data_2LOA # _entry.id 2LOA # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2LOA pdb_00002loa 10.2210/pdb2loa/pdb RCSB RCSB102628 ? ? BMRB 18199 ? ? WWPDB D_1000102628 ? ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 2lo5 PDB . unspecified 2lo8 PDB . unspecified 18199 BMRB . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LOA _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-01-20 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Morrow, J.R.' 1 'Fountain, M.A.' 2 'del Mundo, I.A.' 3 'Siter, K.E.' 4 # _citation.id primary _citation.title 'Structural Basis for Bifunctional Zinc(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA.' _citation.journal_abbrev Inorg.Chem. _citation.journal_volume 51 _citation.page_first 5444 _citation.page_last 5457 _citation.year 2012 _citation.journal_id_ASTM INOCAJ _citation.country US _citation.journal_id_ISSN 0020-1669 _citation.journal_id_CSD 0009 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22507054 _citation.pdbx_database_id_DOI 10.1021/ic3004245 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Del Mundo, I.M.' 1 ? primary 'Siters, K.E.' 2 ? primary 'Fountain, M.A.' 3 ? primary 'Morrow, J.R.' 4 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3') ; 3045.993 1 ? ? ? ? 2 non-polymer syn '4-(1,4,7,10-tetraazacyclododecan-1-ylmethyl)quinoline' 313.440 1 ? ? ? ? 3 non-polymer syn 'ZINC ION' 65.409 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DG)(DC)(DC)(DG)(DC)(DA)(DG)(DT)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCCGCAGTGC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DC n 1 4 DG n 1 5 DC n 1 6 DA n 1 7 DG n 1 8 DT n 1 9 DG n 1 10 DC n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2LOA _struct_ref.pdbx_db_accession 2LOA _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2LOA _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2LOA _struct_ref_seq.db_align_beg 2 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 11 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 2 _struct_ref_seq.pdbx_auth_seq_align_end 11 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight C4Q non-polymer . '4-(1,4,7,10-tetraazacyclododecan-1-ylmethyl)quinoline' ? 'C18 H27 N5' 313.440 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D DQF-COSY' 1 2 1 '2D 1H-1H TOCSY' 1 3 1 '2D 1H-1H NOESY' 2 4 2 '2D 1H-1H NOESY' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.temperature_units 1 0.1 7.5 ambient ? 293 K 2 0.1 7.5 ambient ? 278 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;0.6 mM DNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3'), 100% D2O ; 1 '100% D2O' ;2.0 mM DNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3'), 90% H2O/10% D2O ; 2 '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.field_strength 500 _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Varian INOVA' # _pdbx_nmr_refine.entry_id 2LOA _pdbx_nmr_refine.method 'DGSA-distance geometry simulated annealing, Docking with energy minimization' _pdbx_nmr_refine.details ;One of the structures from PDB 2lo8 was selected and used for docking of of the Zn(cy4q), One conformer was selected from the the cyana calculation above and the Zn(cy4q) docked using energy minimization and distance restraints obtained from NMR data. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with acceptable covalent geometry' _pdbx_nmr_ensemble.conformers_calculated_total_number 1 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2LOA _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2LOA _pdbx_nmr_representative.selection_criteria 'most favorable docked structure' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Guntert, Mumenthaler and Wuthrich' 'geometry optimization' CYANA 2.1 1 Goddard 'chemical shift assignment' Sparky 3.14 2 Goddard 'data analysis' Sparky 3.14 3 'HyperCube, Inc' refinement HyperChem 6 4 'Guntert, Mumenthaler and Wuthrich' refinement CYANA 2.1 5 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details 'NMR structure if a thymine bulge with a Zn 1-(4-quinoylyl)methyl-1,4,7,10-tetraazacyclododecane complex bound' _exptl.entry_id 2LOA _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LOA _struct.title 'Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA' _struct.pdbx_model_details 'most favorable docked structure, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2LOA _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'thymine bulge, BIFUNCTIONAL ZN(II) MACROCYCLIC COMPLEX, DNA, cyclen' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A DT 8 O2 ? ? ? 