data_9VGY # _entry.id 9VGY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.413 _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 9VGY pdb_00009vgy 10.2210/pdb9vgy/pdb WWPDB D_1300060659 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2026-06-17 _pdbx_audit_revision_history.part_number ? # _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 ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9VGY _pdbx_database_status.recvd_initial_deposition_date 2025-06-15 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible N # _pdbx_contact_author.id 2 _pdbx_contact_author.email j.kondo@sophia.ac.jp _pdbx_contact_author.name_first Jiro _pdbx_contact_author.name_last Kondo _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-5682-3685 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kondo, J.' 1 0000-0002-5682-3685 'Atsugi, T.' 2 ? 'Ono, A.' 3 0000-0002-2150-7084 # _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 ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'DNA-Stabilized Triangular Mercury(II) Nanocluster' _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 0000-0002-5682-3685 primary 'Atsugi, T.' 2 ? primary 'Ono, A.' 3 0000-0002-2150-7084 # 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(*CP*GP*CP*GP*AP*XP*XP*(BRU)P*CP*GP*CP*G)-3') ; 3751.380 4 ? ? ? ? 2 non-polymer syn 'MERCURY (II) ION' 200.590 6 ? ? ? ? 3 water nat water 18.015 62 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DG)(DA)(A1AAZ)(A1AAZ)(BRU)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAXXUCGCG _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MERCURY (II) ION' HG 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 DA n 1 6 A1AAZ n 1 7 A1AAZ n 1 8 BRU n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 DG 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 12 _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 A1AAZ 'DNA linking' n 2-thio-thymidine ? 'C10 H15 N2 O7 P S' 338.274 BRU 'DNA linking' n "5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O8 P' 387.078 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 HG non-polymer . 'MERCURY (II) ION' ? 'Hg 2' 200.590 HOH non-polymer . WATER ? 'H2 O' 18.015 # 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 DC 1 1 ? ? ? A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 A1AAZ 6 6 6 A1AAZ NDR A . n A 1 7 A1AAZ 7 7 7 A1AAZ NDR A . n A 1 8 BRU 8 8 8 BRU BRU A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 DC 1 1 1 DC DC B . n B 1 2 DG 2 2 2 DG DG B . n B 1 3 DC 3 3 3 DC DC B . n B 1 4 DG 4 4 4 DG DG B . n B 1 5 DA 5 5 5 DA DA B . n B 1 6 A1AAZ 6 6 6 A1AAZ NDR B . n B 1 7 A1AAZ 7 7 7 A1AAZ NDR B . n B 1 8 BRU 8 8 8 BRU BRU B . n B 1 9 DC 9 9 9 DC DC B . n B 1 10 DG 10 10 10 DG DG B . n B 1 11 DC 11 11 11 DC DC B . n B 1 12 DG 12 12 12 DG DG B . n C 1 1 DC 1 1 ? ? ? C . n C 1 2 DG 2 2 2 DG DG C . n C 1 3 DC 3 3 3 DC DC C . n C 1 4 DG 4 4 4 DG DG C . n C 1 5 DA 5 5 5 DA DA C . n C 1 6 A1AAZ 6 6 6 A1AAZ NDR C . n C 1 7 A1AAZ 7 7 7 A1AAZ NDR C . n C 1 8 BRU 8 8 8 BRU BRU C . n C 1 9 DC 9 9 9 DC DC C . n C 1 10 DG 10 10 10 DG DG C . n C 1 11 DC 11 11 11 DC DC C . n C 1 12 DG 12 12 12 DG DG C . n D 1 1 DC 1 1 1 DC DC D . n D 1 2 DG 2 2 2 DG DG D . n D 1 3 DC 3 3 3 DC DC D . n D 1 4 DG 4 4 4 DG DG D . n D 1 5 DA 5 5 5 DA DA D . n D 1 6 A1AAZ 6 6 6 A1AAZ NDR D . n D 1 7 A1AAZ 7 7 7 A1AAZ NDR D . n D 1 8 BRU 8 8 8 BRU BRU D . n D 1 9 DC 9 9 9 DC DC D . n D 1 10 DG 10 10 10 DG DG D . n D 1 11 DC 11 11 11 DC DC D . n D 1 12 DG 12 12 12 DG DG D . 