
SING C31 C1 ? ?
SING N41 CN1 ? ?
SING N41 C51 ? ?
SING CN1 HN11 ? ?
SING CN1 HN12 ? ?
SING CN1 HN13 ? ?
SING C51 H51 ? ?
DOUB C1 O1 ? ?
SING C1 N2 ? ?
SING N2 C12 ? ?
SING N2 HN2 ? ?
SING C12 N22 ? ?
DOUB C12 C52 ? ?
DOUB N22 C32 ? ?
SING C32 N42 ? ?
SING C32 C2 ? ?
SING N42 CN2 ? ?
SING N42 C52 ? ?
SING CN2 HN21 ? ?
SING CN2 HN22 ? ?
SING CN2 HN23 ? ?
SING C52 H52 ? ?
DOUB C2 O2 ? ?
SING C2 N3 ? ?
SING N3 C13 ? ?
SING N3 HN3 ? ?
SING C13 N23 ? ?
DOUB C13 C53 ? ?
DOUB N23 C33 ? ?
SING C33 N43 ? ?
SING C33 C3 ? ?
SING N43 CN3 ? ?
SING N43 C53 ? ?
SING CN3 HN31 ? ?
SING CN3 HN32 ? ?
SING CN3 HN33 ? ?
SING C53 H53 ? ?
DOUB C3 O3 ? ?
SING C3 NT ? ?
SING NT C1T ? ?
SING NT HT ? ?
SING C1T C2T ? ?
SING C1T H1T1 ? ?
SING C1T H1T2 ? ?
SING C2T N3T ? ?
SING C2T H2T1 ? ?
SING C2T H2T2 ? ?
SING N3T CNT ? ?
SING N3T CMT ? ?
SING N3T HNT ? ?
SING CNT HNT1 ? ?
SING CNT HNT2 ? ?
SING CNT HNT3 ? ?
SING CMT HMT1 ? ?
SING CMT HMT2 ? ?
SING CMT HMT3 ? ?
stop_
_Mol_thiol_state .
_Sequence_homology_query_date .
save_
####################
# Natural source #
####################
save_natural_source
_Saveframe_category natural_source
loop_
_Mol_label
_Organism_name_common
_NCBI_taxonomy_ID
_Superkingdom
_Kingdom
_Genus
_Species
$DNA_strand . . . . . .
$entity_AR1 . . . . . .
stop_
save_
#########################
# Experimental source #
#########################
save_experimental_source
_Saveframe_category experimental_source
loop_
_Mol_label
_Production_method
_Host_organism_name_common
_Genus
_Species
_Strain
_Vector_name
$DNA_strand 'chemically synthesized' . . . . .
$entity_AR1 'chemically synthesized' . . . . .
stop_
save_
#####################################
# Sample contents and methodology #
#####################################
########################
# Sample description #
########################
save_sample_1
_Saveframe_category sample
_Sample_type solution
_Details .
loop_
_Mol_label
_Concentration_value
_Concentration_value_units
_Isotopic_labeling
$MGB 1.25 mM .
stop_
save_
#########################
# Experimental detail #
#########################
##################################
# NMR Spectrometer definitions #
##################################
save_spectrometer_1
_Saveframe_category NMR_spectrometer
_Manufacturer VARIAN
_Model Unity
_Field_strength 750
_Details .
save_
save_spectrometer_2
_Saveframe_category NMR_spectrometer
_Manufacturer VARIAN
_Model VXR
_Field_strength 500
_Details .
save_
#############################
# NMR applied experiments #
#############################
save_NOESY_1
_Saveframe_category NMR_applied_experiment
_Experiment_name NOESY
_Sample_label $sample_1
save_
save_TOCSY_2
_Saveframe_category NMR_applied_experiment
_Experiment_name TOCSY
_Sample_label $sample_1
save_
#######################
# Sample conditions #
#######################
save_sample_conditions_set_1
_Saveframe_category sample_conditions
_Details .
