data_6DY5 # _entry.id 6DY5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 6DY5 pdb_00006dy5 10.2210/pdb6dy5/pdb WWPDB D_1000235405 ? ? # 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 2019-01-23 2 'Structure model' 1 1 2019-12-04 3 'Structure model' 1 2 2024-03-13 # _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' 'Author supporting evidence' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # 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 2 'Structure model' pdbx_audit_support 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 'Structure model' pdbx_struct_conn_angle 6 3 'Structure model' struct_conn # 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 2 'Structure model' '_pdbx_audit_support.funding_organization' 2 2 'Structure model' '_pdbx_audit_support.grant_number' 3 3 'Structure model' '_database_2.pdbx_DOI' 4 3 'Structure model' '_database_2.pdbx_database_accession' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.value' 8 3 'Structure model' '_struct_conn.pdbx_dist_value' 9 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 10 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 11 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 12 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 13 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 14 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 15 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 16 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 17 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 18 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 19 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 20 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 21 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6DY5 _pdbx_database_status.recvd_initial_deposition_date 2018-07-01 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Hou, C.' 1 ? 'Tsodikov, O.V.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country DK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_id_ASTM ABCRE6 _citation.journal_id_CSD 0766 _citation.journal_id_ISSN 0907-4449 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 75 _citation.language ? _citation.page_first 32 _citation.page_last ? _citation.title 'Utilizing guanine coordinated Zn2+ to determine DNA crystal structures by single-wavelength anomalous diffraction' _citation.year 2019 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hou, C.' 1 ? primary 'Tsodikov, O.V.' 2 ? # 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(*AP*GP*GP*GP*AP*TP*CP*CP*CP*T)-3') ; 3045.005 2 ? ? ? ? 2 non-polymer syn SPERMIDINE 145.246 1 ? ? ? ? 3 non-polymer syn 'ZINC ION' 65.409 3 ? ? ? ? 4 water nat water 18.015 96 ? ? ? ? # _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 '(DA)(DG)(DG)(DG)(DA)(DT)(DC)(DC)(DC)(DT)' _entity_poly.pdbx_seq_one_letter_code_can AGGGATCCCT _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 SPERMIDINE SPD 3 'ZINC ION' ZN 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DG n 1 3 DG n 1 4 DG n 1 5 DA n 1 6 DT n 1 7 DC n 1 8 DC n 1 9 DC n 1 10 DT n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 10 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # 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 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 HOH non-polymer . WATER ? 