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 E 2 HG 1 101 1 HG HG A . F 2 HG 1 102 2 HG HG A . G 2 HG 1 103 3 HG HG A . H 2 HG 1 101 6 HG HG C . I 2 HG 1 101 4 HG HG D . J 2 HG 1 102 5 HG HG D . K 3 HOH 1 201 46 HOH HOH A . K 3 HOH 2 202 12 HOH HOH A . K 3 HOH 3 203 62 HOH HOH A . K 3 HOH 4 204 30 HOH HOH A . K 3 HOH 5 205 35 HOH HOH A . K 3 HOH 6 206 53 HOH HOH A . K 3 HOH 7 207 37 HOH HOH A . K 3 HOH 8 208 63 HOH HOH A . K 3 HOH 9 209 39 HOH HOH A . K 3 HOH 10 210 4 HOH HOH A . K 3 HOH 11 211 52 HOH HOH A . K 3 HOH 12 212 57 HOH HOH A . K 3 HOH 13 213 47 HOH HOH A . K 3 HOH 14 214 65 HOH HOH A . K 3 HOH 15 215 38 HOH HOH A . L 3 HOH 1 101 1 HOH HOH B . L 3 HOH 2 102 15 HOH HOH B . L 3 HOH 3 103 50 HOH HOH B . L 3 HOH 4 104 18 HOH HOH B . L 3 HOH 5 105 19 HOH HOH B . L 3 HOH 6 106 3 HOH HOH B . L 3 HOH 7 107 22 HOH HOH B . L 3 HOH 8 108 64 HOH HOH B . L 3 HOH 9 109 17 HOH HOH B . L 3 HOH 10 110 14 HOH HOH B . L 3 HOH 11 111 9 HOH HOH B . L 3 HOH 12 112 20 HOH HOH B . L 3 HOH 13 113 28 HOH HOH B . L 3 HOH 14 114 33 HOH HOH B . L 3 HOH 15 115 58 HOH HOH B . L 3 HOH 16 116 27 HOH HOH B . M 3 HOH 1 201 43 HOH HOH C . M 3 HOH 2 202 49 HOH HOH C . M 3 HOH 3 203 21 HOH HOH C . M 3 HOH 4 204 31 HOH HOH C . M 3 HOH 5 205 16 HOH HOH C . M 3 HOH 6 206 6 HOH HOH C . M 3 HOH 7 207 51 HOH HOH C . M 3 HOH 8 208 10 HOH HOH C . M 3 HOH 9 209 7 HOH HOH C . M 3 HOH 10 210 32 HOH HOH C . M 3 HOH 11 211 25 HOH HOH C . M 3 HOH 12 212 5 HOH HOH C . M 3 HOH 13 213 66 HOH HOH C . N 3 HOH 1 201 2 HOH HOH D . N 3 HOH 2 202 45 HOH HOH D . N 3 HOH 3 203 54 HOH HOH D . N 3 HOH 4 204 40 HOH HOH D . N 3 HOH 5 205 36 HOH HOH D . N 3 HOH 6 206 13 HOH HOH D . N 3 HOH 7 207 26 HOH HOH D . N 3 HOH 8 208 41 HOH HOH D . N 3 HOH 9 209 59 HOH HOH D . N 3 HOH 10 210 23 HOH HOH D . N 3 HOH 11 211 8 HOH HOH D . N 3 HOH 12 212 24 HOH HOH D . N 3 HOH 13 213 61 HOH HOH D . N 3 HOH 14 214 42 HOH HOH D . N 3 HOH 15 215 56 HOH HOH D . N 3 HOH 16 216 44 HOH HOH D . N 3 HOH 17 217 11 HOH HOH D . N 3 HOH 18 218 29 HOH HOH D . # 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_reference_DOI _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(1.20.1_4487: ???)' ? 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . ? 2 ? phasing ? ? ? ? ? ? ? ? ? ? ? AutoSol ? ? ? . ? 3 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? . ? 4 # _cell.entry_id 9VGY _cell.length_a 38.781 _cell.length_b 47.283 _cell.length_c 66.556 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9VGY _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # _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 9VGY _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 1.78 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 30.93 _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.