loop_
_Variable_type
_Variable_value
_Variable_value_error
_Variable_value_units
pH 7.0 0.2 n/a
temperature 275 1 K
stop_
save_
####################
# NMR parameters #
####################
##############################
# Assigned chemical shifts #
##############################
################################
# Chemical shift referencing #
################################
save_chemical_shift_reference_set_1
_Saveframe_category chemical_shift_reference
_Details .
loop_
_Mol_common_name
_Atom_type
_Atom_isotope_number
_Atom_group
_Chem_shift_units
_Chem_shift_value
_Reference_method
_Reference_type
_External_reference_sample_geometry
_External_reference_location
_External_reference_axis
_Indirect_shift_ratio
DSS H 1 'methyl protons' ppm 0.0 internal direct . . . 1.0
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_set_1
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Sample_label
$sample_1
stop_
_Sample_conditions_label $sample_conditions_set_1
_Chem_shift_reference_set_label $chemical_shift_reference_set_1
_Mol_system_component_name 'DNA strand A'
_Text_data_format .
_Text_data .
loop_
_Atom_shift_assign_ID
_Residue_author_seq_code
_Residue_seq_code
_Residue_label
_Atom_name
_Atom_type
_Chem_shift_value
_Chem_shift_value_error
_Chem_shift_ambiguity_code
1 . 1 DG H5'' H 3.681 . 1
2 . 1 DG H5' H 3.681 . 1
3 . 1 DG H4' H 4.134 . 1
4 . 1 DG H3' H 4.823 . 1
5 . 1 DG H2' H 2.695 . 1
6 . 1 DG H1' H 5.527 . 1
7 . 1 DG H8 H 7.821 . 1
8 . 2 DA H5'' H 4.030 . 1
9 . 2 DA H5' H 4.172 . 1
10 . 2 DA H4' H 4.422 . 1
11 . 2 DA H3' H 5.068 . 1
12 . 2 DA H2' H 3.009 . 1
13 . 2 DA H1' H 6.117 . 1
14 . 2 DA H2 H 7.545 . 1
15 . 2 DA H8 H 8.157 . 1
16 . 3 DA H5'' H 4.239 . 1
17 . 3 DA H5' H 4.239 . 1
18 . 3 DA H4' H 4.411 . 1
19 . 3 DA H3' H 5.005 . 1
20 . 3 DA H2' H 2.591 . 1
21 . 3 DA H1' H 5.920 . 1
22 . 3 DA H2 H 7.699 . 1
23 . 3 DA H8 H 8.138 . 1
24 . 4 DC H5'' H 4.143 . 1
25 . 4 DC H5' H 4.142 . 1
26 . 4 DC H4' H 4.217 . 1
27 . 4 DC H3' H 4.951 . 1
28 . 4 DC H2' H 2.278 . 1
29 . 4 DC H1' H 6.223 . 1
30 . 4 DC H5 H 5.131 . 1
31 . 4 DC H6 H 7.485 . 1
32 . 5 DC H5'' H 3.694 . 1
33 . 5 DC H5' H 3.899 . 1
34 . 5 DC H4' H 3.329 . 1
35 . 5 DC H3' H 4.616 . 1
36 . 5 DC H2' H 2.543 . 1
37 . 5 DC H1' H 4.803 . 1
38 . 5 DC H5 H 5.376 . 1
39 . 5 DC H6 H 7.420 . 1
40 . 6 DG H5'' H 3.202 . 1
41 . 6 DG H5' H 3.716 . 1
42 . 6 DG H4' H 3.274 . 1
43 . 6 DG H3' H 4.718 . 1
44 . 6 DG H2' H 2.671 . 1
45 . 6 DG H1' H 5.430 . 1
46 . 6 DG H8 H 7.457 . 1
47 . 7 DG H5'' H 3.539 . 1
48 . 7 DG H5' H 3.539 . 1