'H2 O' 18.015 SPD non-polymer . SPERMIDINE 'N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)' 'C7 H19 N3' 145.246 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # 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 DA 1 0 0 DA DA A . n A 1 2 DG 2 1 1 DG DG A . n A 1 3 DG 3 2 2 DG DG A . n A 1 4 DG 4 3 3 DG DG A . n A 1 5 DA 5 4 4 DA DA A . n A 1 6 DT 6 5 5 DT DT A . n A 1 7 DC 7 6 6 DC DC A . n A 1 8 DC 8 7 7 DC DC A . n A 1 9 DC 9 8 8 DC DC A . n A 1 10 DT 10 9 9 DT DT A . n B 1 1 DA 1 8 8 DA DA B . n B 1 2 DG 2 9 9 DG DG B . n B 1 3 DG 3 10 10 DG DG B . n B 1 4 DG 4 11 11 DG DG B . n B 1 5 DA 5 12 12 DA DA B . n B 1 6 DT 6 13 13 DT DT B . n B 1 7 DC 7 14 14 DC DC B . n B 1 8 DC 8 15 15 DC DC B . n B 1 9 DC 9 16 16 DC DC B . n B 1 10 DT 10 17 17 DT DT B . 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 C 2 SPD 1 101 500 SPD SPD A . D 3 ZN 1 102 1 ZN ZN A . E 3 ZN 1 101 1 ZN ZN B . F 3 ZN 1 102 1 ZN ZN B . G 4 HOH 1 201 8 HOH HOH A . G 4 HOH 2 202 23 HOH HOH A . G 4 HOH 3 203 106 HOH HOH A . G 4 HOH 4 204 66 HOH HOH A . G 4 HOH 5 205 103 HOH HOH A . G 4 HOH 6 206 7 HOH HOH A . G 4 HOH 7 207 83 HOH HOH A . G 4 HOH 8 208 80 HOH HOH A . G 4 HOH 9 209 105 HOH HOH A . G 4 HOH 10 210 122 HOH HOH A . G 4 HOH 11 211 81 HOH HOH A . G 4 HOH 12 212 51 HOH HOH A . G 4 HOH 13 213 19 HOH HOH A . G 4 HOH 14 214 30 HOH HOH A . G 4 HOH 15 215 12 HOH HOH A . G 4 HOH 16 216 36 HOH HOH A . G 4 HOH 17 217 111 HOH HOH A . G 4 HOH 18 218 25 HOH HOH A . G 4 HOH 19 219 24 HOH HOH A . G 4 HOH 20 220 68 HOH HOH A . G 4 HOH 21 221 91 HOH HOH A . G 4 HOH 22 222 4 HOH HOH A . G 4 HOH 23 223 90 HOH HOH A . G 4 HOH 24 224 39 HOH HOH A . G 4 HOH 25 225 6 HOH HOH A . G 4 HOH 26 226 57 HOH HOH A . G 4 HOH 27 227 89 HOH HOH A . G 4 HOH 28 228 58 HOH HOH A . G 4 HOH 29 229 28 HOH HOH A . G 4 HOH 30 230 29 HOH HOH A . G 4 HOH 31 231 104 HOH HOH A . G 4 HOH 32 232 42 HOH HOH A . G 4 HOH 33 233 69 HOH HOH A . G 4 HOH 34 234 72 HOH HOH A . G 4 HOH 35 235 108 HOH HOH A . G 4 HOH 36 236 61 HOH HOH A . G 4 HOH 37 237 71 HOH HOH A . G 4 HOH 38 238 20 HOH HOH A . G 4 HOH 39 239 45 HOH HOH A . G 4 HOH 40 240 34 HOH HOH A . G 4 HOH 41 241 63 HOH HOH A . G 4 HOH 42 242 88 HOH HOH A . G 4 HOH 43 243 49 HOH HOH A . G 4 HOH 44 244 82 HOH HOH A . G 4 HOH 45 245 31 HOH HOH A . G 4 HOH 46 246 75 HOH HOH A . G 4 HOH 47 247 43 HOH HOH A . G 4 HOH 48 248 107 HOH HOH A . G 4 HOH 49 249 112 HOH HOH A . G 4 HOH 50 250 73 HOH HOH A . G 4 HOH 51 251 53 HOH HOH A . H 4 HOH 1 201 84 HOH HOH B . H 4 HOH 2 202 85 HOH HOH B . H 4 HOH 3 203 98 HOH HOH B . H 4 HOH 4 204 115 HOH HOH B . H 4 HOH 5 205 14 HOH HOH B . H 4 HOH 6 206 114 HOH HOH B . H 4 HOH 7 207 67 HOH HOH B . H 4 HOH 8 208 101 HOH HOH B . H 4 HOH 9 209 2 HOH HOH B . H 4 HOH 10 210 17 HOH HOH B . H 4 HOH 11 211 120 HOH HOH B . H 4 HOH 12 212 95 HOH HOH B . H 4 HOH 13 213 10 HOH HOH B . H 4 HOH 14 214 21 HOH HOH B . H 4 HOH 15 215 119 HOH HOH B . H 4 HOH 16 216 16 HOH HOH B . H 4 HOH 17 217 32 HOH HOH B . H 4 HOH 18 218 48 HOH HOH B . H 4 HOH 19 219 94 HOH HOH B . H 4 HOH 20 220 99 HOH HOH B . H 4 HOH 21 221 54 HOH HOH B . H 4 HOH 22 222 93 HOH HOH B . H 4 HOH 23 223 109 HOH HOH B . H 4 HOH 24 224 38 HOH HOH B . H 4 HOH 25 225 92 HOH HOH B . H 4 HOH 26 226 102 HOH HOH B . H 4 HOH 27 227 37 HOH HOH B . H 4 HOH 28 228 121 HOH HOH B . H 4 HOH 29 229 117 HOH HOH B . H 4 HOH 30 230 27 HOH HOH B . H 4 HOH 