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_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_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'MOPS, Spermine, MPD, NaNO3' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293 # _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 N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 2M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2016-12-10 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _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 0.91915 _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 'PHOTON FACTORY BEAMLINE BL-17A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.91915 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-17A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 9VGY _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 38.600 _reflns.d_resolution_high 1.910 _reflns.number_obs 18414 _reflns.number_all ? _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.06200 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 19.7900 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.800 _reflns.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_Rrim_I_all ? # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.91 _reflns_shell.d_res_low 1.96 _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_obs 0.25200 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_Rrim_I_all ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 9VGY _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 18409 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.420 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 38.55 _refine.ls_d_res_high 1.91 _refine.ls_percent_reflns_obs 99.9 _refine.ls_R_factor_obs 0.173 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.169 _refine.ls_R_factor_R_free 0.204 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.020 _refine.ls_number_reflns_R_free 1845 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.10 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.150 _refine.pdbx_overall_phase_error 18.790 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 936 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 62 _refine_hist.number_atoms_total 1004 _refine_hist.d_res_high 1.91 _refine_hist.d_res_low 38.55 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function f_bond_d 0.010 ? ? 1044 'X-RAY DIFFRACTION' ? f_angle_d 1.692 ? ? 1604 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 32.727 ? ? 374 'X-RAY DIFFRACTION' ? f_chiral_restr 0.075 ? ? 170 'X-RAY DIFFRACTION' ? f_plane_restr 0.013 ? ? 46 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.number_reflns_obs 'X-RAY DIFFRACTION' . 1.9100 1.9600 1261 0.1722 99.00 0.2446 . . 135 . . . . 'X-RAY DIFFRACTION' . 1.9600 2.0200 1286 0.1665 100.00 0.2071 . . 137 . . . . 'X-RAY DIFFRACTION' . 2.0200 2.0800 1275 0.1702 100.00 0.2171 . . 137 . . . . 'X-RAY DIFFRACTION' . 2.0800 2.1600 1298 0.1648 100.00 0.2012 . . 142 . . . . 'X-RAY DIFFRACTION' . 2.1600 2.2400 1258 0.1675 100.00 0.1840 . . 147 . . . . 'X-RAY DIFFRACTION' . 2.2400 2.3400 1273 0.1664 100.00 0.1995 . . 143 . . . . 'X-RAY DIFFRACTION' . 2.3400 2.4700 1281 0.1760 100.00 0.1891 . . 141 . . . . 'X-RAY DIFFRACTION' . 2.4700 2.6200 1283 0.1708 100.00 0.1977 . . 144 . . . . 'X-RAY DIFFRACTION' . 2.6200 2.8200 1271 0.1964 100.00 0.2589 . . 