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_