31 231 5 HOH HOH B . H 4 HOH 32 232 1 HOH HOH B . H 4 HOH 33 233 113 HOH HOH B . H 4 HOH 34 234 110 HOH HOH B . H 4 HOH 35 235 70 HOH HOH B . H 4 HOH 36 236 116 HOH HOH B . H 4 HOH 37 237 100 HOH HOH B . H 4 HOH 38 238 118 HOH HOH B . H 4 HOH 39 239 22 HOH HOH B . H 4 HOH 40 240 55 HOH HOH B . H 4 HOH 41 241 26 HOH HOH B . H 4 HOH 42 242 52 HOH HOH B . H 4 HOH 43 243 78 HOH HOH B . H 4 HOH 44 244 97 HOH HOH B . H 4 HOH 45 245 76 HOH HOH B . # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag N _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 1 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id A _pdbx_unobs_or_zero_occ_atoms.auth_comp_id SPD _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 101 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id N1 _pdbx_unobs_or_zero_occ_atoms.label_alt_id ? _pdbx_unobs_or_zero_occ_atoms.label_asym_id C _pdbx_unobs_or_zero_occ_atoms.label_comp_id SPD _pdbx_unobs_or_zero_occ_atoms.label_seq_id 1 _pdbx_unobs_or_zero_occ_atoms.label_atom_id N1 # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.8.0135 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? AutoSol ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 6DY5 _cell.details ? _cell.formula_units_Z ? _cell.length_a 25.567 _cell.length_a_esd ? _cell.length_b 42.451 _cell.length_b_esd ? _cell.length_c 49.212 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DY5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 6DY5 _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.19 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 43.90 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 294 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details ;1 mM ds DNA containing 5 mM zinc acetate, 2 mM spermine and 50 mM NaCl, incubated against 55% (v/v) 2-methyl-2,4-pentanediol (MPD) ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment ? # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MARMOSAIC 300 mm CCD' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-07-12 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9786 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 21-ID-G' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9786 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 21-ID-G _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 6DY5 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.25 _reflns.d_resolution_low 50.00 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 14675 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 97.3 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 6.8 _reflns.pdbx_Rmerge_I_obs 0.06 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 54 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 1.25 _reflns_shell.d_res_low 1.27 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 705 _reflns_shell.percent_possible_all 94.1 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 0.62 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy 5.1 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_R_split ? # _refine.aniso_B[1][1] 4.50 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][2] -2.23 _refine.aniso_B[2][3] 0.00 _refine.aniso_B[3][3] -2.27 _refine.B_iso_max ? _refine.B_iso_mean 25.919 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.955 _refine.correlation_coeff_Fo_to_Fc_free 0.943 