141 . . . . 'X-RAY DIFFRACTION' . 2.8200 3.1100 1259 0.2234 100.00 0.2337 . . 146 . . . . 'X-RAY DIFFRACTION' . 3.1100 3.5600 1275 0.1639 100.00 0.2211 . . 146 . . . . 'X-RAY DIFFRACTION' . 3.5600 4.4800 1269 0.1565 100.00 0.1946 . . 141 . . . . 'X-RAY DIFFRACTION' . 4.4900 38.5500 1275 0.1470 100.00 0.1695 . . 145 . . . . # _struct.entry_id 9VGY _struct.title 'DNA duplex containing Mercury(II)-mediated base pairs with 2-Thiothymine and 5-bromouracyl' _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 9VGY _struct_keywords.text 'Mercury, metal-mediated base pair, DNA, X-ray analysis' _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 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 2 ? K N N 3 ? L N N 3 ? M N N 3 ? N N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 9VGY _struct_ref.pdbx_db_accession 9VGY _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 9VGY A 1 ? 12 ? 9VGY 1 ? 12 ? 1 12 2 1 9VGY B 1 ? 12 ? 9VGY 1 ? 12 ? 1 12 3 1 9VGY C 1 ? 12 ? 9VGY 1 ? 12 ? 1 12 4 1 9VGY D 1 ? 12 ? 9VGY 1 ? 12 ? 1 12 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _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,I,J,K,L,M,N # _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 ? # _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 covale1 covale both ? A DA 5 "O3'" ? ? ? 1_555 A A1AAZ 6 P ? ? A DA 5 A A1AAZ 6 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale2 covale one ? A A1AAZ 6 "O3'" ? ? ? 1_555 A A1AAZ 7 P ? ? A A1AAZ 6 A A1AAZ 7 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale3 covale one ? A A1AAZ 7 "O3'" ? ? ? 1_555 A BRU 8 P ? ? A A1AAZ 7 A BRU 8 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale4 covale both ? A BRU 8 "O3'" ? ? ? 1_555 A DC 9 P ? ? A BRU 8 A DC 9 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale5 covale both ? B DA 5 "O3'" ? ? ? 1_555 B A1AAZ 6 P ? ? B DA 5 B A1AAZ 6 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale6 covale one ? B A1AAZ 6 "O3'" ? ? ? 1_555 B A1AAZ 7 P ? ? B A1AAZ 6 B A1AAZ 7 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale7 covale one ? B A1AAZ 7 "O3'" ? ? ? 1_555 B BRU 8 P ? ? B A1AAZ 7 B BRU 8 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale8 covale both ? B BRU 8 "O3'" ? ? ? 1_555 B DC 9 P ? ? B BRU 8 B DC 9 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale9 covale both ? C DA 5 "O3'" ? ? ? 1_555 C A1AAZ 6 P ? ? C DA 5 C A1AAZ 6 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale10 covale one ? C A1AAZ 6 "O3'" ? ? ? 1_555 C A1AAZ 7 P ? ? C A1AAZ 6 C A1AAZ 7 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale11 covale one ? C A1AAZ 7 "O3'" ? ? ? 1_555 C BRU 8 P ? ? C A1AAZ 7 C BRU 8 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale12 covale both ? C BRU 8 "O3'" ? ? ? 1_555 C DC 9 P ? ? C BRU 8 C DC 9 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale13 covale both ? D DA 5 "O3'" ? ? ? 1_555 D A1AAZ 6 P ? ? D DA 5 D A1AAZ 6 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale14 covale one ? D A1AAZ 6 "O3'" ? ? ? 1_555 D A1AAZ 7 P ? ? D A1AAZ 6 D A1AAZ 7 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale15 covale one ? D A1AAZ 7 "O3'" ? ? ? 