1_555 C ZN . ZN ? ? A DT 9 A ZN 102 1_555 ? ? ? ? ? ? ? 1.885 ? ? metalc2 metalc ? ? B C4Q . "N4'" ? ? ? 1_555 C ZN . ZN ? ? A C4Q 101 A ZN 102 1_555 ? ? ? ? ? ? ? 2.635 ? ? metalc3 metalc ? ? B C4Q . "N3'" ? ? ? 1_555 C ZN . ZN ? ? A C4Q 101 A ZN 102 1_555 ? ? ? ? ? ? ? 2.670 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DC 10 N3 ? ? A DG 2 A DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 10 O2 ? ? A DG 2 A DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 10 N4 ? ? A DG 2 A DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 3 A DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 3 A DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 3 A DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 A DG 7 N1 ? ? A DC 4 A DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 A DG 7 O6 ? ? A DC 4 A DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 A DG 7 N2 ? ? A DC 4 A DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DA 6 N7 ? ? A DG 5 A DA 7 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog11 hydrog ? ? A DG 4 N3 ? ? ? 1_555 A DA 6 N6 ? ? A DG 5 A DA 7 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A C4Q 101 ? 3 'BINDING SITE FOR RESIDUE C4Q A 101' AC2 Software A ZN 102 ? 2 'BINDING SITE FOR RESIDUE ZN A 102' 1 ? ? ? ? ? ? ? # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 3 DG A 7 ? DG A 8 . ? 1_555 ? 2 AC1 3 DT A 8 ? DT A 9 . ? 1_555 ? 3 AC1 3 ZN C . ? ZN A 102 . ? 1_555 ? 4 AC2 2 DT A 8 ? DT A 9 . ? 1_555 ? 5 AC2 2 C4Q B . ? C4Q A 101 . ? 1_555 ? # _atom_sites.entry_id 2LOA _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P ZN # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 2 2 DG DG A . n A 1 2 DC 2 3 3 DC DC A . n A 1 3 DC 3 4 4 DC DC A . n A 1 4 DG 4 5 5 DG DG A . n A 1 5 DC 5 6 6 DC DC A . n A 1 6 DA 6 7 7 DA DA A . n A 1 7 DG 7 8 8 DG DG A . n A 1 8 DT 8 9 9 DT DT A . n A 1 9 DG 9 10 10 DG DG A . n A 1 10 DC 10 11 11 DC DC A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 C4Q 1 101 12 C4Q C4Q A . C 3 ZN 1 102 13 ZN C4Q A . # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'OUTSIDE BINDER' # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O2 ? A DT 8 ? A DT 9 ? 1_555 ZN ? C ZN . ? A ZN 102 ? 1_555 "N4'" ? B C4Q . ? A C4Q 101 ? 1_555 171.4 ? 2 O2 ? A DT 8 ? A DT 9 ? 1_555 ZN ? C ZN . ? A ZN 102 ? 1_555 "N3'" ? B C4Q . ? A C4Q 101 ? 1_555 108.3 ? 3 "N4'" ? B C4Q . ? A C4Q 101 ? 1_555 ZN ? C ZN . ? A ZN 102 ? 1_555 "N3'" ? B C4Q . ? A C4Q 101 ? 1_555 64.6 ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2012-03-14 2 'Structure model' 1 1 2012-05-23 3 'Structure model' 1 2 2023-06-14 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' database_2 2 3 'Structure model' pdbx_database_status 3 3 'Structure model' pdbx_nmr_software 4 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 3 'Structure model' '_pdbx_nmr_software.name' 5 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id ;DNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3')-1 ; 0.6 ? mM ? 1 ;DNA (5'-D(*GP*CP*CP*GP*CP*AP*GP*TP*GP*C)-3')-2 ; 2.0 ? mM ? 2 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2LOA _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count 4 _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count 4 _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count 8 _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count 6 _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count 4 _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count 4 _pdbx_nmr_constraints.NA_other-angle_constraints_total_count 0 _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count 0 _pdbx_nmr_constraints.NOE_constraints_total 118 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count ? _pdbx_nmr_constraints.NOE_long_range_total_count 64 _pdbx_nmr_constraints.NOE_medium_range_total_count ? _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count ? _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 N3 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 DT _pdbx_validate_close_contact.auth_seq_id_1 9 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 ZN _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 ZN _pdbx_validate_close_contact.auth_seq_id_2 102 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.50 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O4'" A DG 8 ? ? "C4'" A DG 8 ? ? 