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 6DY5 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.26 _refine.ls_d_res_low 30.00 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 13820 _refine.ls_number_reflns_R_free 791 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 96.99 _refine.ls_percent_reflns_R_free 5.4 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.21649 _refine.ls_R_factor_R_free 0.25374 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.21430 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.066 _refine.pdbx_overall_ESU_R_Free 0.063 _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B 4.399 _refine.overall_SU_ML 0.076 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id 1 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 404 _refine_hist.pdbx_number_atoms_ligand 12 _refine_hist.number_atoms_solvent 96 _refine_hist.number_atoms_total 512 _refine_hist.d_res_high 1.26 _refine_hist.d_res_low 30.00 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.008 0.011 472 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.005 0.020 262 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 1.146 1.183 701 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 1.955 3.000 580 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_1_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_2_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_3_deg ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_dihedral_angle_4_deg ? ? 'X-RAY DIFFRACTION' ? 0.071 0.200 60 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.017 0.020 243 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.012 0.020 103 ? r_gen_planes_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_nbtor_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_xyhbond_nbd_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_vdw_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_hbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_refined ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_symmetry_metal_ion_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcbond_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcangle_it ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_mcangle_other ? ? 'X-RAY DIFFRACTION' ? 1.860 2.394 472 ? r_scbond_it ? ? 'X-RAY DIFFRACTION' ? 1.861 2.394 473 ? r_scbond_other ? ? 'X-RAY DIFFRACTION' ? ? ? ? ? r_scangle_it ? ? 'X-RAY DIFFRACTION' ? 2.170 23.043 702 ? r_scangle_other ? ? 'X-RAY DIFFRACTION' ? 4.270 25.279 706 ? r_long_range_B_refined ? ? 'X-RAY DIFFRACTION' ? 4.186 ? 700 ? r_long_range_B_other ? ? 'X-RAY DIFFRACTION' ? 2.084 3.000 724 ? r_rigid_bond_restr ? ? 'X-RAY DIFFRACTION' ? 51.989 5.000 18 ? r_sphericity_free ? ? 'X-RAY DIFFRACTION' ? 16.842 5.000 746 ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.260 _refine_ls_shell.d_res_low 1.293 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 66 _refine_ls_shell.number_reflns_R_work 946 _refine_ls_shell.percent_reflns_obs 91.58 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free 0.514 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work 0.645 _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 6DY5 _struct.title 'Crystal structure of double-stranded DNA AGGGATCCCT in complex with Zn2+' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 6DY5 _struct_keywords.text 'palindrome, Zn-N7 coordination, mithramycin binding, ETS factor binding, DNA' _struct_keywords.pdbx_keywords DNA # 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 1 ? C N N 2 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 4 ? H N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 6DY5 _struct_ref.pdbx_db_accession 6DY5 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 6DY5 A 1 ? 