1_555 D BRU 8 P ? ? D A1AAZ 7 D BRU 8 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale16 covale both ? D BRU 8 "O3'" ? ? ? 1_555 D DC 9 P ? ? D BRU 8 D DC 9 1_555 ? ? ? ? ? ? ? 1.606 ? ? metalc1 metalc ? ? A A1AAZ 6 N3 ? ? ? 1_555 G HG . HG ? ? A A1AAZ 6 A HG 103 1_555 ? ? ? ? ? ? ? 2.714 ? ? metalc2 metalc ? ? A A1AAZ 6 S1 ? ? ? 1_555 G HG . HG ? ? A A1AAZ 6 A HG 103 1_555 ? ? ? ? ? ? ? 2.415 ? ? metalc3 metalc ? ? A A1AAZ 7 N3 ? ? ? 1_555 F HG . HG ? ? A A1AAZ 7 A HG 102 1_555 ? ? ? ? ? ? ? 2.169 ? ? metalc4 metalc ? ? A A1AAZ 7 S1 ? ? ? 1_555 F HG . HG ? ? A A1AAZ 7 A HG 102 1_555 ? ? ? ? ? ? ? 3.057 ? ? metalc5 metalc ? ? A A1AAZ 7 S1 ? ? ? 1_555 G HG . HG ? ? A A1AAZ 7 A HG 103 1_555 ? ? ? ? ? ? ? 2.788 ? ? metalc6 metalc ? ? A BRU 8 N3 ? ? ? 1_555 E HG . HG ? ? A BRU 8 A HG 101 1_555 ? ? ? ? ? ? ? 2.056 ? ? metalc7 metalc ? ? A BRU 8 O2 ? ? ? 1_555 E HG . HG ? ? A BRU 8 A HG 101 1_555 ? ? ? ? ? ? ? 3.192 ? ? metalc8 metalc ? ? A BRU 8 O4 ? ? ? 1_555 E HG . HG ? ? A BRU 8 A HG 101 1_555 ? ? ? ? ? ? ? 2.962 ? ? metalc9 metalc ? ? E HG . HG ? ? ? 1_555 B A1AAZ 6 N3 ? ? A HG 101 B A1AAZ 6 1_555 ? ? ? ? ? ? ? 2.761 ? ? metalc10 metalc ? ? E HG . HG ? ? ? 1_555 B A1AAZ 6 S1 ? ? A HG 101 B A1AAZ 6 1_555 ? ? ? ? ? ? ? 2.458 ? ? metalc11 metalc ? ? E HG . HG ? ? ? 1_555 B A1AAZ 7 S1 ? ? A HG 101 B A1AAZ 7 1_555 ? ? ? ? ? ? ? 2.886 ? ? metalc12 metalc ? ? F HG . HG ? ? ? 1_555 B A1AAZ 7 N3 ? ? A HG 102 B A1AAZ 7 1_555 ? ? ? ? ? ? ? 2.231 ? ? metalc13 metalc ? ? F HG . HG ? ? ? 1_555 B A1AAZ 7 S1 ? ? A HG 102 B A1AAZ 7 1_555 ? ? ? ? ? ? ? 3.046 ? ? metalc14 metalc ? ? G HG . HG ? ? ? 1_555 B BRU 8 N3 ? ? A HG 103 B BRU 8 1_555 ? ? ? ? ? ? ? 2.015 ? ? metalc15 metalc ? ? G HG . HG ? ? ? 1_555 B BRU 8 O2 ? ? A HG 103 B BRU 8 1_555 ? ? ? ? ? ? ? 2.968 ? ? metalc16 metalc ? ? G HG . HG ? ? ? 1_555 B BRU 8 O4 ? ? A HG 103 B BRU 8 1_555 ? ? ? ? ? ? ? 3.187 ? ? metalc17 metalc ? ? C A1AAZ 6 N3 ? ? ? 1_555 I HG . HG ? ? C A1AAZ 6 D HG 101 1_555 ? ? ? ? ? ? ? 2.733 ? ? metalc18 metalc ? ? C A1AAZ 6 S1 ? ? ? 1_555 I HG . HG ? ? C A1AAZ 6 D HG 101 1_555 ? ? ? ? ? ? ? 2.346 ? ? metalc19 metalc ? ? C A1AAZ 7 S1 ? ? ? 1_555 I HG . HG ? ? C A1AAZ 7 D HG 101 1_555 ? ? ? ? ? ? ? 2.807 ? ? metalc20 metalc ? ? C A1AAZ 7 N3 ? ? ? 1_555 J HG . HG ? ? C A1AAZ 7 D HG 102 1_555 ? ? ? ? ? ? ? 2.168 ? ? metalc21 metalc ? ? C A1AAZ 7 S1 ? ? ? 1_555 J HG . HG ? ? C A1AAZ 7 D HG 102 1_555 ? ? ? ? ? ? ? 2.972 ? ? metalc22 metalc ? ? C BRU 8 O2 ? ? ? 1_555 H HG . HG ? ? C BRU 8 C HG 101 1_555 ? ? ? ? ? ? ? 3.054 ? ? metalc23 metalc ? ? C BRU 8 O4 ? ? ? 1_555 H HG . HG ? ? C BRU 8 C HG 101 1_555 ? ? ? ? ? ? ? 3.147 ? ? metalc24 metalc ? ? H HG . HG ? ? ? 1_555 D A1AAZ 6 N3 ? ? C HG 101 D A1AAZ 6 1_555 ? ? ? ? ? ? ? 2.550 ? ? metalc25 metalc ? ? H HG . HG ? ? ? 1_555 D A1AAZ 6 S1 ? ? C HG 101 D A1AAZ 6 1_555 ? ? ? ? ? ? ? 2.413 ? ? metalc26 metalc ? ? H HG . HG ? ? ? 1_555 D A1AAZ 7 S1 ? ? C HG 101 D A1AAZ 7 1_555 ? ? ? ? ? ? ? 2.803 ? ? metalc27 metalc ? ? D A1AAZ 6 O4 ? ? ? 1_555 J HG . HG ? ? D A1AAZ 6 D HG 102 1_555 ? ? ? ? ? ? ? 3.155 ? ? metalc28 metalc ? ? D A1AAZ 7 N3 ? ? ? 1_555 J HG . HG ? ? D A1AAZ 7 D HG 102 1_555 ? ? ? ? ? ? ? 2.188 ? ? metalc29 metalc ? ? D A1AAZ 7 S1 ? ? ? 1_555 J HG . HG ? ? D A1AAZ 7 D HG 102 1_555 ? ? ? ? ? ? ? 