1.375 1.446 -0.071 0.010 N 2 1 "O4'" A DT 9 ? ? "C4'" A DT 9 ? ? 1.377 1.446 -0.069 0.010 N 3 1 C4 A DT 9 ? ? O4 A DT 9 ? ? 1.121 1.228 -0.107 0.009 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? 102.03 104.50 -2.47 0.40 N 2 1 "C1'" A DG 2 ? ? "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? 115.09 110.30 4.79 0.70 N 3 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.21 108.30 2.91 0.30 N 4 1 C6 A DG 2 ? ? N1 A DG 2 ? ? C2 A DG 2 ? ? 118.50 125.10 -6.60 0.60 N 5 1 N1 A DG 2 ? ? C2 A DG 2 ? ? N3 A DG 2 ? ? 129.11 123.90 5.21 0.60 N 6 1 C5 A DG 2 ? ? C6 A DG 2 ? ? N1 A DG 2 ? ? 117.40 111.50 5.90 0.50 N 7 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 111.15 108.30 2.85 0.30 N 8 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 111.17 108.30 2.87 0.30 N 9 1 "C1'" A DG 5 ? ? "O4'" A DG 5 ? ? "C4'" A DG 5 ? ? 115.20 110.30 4.90 0.70 N 10 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 111.15 108.30 2.85 0.30 N 11 1 C6 A DG 5 ? ? N1 A DG 5 ? ? C2 A DG 5 ? ? 118.46 125.10 -6.64 0.60 N 12 1 N1 A DG 5 ? ? C2 A DG 5 ? ? N3 A DG 5 ? ? 129.13 123.90 5.23 0.60 N 13 1 C5 A DG 5 ? ? C6 A DG 5 ? ? N1 A DG 5 ? ? 117.44 111.50 5.94 0.50 N 14 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 111.15 108.30 2.85 0.30 N 15 1 "O4'" A DA 7 ? ? "C4'" A DA 7 ? ? "C3'" A DA 7 ? ? 98.98 104.50 -5.52 0.40 N 16 1 "C1'" A DA 7 ? ? "O4'" A DA 7 ? ? "C4'" A DA 7 ? ? 117.32 110.30 7.02 0.70 N 17 1 "O4'" A DA 7 ? ? "C1'" A DA 7 ? ? N9 A DA 7 ? ? 111.17 108.30 2.87 0.30 N 18 1 "O4'" A DG 8 ? ? "C4'" A DG 8 ? ? "C3'" A DG 8 ? ? 97.93 104.50 -6.57 0.40 N 19 1 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 111.23 108.30 2.93 0.30 N 20 1 C6 A DG 8 ? ? N1 A DG 8 ? ? C2 A DG 8 ? ? 118.55 125.10 -6.55 0.60 N 21 1 N1 A DG 8 ? ? C2 A DG 8 ? ? N3 A DG 8 ? ? 129.08 123.90 5.18 0.60 N 22 1 C5 A DG 8 ? ? C6 A DG 8 ? ? N1 A DG 8 ? ? 117.35 111.50 5.85 0.50 N 23 1 "O4'" A DT 9 ? ? "C4'" A DT 9 ? ? "C3'" A DT 9 ? ? 94.90 104.50 -9.60 0.40 N 24 1 "C5'" A DT 9 ? ? "C4'" A DT 9 ? ? "O4'" A DT 9 ? ? 120.56 109.80 10.76 1.10 N 25 1 "C1'" A DT 9 ? ? "O4'" A DT 9 ? ? "C4'" A DT 9 ? ? 116.85 110.30 6.55 0.70 N 26 1 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.20 108.30 2.90 0.30 N 27 1 C2 A DT 9 ? ? N3 A DT 9 ? ? C4 A DT 9 ? ? 123.60 127.20 -3.60 0.60 N 28 1 N3 A DT 9 ? ? C4 A DT 9 ? ? O4 A DT 9 ? ? 113.12 119.90 -6.78 0.60 N 29 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 111.17 108.30 2.87 0.30 N 30 1 C6 A DG 10 ? ? N1 A DG 10 ? ? C2 A DG 10 ? ? 118.52 125.10 -6.58 0.60 N 31 1 N1 A DG 10 ? ? C2 A DG 10 ? ? N3 A DG 10 ? ? 129.11 123.90 5.21 0.60 N 32 1 C5 A DG 10 ? ? C6 A DG 10 ? ? N1 A DG 10 ? ? 117.35 111.50 5.85 0.50 N 33 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? N1 A DC 11 ? ? 111.18 108.30 2.88 0.30 N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id DT _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 9 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.055 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2LOA 'b-form double helix' 2LOA 'hairpin loop' 2LOA 'bulge loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 1 1_555 A DC 10 1_555 -0.668 -0.248 0.120 -9.153 3.262 -1.043 1 A_DG2:DC11_A A 2 ? A 11 ? 19 1 1 A DC 2 1_555 A DG 9 1_555 0.341 -0.494 -1.345 12.565 4.885 -9.782 2 A_DC3:DG10_A A 3 ? A 10 ? 19 1 1 A DC 3 1_555 A DG 7 1_555 -0.301 -0.037 -0.531 20.181 7.230 -2.950 3 A_DC4:DG8_A A 4 ? A 8 ? 19 1 1 A DG 4 1_555 A DA 6 1_555 6.175 -4.327 1.867 16.520 -27.091 7.512 4 A_DG5:DA7_A A 5 ? A 7 ? 11 9 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 1 1_555 A DC 10 1_555 A DC 2 1_555 A DG 9 1_555 -0.523 0.743 3.360 4.109 -11.485 39.679 2.265 1.174 2.976 -16.454 -5.888 41.439 1 AA_DG2DC3:DG10DC11_AA A 2 ? A 11 ? A 3 ? A 10 ? 1 A DC 2 1_555 A DG 9 1_555 A DC 3 1_555 A DG 7 1_555 1.223 1.593 4.216 -8.317 32.068 21.713 -3.440 -3.317 3.378 55.809 14.474 39.443 2 AA_DC3DC4:DG8DG10_AA A 3 ? A 10 ? A 4 ? A 8 ? 1 A DC 3 1_555 A DG 7 1_555 A DG 4 1_555 A DA 6 1_555 -0.443 2.133 3.416 2.760 19.612 34.508 0.354 1.047 3.981 30.183 -4.247 39.637 3 AA_DC4DG5:DA7DG8_AA A 4 ? A 8 ? A 5 ? A 7 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '4-(1,4,7,10-tetraazacyclododecan-1-ylmethyl)quinoline' C4Q 3 'ZINC ION' ZN #