10 ? 6DY5 0 ? 9 ? 0 9 2 1 6DY5 B 1 ? 10 ? 6DY5 8 ? 17 ? 8 17 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1390 ? 1 MORE -77 ? 1 'SSA (A^2)' 4030 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details 'double-stranded DNA' # _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_ _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 DG 3 N7 ? ? ? 1_555 D ZN . ZN ? ? A DG 2 A ZN 102 1_555 ? ? ? ? ? ? ? 2.135 ? ? metalc2 metalc ? ? D ZN . ZN ? ? ? 1_555 G HOH . O ? ? A ZN 102 A HOH 204 1_555 ? ? ? ? ? ? ? 2.020 ? ? metalc3 metalc ? ? D ZN . ZN ? ? ? 1_555 G HOH . O ? ? A ZN 102 A HOH 221 1_555 ? ? ? ? ? ? ? 2.007 ? ? metalc4 metalc ? ? D ZN . ZN ? ? ? 1_555 G HOH . O ? ? A ZN 102 A HOH 223 1_555 ? ? ? ? ? ? ? 2.029 ? ? metalc5 metalc ? ? D ZN . ZN ? ? ? 1_555 G HOH . O ? ? A ZN 102 A HOH 227 1_555 ? ? ? ? ? ? ? 2.015 ? ? metalc6 metalc ? ? D ZN . ZN ? ? ? 1_555 G HOH . O ? ? A ZN 102 A HOH 242 1_555 ? ? ? ? ? ? ? 2.035 ? ? metalc7 metalc ? ? B DG 2 N7 ? ? ? 1_555 E ZN . ZN ? ? B DG 9 B ZN 101 1_555 ? ? ? ? ? ? ? 2.117 ? ? metalc8 metalc ? ? B DG 4 N7 ? ? ? 1_555 F ZN . ZN ? ? B DG 11 B ZN 102 1_555 ? ? ? ? ? ? ? 2.488 ? ? metalc9 metalc ? ? E ZN . ZN ? ? ? 1_555 H HOH . O ? ? B ZN 101 B HOH 208 1_555 ? ? ? ? ? ? ? 1.913 ? ? metalc10 metalc ? ? E ZN . ZN ? ? ? 1_555 H HOH . O ? ? B ZN 101 B HOH 212 1_555 ? ? ? ? ? ? ? 1.990 ? ? metalc11 metalc ? ? E ZN . ZN ? ? ? 1_555 H HOH . O ? ? B ZN 101 B HOH 220 1_555 ? ? ? ? ? ? ? 1.983 ? ? metalc12 metalc ? ? E ZN . ZN ? ? ? 1_555 H HOH . O ? ? B ZN 101 B HOH 226 1_555 ? ? ? ? ? ? ? 1.999 ? ? metalc13 metalc ? ? E ZN . ZN ? ? ? 1_555 H HOH . O ? ? B ZN 101 B HOH 237 1_555 ? ? ? ? ? ? ? 2.000 ? ? metalc14 metalc ? ? F ZN . ZN ? ? ? 1_555 H HOH . O ? ? B ZN 102 B HOH 213 1_555 ? ? ? ? ? ? ? 2.514 ? ? metalc15 metalc ? ? F ZN . ZN ? ? ? 1_555 H HOH . O ? ? B ZN 102 B HOH 222 1_555 ? ? ? ? ? ? ? 2.136 ? ? metalc16 metalc ? ? F ZN . ZN ? ? ? 1_555 H HOH . O ? ? B ZN 102 B HOH 243 1_555 ? ? ? ? ? ? ? 2.178 ? ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 10 N3 ? ? A DA 0 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 10 O4 ? ? A DA 0 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 1 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 1 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 1 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 2 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 2 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 2 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 3 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 3 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 3 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 6 N3 ? ? A DA 4 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 4 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 5 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 5 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 6 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 6 