3.034 ? ? metalc30 metalc ? ? D BRU 8 O2 ? ? ? 1_555 I HG . HG ? ? D BRU 8 D HG 101 1_555 ? ? ? ? ? ? ? 3.083 ? ? metalc31 metalc ? ? D BRU 8 O4 ? ? ? 1_555 I HG . HG ? ? D BRU 8 D HG 101 1_555 ? ? ? ? ? ? ? 3.086 ? ? hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N2 ? ? ? 1_555 D DG 12 N3 ? ? A DG 2 D DG 12 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog5 hydrog ? ? A DG 2 N3 ? ? ? 1_555 D DG 12 N2 ? ? A DG 2 D DG 12 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog6 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A BRU 8 O4 ? ? ? 1_555 B A1AAZ 6 N3 ? ? A BRU 8 B A1AAZ 6 1_555 ? ? ? ? ? ? 'BRU-A1AAZ MISPAIR' ? ? ? hydrog13 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B DG 12 N2 ? ? ? 1_555 C DG 2 N3 ? ? B DG 12 C DG 2 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog26 hydrog ? ? B DG 12 N3 ? ? ? 1_555 C DG 2 N2 ? ? B DG 12 C DG 2 1_555 ? ? ? ? ? ? TYPE_4_PAIR ? ? ? hydrog27 hydrog ? ? C DG 2 N1 ? ? ? 1_555 D DC 11 N3 ? ? C DG 2 D DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C DG 2 N2 ? ? ? 1_555 D DC 11 O2 ? ? C DG 2 D DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C DG 2 O6 ? ? ? 1_555 D DC 11 N4 ? ? C DG 2 D DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C DC 3 N3 ? ? ? 1_555 D DG 10 N1 ? ? C DC 3 D DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C DC 3 N4 ? ? ? 1_555 D DG 10 O6 ? ? C DC 3 D DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C DC 3 O2 ? ? ? 1_555 D DG 10 N2 ? ? C DC 3 D DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? C DG 4 N1 ? ? ? 1_555 D DC 9 N3 ? ? C DG 4 D DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? C DG 4 N2 ? ? ? 1_555 D DC 9 O2 ? ? C DG 4 D DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? C DG 4 O6 ? ? ? 1_555 D DC 9 N4 ? ? C DG 4 D DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? C A1AAZ 6 N3 ? ? ? 1_555 D BRU 8 O4 ? ? C A1AAZ 6 D BRU 8 1_555 ? ? ? ? ? ? 'A1AAZ-BRU MISPAIR' ? ? ? hydrog37 hydrog ? ? C BRU 8 O4 ? ? ? 1_555 D A1AAZ 6 N3 ? ? C BRU 8 D A1AAZ 6 1_555 ? ? ? ? ? ? 'BRU-A1AAZ MISPAIR' ? ? ? hydrog38 hydrog ? ? C DC 9 N3 ? ? ? 1_555 D DG 4 N1 ? ? C DC 9 D DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C DC 9 N4 ? ? ? 1_555 D DG 4 O6 ? ? C DC 9 D DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C DC 9 O2 ? ? ? 1_555 D DG 4 N2 ? ? C DC 9 D DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C DG 10 N1 ? ? ? 1_555 D DC 3 N3 ? ? C DG 10 D DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C DG 10 N2 ? ? ? 1_555 D DC 3 O2 ? ? C DG 10 D DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C DG 10 O6 ? ? ? 1_555 D DC 3 N4 ? ? C DG 10 D DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C DC 11 N3 ? ? ? 1_555 D DG 2 N1 ? ? C DC 11 D DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C DC 11 N4 ? ? ? 1_555 D DG 2 O6 ? ? C DC 11 D DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C DC 11 O2 ? ? ? 1_555 D DG 2 N2 ? ? C DC 11 D DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? C DG 12 N1 ? ? ? 1_555 D DC 1 N3 ? ? C DG 12 D DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? C DG 12 N2 ? ? ? 1_555 D DC 1 O2 ? ? C DG 12 D DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? C DG 12 O6 ? ? ? 