49 . 7 DG H4' H 3.868 . 1
50 . 7 DG H3' H 4.619 . 1
51 . 7 DG H2' H 1.986 . 1
52 . 7 DG H1' H 5.221 . 1
53 . 7 DG H8 H 7.511 . 1
54 . 8 DT H5'' H 3.610 . 1
55 . 8 DT H5' H 3.805 . 1
56 . 8 DT H4' H 2.041 . 1
57 . 8 DT H3' H 4.427 . 1
58 . 8 DT H2' H 1.870 . 1
59 . 8 DT H1' H 5.415 . 1
60 . 8 DT H71 H 1.518 . 1
61 . 8 DT H72 H 1.518 . 1
62 . 8 DT H73 H 1.518 . 1
63 . 8 DT H6 H 6.881 . 1
64 . 9 DT H5'' H 3.693 . 1
65 . 9 DT H5' H 4.077 . 1
66 . 9 DT H4' H 4.305 . 1
67 . 9 DT H3' H 4.903 . 1
68 . 9 DT H2' H 2.469 . 1
69 . 9 DT H1' H 6.146 . 1
70 . 9 DT H71 H 1.558 . 1
71 . 9 DT H72 H 1.558 . 1
72 . 9 DT H73 H 1.558 . 1
73 . 9 DT H6 H 7.376 . 1
74 . 10 DC H5'' H 4.040 . 1
75 . 10 DC H5' H 4.040 . 1
76 . 10 DC H4' H 3.976 . 1
77 . 10 DC H3' H 4.511 . 1
78 . 10 DC H2' H 2.179 . 1
79 . 10 DC H1' H 6.160 . 1
80 . 10 DC H5 H 5.650 . 1
81 . 10 DC H6 H 7.535 . 1
stop_
save_
save_assigned_chemical_shifts_set_2
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Sample_label
$sample_1
stop_
_Sample_conditions_label $sample_conditions_set_1
_Chem_shift_reference_set_label $chemical_shift_reference_set_1
_Mol_system_component_name 'DNA strand A'
_Text_data_format .
_Text_data .
loop_
_Atom_shift_assign_ID
_Residue_author_seq_code
_Residue_seq_code
_Residue_label
_Atom_name
_Atom_type
_Chem_shift_value
_Chem_shift_value_error
_Chem_shift_ambiguity_code
1 . 1 DG H2' H 2.447 . 1
2 . 2 DA H2' H 2.732 . 1
3 . 3 DA H2' H 2.659 . 1
4 . 4 DC H2' H 2.109 . 1
5 . 5 DC H2' H 2.005 . 1
6 . 6 DG H2' H 2.277 . 1
7 . 7 DG H2' H 2.648 . 1
8 . 8 DT H2' H 1.518 . 1
9 . 9 DT H2' H 2.239 . 1
10 . 10 DC H2' H 2.179 . 1
stop_
save_
save_assigned_chemical_shifts_set_3
_Saveframe_category assigned_chemical_shifts
_Details .
loop_
_Sample_label
$sample_1
stop_
_Sample_conditions_label $sample_conditions_set_1
_Chem_shift_reference_set_label $chemical_shift_reference_set_1
_Mol_system_component_name AR-1-144
_Text_data_format .
_Text_data .
loop_
_Atom_shift_assign_ID
_Residue_author_seq_code
_Residue_seq_code
_Residue_label
_Atom_name
_Atom_type
_Chem_shift_value
_Chem_shift_value_error
_Chem_shift_ambiguity_code
1 . 1 AR1 1FOR_H1 H 7.703 . 1
2 . 1 AR1 2MIM_H5 H 6.684 . 1
3 . 1 AR1 2MIM_HNA H 3.871 . 1
4 . 1 AR1 3MIM_H5 H 7.626 . 1
5 . 1 AR1 3MIM_HNA H 4.062 . 1
6 . 1 AR1 4MIM_H5 H 7.638 . 1
7 . 1 AR1 4MIM_HNA H 4.062 . 1
8 . 1 AR1 TAI_H11 H 3.474 . 1
9 . 1 AR1 TAI_H12 H 3.431 . 1
10 . 1 AR1 TAI_H21 H 3.955 . 1
11 . 1 AR1 TAI_H22 H 3.340 . 1
12 . 1 AR1 TAI_H1 H 3.170 . 1
13 . 1 AR1 TAI_H2 H 2.982 . 1
stop_
save_