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 6 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 7 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 7 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 7 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 8 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 8 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 8 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 9 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 9 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # 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 N7 ? A DG 3 ? A DG 2 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 204 ? 1_555 89.7 ? 2 N7 ? A DG 3 ? A DG 2 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 221 ? 1_555 93.8 ? 3 O ? G HOH . ? A HOH 204 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 221 ? 1_555 97.8 ? 4 N7 ? A DG 3 ? A DG 2 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 223 ? 1_555 95.9 ? 5 O ? G HOH . ? A HOH 204 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 223 ? 1_555 174.2 ? 6 O ? G HOH . ? A HOH 221 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 223 ? 1_555 80.7 ? 7 N7 ? A DG 3 ? A DG 2 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 227 ? 1_555 90.4 ? 8 O ? G HOH . ? A HOH 204 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 227 ? 1_555 88.6 ? 9 O ? G HOH . ? A HOH 221 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 227 ? 1_555 172.3 ? 10 O ? G HOH . ? A HOH 223 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 227 ? 1_555 92.4 ? 11 N7 ? A DG 3 ? A DG 2 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 242 ? 1_555 178.7 ? 12 O ? G HOH . ? A HOH 204 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 242 ? 1_555 89.4 ? 13 O ? G HOH . ? A HOH 221 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 242 ? 1_555 87.3 ? 14 O ? G HOH . ? A HOH 223 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 242 ? 1_555 84.9 ? 15 O ? G HOH . ? A HOH 227 ? 1_555 ZN ? D ZN . ? A ZN 102 ? 1_555 O ? G HOH . ? A HOH 242 ? 1_555 88.6 ? 16 N7 ? B DG 2 ? B DG 9 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 208 ? 1_555 86.6 ? 17 N7 ? B DG 2 ? B DG 9 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 212 ? 1_555 90.9 ? 18 O ? H HOH . ? B HOH 208 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 212 ? 1_555 80.0 ? 19 N7 ? B DG 2 ? B DG 9 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 220 ? 1_555 97.5 ? 20 O ? H HOH . ? B HOH 208 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 220 ? 1_555 175.8 ? 21 O ? H HOH . ? B HOH 212 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 220 ? 1_555 100.3 ? 22 N7 ? B DG 2 ? B DG 9 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 226 ? 1_555 92.7 ? 23 O ? H HOH . ? B HOH 208 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 226 ? 1_555 88.0 ? 24 O ? H HOH . ? B HOH 212 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 226 ? 1_555 167.2 ? 25 O ? H HOH . ? B HOH 220 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 226 ? 1_555 91.4 ? 26 N7 ? B DG 2 ? B DG 9 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 237 ? 1_555 170.9 ? 27 O ? H HOH . ? B HOH 208 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 237 ? 1_555 84.3 ? 28 O ? H HOH . ? B HOH 212 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 237 ? 1_555 87.1 ? 29 O ? H HOH . ? B HOH 220 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 237 ? 1_555 91.6 ? 30 O ? H HOH . ? B HOH 226 ? 1_555 ZN ? E ZN . ? B ZN 101 ? 1_555 O ? H HOH . ? B HOH 237 ? 1_555 87.4 ? 31 N7 ? B DG 4 ? B DG 11 ? 1_555 ZN ? F ZN . ? B ZN 102 ? 1_555 O ? H HOH . ? B HOH 213 ? 1_555 95.8 ? 32 N7 ? B DG 4 ? B DG 11 ? 1_555 ZN ? F ZN . ? B ZN 102 ? 1_555 O ? H HOH . ? B HOH 222 ? 1_555 98.4 ? 33 O ? H HOH . ? B HOH 213 ? 1_555 ZN ? F ZN . ? B ZN 102 ? 1_555 O ? H HOH . ? B HOH 222 ? 1_555 77.7 ? 34 N7 ? B DG 4 ? B DG 11 ? 1_555 ZN ? F ZN . ? B ZN 102 ? 1_555 O ? H HOH . ? B HOH 243 ? 1_555 172.8 ? 35 O ? H HOH . ? B HOH 213 ? 1_555 ZN ? F ZN . ? B ZN 102 ? 1_555 O ? H HOH . ? B HOH 243 ? 1_555 88.7 ? 36 O ? H HOH . ? B HOH 222 ? 1_555 ZN ? F ZN . ? B ZN 102 ? 1_555 O ? H HOH . ? B HOH 243 ? 1_555 88.1 ? # 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 SPD 101 ? 2 'binding site for residue SPD A 101' AC2 Software A ZN 102 ? 6 'binding site for residue ZN A 102' AC3 Software B ZN 101 ? 6 'binding site for residue ZN B 101' AC4 Software B ZN 102 ? 4 'binding site for residue ZN B 102' # 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 2 DA A 5 ? DA A 4 . ? 1_555 ? 2 AC1 2 DT A 6 ? DT A 5 . ? 1_555 ? 3 AC2 6 DG A 3 ? DG A 2 . ? 1_555 ? 4 AC2 6 HOH G . ? HOH A 204 . ? 1_555 ? 5 AC2 6 HOH G . ? HOH A 221 . ? 1_555 ? 6 AC2 6 HOH G . ? HOH A 223 . ? 1_555 ? 7 AC2 6 HOH G . ? HOH A 227 . ? 1_555 ? 8 AC2 6 HOH G . ? HOH A 242 . ? 1_555 ? 9 AC3 6 DG B 2 ? DG B 9 . ? 1_555 ? 10 AC3 6 HOH H . ? HOH B 208 . ? 1_555 ? 11 AC3 6 HOH H . ? HOH B 212 . ? 1_555 ? 12 AC3 6 HOH H . ? HOH B 220 . ? 1_555 ? 13 AC3 6 HOH H . ? HOH B 226 . ? 1_555 ? 14 AC3 6 HOH H . ? HOH B 237 . ? 1_555 ? 15 AC4 4 DG B 4 ? DG B 11 . ? 1_555 ? 16 AC4 4 HOH H . ? HOH B 213 . ? 1_555 ? 17 AC4 4 HOH H . ? HOH B 222 . ? 1_555 ? 18 AC4 4 HOH H . ? HOH B 243 . ? 1_555 ? # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id B _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 245 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.19 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 SPD N1 N N N 147 SPD C2 C N N 148 SPD C3 C N N 149 SPD C4 C N N 150 SPD C5 C N N 151 SPD N6 N N N 152 SPD C7 C N N 153 SPD C8 C N N 154 SPD C9 C N N 155 SPD N10 N N N 156 SPD HN11 H N N 157 SPD HN12 H N N 158 SPD H21 H N N 159 SPD H22 H N N 160 SPD H31 H N N 161 SPD H32 H N N 162 SPD H41 H N N 163 SPD H42 H N N 164 SPD H51 H N N 165 SPD H52 H N N 166 SPD HN6 H N N 167 SPD H71 H N N 168 SPD H72 H N N 169 SPD H81 H N N 170 SPD H82 H N N 171 SPD H91 H N N 172 SPD H92 H N N 173 SPD H101 H N N 174 SPD H102 H N N 175 ZN ZN ZN N N 176 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 SPD N1 C2 sing N N 152 SPD N1 HN11 sing N N 153 SPD N1 HN12 sing N N 154 SPD C2 C3 sing N N 155 SPD C2 H21 sing N N 156 SPD C2 H22 sing N N 157 SPD C3 C4 sing N N 158 SPD C3 H31 sing N N 159 SPD C3 H32 sing N N 160 SPD C4 C5 sing N N 161 SPD C4 H41 sing N N 162 SPD C4 H42 sing N N 163 SPD C5 N6 sing N N 164 SPD C5 H51 sing N N 165 SPD C5 H52 sing N N 166 SPD N6 C7 sing N N 167 SPD N6 HN6 sing N N 168 SPD C7 C8 sing N N 169 SPD C7 H71 sing N N 170 SPD C7 H72 sing N N 171 SPD C8 C9 sing N N 172 SPD C8 H81 sing N N 173 SPD C8 H82 sing N N 174 SPD C9 N10 sing N N 175 SPD C9 H91 sing N N 176 SPD C9 H92 sing N N 177 SPD N10 H101 sing N N 178 SPD N10 H102 sing N N 179 # _ndb_struct_conf_na.entry_id 6DY5 _ndb_struct_conf_na.feature 'a-form double helix' # 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 DA 1 1_555 B DT 10 1_555 -0.210 -0.189 -0.295 -13.494 -9.985 4.041 1 A_DA0:DT17_B A 0 ? B 17 ? 20 1 1 A DG 2 1_555 B DC 9 1_555 -0.250 -0.146 0.202 -3.220 -10.023 1.253 2 A_DG1:DC16_B A 1 ? B 16 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.298 -0.069 -0.076 -14.293 -9.905 0.515 3 A_DG2:DC15_B A 2 ? B 15 ? 19 1 1 A DG 4 1_555 B DC 7 1_555 -0.240 -0.080 -0.227 -7.165 -15.149 0.841 4 A_DG3:DC14_B A 3 ? B 14 ? 19 1 1 A DA 5 1_555 B DT 6 1_555 0.008 -0.064 0.076 -1.360 -10.281 -1.316 5 A_DA4:DT13_B A 4 ? B 13 ? 20 1 1 A DT 6 1_555 B DA 5 1_555 -0.041 -0.039 -0.043 13.033 -9.986 6.056 6 A_DT5:DA12_B A 5 ? B 12 ? 20 1 1 A DC 7 1_555 B DG 4 1_555 0.418 -0.063 -0.175 10.678 -13.808 2.842 7 A_DC6:DG11_B A 6 ? B 11 ? 19 1 1 A DC 8 1_555 B DG 3 1_555 0.387 -0.150 -0.023 -0.097 -5.311 -0.230 8 A_DC7:DG10_B A 7 ? B 10 ? 19 1 1 A DC 9 1_555 B DG 2 1_555 0.281 -0.076 0.046 -1.573 -8.668 1.816 9 A_DC8:DG9_B A 8 ? B 9 ? 19 1 1 A DT 10 1_555 B DA 1 1_555 0.064 -0.123 0.009 15.543 4.159 -0.201 10 A_DT9:DA8_B A 9 ? B 8 ? 20 1 # 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 DA 1 1_555 B DT 10 1_555 A DG 2 1_555 B DC 9 1_555 0.847 -1.915 3.062 -1.065 2.802 22.791 -5.691 -2.461 2.767 7.052 2.681 22.984 1 AA_DA0DG1:DC16DT17_BB A 0 ? B 17 ? A 1 ? B 16 ? 1 A DG 2 1_555 B DC 9 1_555 A DG 3 1_555 B DC 8 1_555 0.127 -1.614 3.592 7.316 0.089 33.331 -2.767 1.063 3.535 0.153 -12.568 34.102 2 AA_DG1DG2:DC15DC16_BB A 1 ? B 16 ? A 2 ? B 15 ? 1 A DG 3 1_555 B DC 8 1_555 A DG 4 1_555 B DC 7 1_555 -0.514 -0.583 3.160 -2.029 13.456 35.065 -2.562 0.550 2.784 21.365 3.222 37.536 3 AA_DG2DG3:DC14DC15_BB A 2 ? B 15 ? A 3 ? B 14 ? 1 A DG 4 1_555 B DC 7 1_555 A DA 5 1_555 B DT 6 1_555 1.116 -1.578 3.180 2.453 17.227 23.778 -6.216 -1.757 1.763 36.238 -5.160 29.391 4 AA_DG3DA4:DT13DC14_BB A 3 ? B 14 ? A 4 ? B 13 ? 1 A DA 5 1_555 B DT 6 1_555 A DT 6 1_555 B DA 5 1_555 0.722 -0.972 2.971 1.455 6.320 31.361 -2.772 -1.077 2.757 11.538 -2.656 32.008 5 AA_DA4DT5:DA12DT13_BB A 4 ? B 13 ? A 5 ? B 12 ? 1 A DT 6 1_555 B DA 5 1_555 A DC 7 1_555 B DG 4 1_555 0.524 -2.185 3.179 3.493 11.489 27.410 -6.272 -0.397 2.157 22.903 -6.963 29.879 6 AA_DT5DC6:DG11DA12_BB A 5 ? B 12 ? A 6 ? B 11 ? 1 A DC 7 1_555 B DG 4 1_555 A DC 8 1_555 B DG 3 1_555 -0.339 -2.351 3.482 -1.267 8.559 33.874 -5.186 0.376 2.833 14.400 2.132 34.930 7 AA_DC6DC7:DG10DG11_BB A 6 ? B 11 ? A 7 ? B 10 ? 1 A DC 8 1_555 B DG 3 1_555 A DC 9 1_555 B DG 2 1_555 -0.392 -2.392 3.232 0.911 9.102 24.103 -7.549 1.098 2.181 20.860 -2.088 25.756 8 AA_DC7DC8:DG9DG10_BB A 7 ? B 10 ? A 8 ? B 9 ? 1 A DC 9 1_555 B DG 2 1_555 A DT 10 1_555 B DA 1 1_555 -0.572 -1.834 3.146 -3.538 -3.503 27.690 -2.945 0.341 3.393 -7.246 7.318 28.126 9 AA_DC8DT9:DA8DG9_BB A 8 ? B 9 ? A 9 ? B 8 ? # _pdbx_audit_support.funding_organization 'Department of Defense (DOD, United States)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number PC150300P1 _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 6DY5 _atom_sites.fract_transf_matrix[1][1] 0.039113 _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] 0.023557 _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] 0.020320 _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 N O P ZN # loop_