1_555 D DC 1 N4 ? ? C DG 12 D DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 N3 ? A A1AAZ 6 ? A A1AAZ 6 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 S1 ? A A1AAZ 6 ? A A1AAZ 6 ? 1_555 64.5 ? 2 N3 ? A A1AAZ 6 ? A A1AAZ 6 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 S1 ? A A1AAZ 7 ? A A1AAZ 7 ? 1_555 94.7 ? 3 S1 ? A A1AAZ 6 ? A A1AAZ 6 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 S1 ? A A1AAZ 7 ? A A1AAZ 7 ? 1_555 106.7 ? 4 N3 ? A A1AAZ 6 ? A A1AAZ 6 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 N3 ? B BRU 8 ? B BRU 8 ? 1_555 128.1 ? 5 S1 ? A A1AAZ 6 ? A A1AAZ 6 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 N3 ? B BRU 8 ? B BRU 8 ? 1_555 160.0 ? 6 S1 ? A A1AAZ 7 ? A A1AAZ 7 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 N3 ? B BRU 8 ? B BRU 8 ? 1_555 88.8 ? 7 N3 ? A A1AAZ 6 ? A A1AAZ 6 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 O2 ? B BRU 8 ? B BRU 8 ? 1_555 175.7 ? 8 S1 ? A A1AAZ 6 ? A A1AAZ 6 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 O2 ? B BRU 8 ? B BRU 8 ? 1_555 117.9 ? 9 S1 ? A A1AAZ 7 ? A A1AAZ 7 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 O2 ? B BRU 8 ? B BRU 8 ? 1_555 81.2 ? 10 N3 ? B BRU 8 ? B BRU 8 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 O2 ? B BRU 8 ? B BRU 8 ? 1_555 50.8 ? 11 N3 ? A A1AAZ 6 ? A A1AAZ 6 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 O4 ? B BRU 8 ? B BRU 8 ? 1_555 83.1 ? 12 S1 ? A A1AAZ 6 ? A A1AAZ 6 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 O4 ? B BRU 8 ? B BRU 8 ? 1_555 141.5 ? 13 S1 ? A A1AAZ 7 ? A A1AAZ 7 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 O4 ? B BRU 8 ? B BRU 8 ? 1_555 95.6 ? 14 N3 ? B BRU 8 ? B BRU 8 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 O4 ? B BRU 8 ? B BRU 8 ? 1_555 45.1 ? 15 O2 ? B BRU 8 ? B BRU 8 ? 1_555 HG ? G HG . ? A HG 103 ? 1_555 O4 ? B BRU 8 ? B BRU 8 ? 1_555 95.9 ? 16 N3 ? A A1AAZ 7 ? A A1AAZ 7 ? 1_555 HG ? F HG . ? A HG 102 ? 1_555 S1 ? A A1AAZ 7 ? A A1AAZ 7 ? 1_555 60.1 ? 17 N3 ? A A1AAZ 7 ? A A1AAZ 7 ? 1_555 HG ? F HG . ? A HG 102 ? 1_555 N3 ? B A1AAZ 7 ? B A1AAZ 7 ? 1_555 177.6 ? 18 S1 ? A A1AAZ 7 ? A A1AAZ 7 ? 1_555 HG ? F HG . ? A HG 102 ? 1_555 N3 ? B A1AAZ 7 ? B A1AAZ 7 ? 1_555 120.5 ? 19 N3 ? A A1AAZ 7 ? A A1AAZ 7 ? 1_555 HG ? F HG . ? A HG 102 ? 1_555 S1 ? B A1AAZ 7 ? B A1AAZ 7 ? 1_555 120.6 ? 20 S1 ? A A1AAZ 7 ? A A1AAZ 7 ? 1_555 HG ? F HG . ? A HG 102 ? 1_555 S1 ? B A1AAZ 7 ? B A1AAZ 7 ? 1_555 73.2 ? 21 N3 ? B A1AAZ 7 ? B A1AAZ 7 ? 1_555 HG ? F HG . ? A HG 102 ? 1_555 S1 ? B A1AAZ 7 ? B A1AAZ 7 ? 1_555 58.3 ? 22 N3 ? A BRU 8 ? A BRU 8 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 O2 ? A BRU 8 ? A BRU 8 ? 1_555 46.4 ? 23 N3 ? A BRU 8 ? A BRU 8 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 O4 ? A BRU 8 ? A BRU 8 ? 1_555 50.0 ? 24 O2 ? A BRU 8 ? A BRU 8 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 O4 ? A BRU 8 ? A BRU 8 ? 1_555 96.4 ? 25 N3 ? A BRU 8 ? A BRU 8 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 N3 ? B A1AAZ 6 ? B A1AAZ 6 ? 1_555 128.9 ? 26 O2 ? A BRU 8 ? A BRU 8 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 N3 ? B A1AAZ 6 ? B A1AAZ 6 ? 1_555 173.0 ? 27 O4 ? A BRU 8 ? A BRU 8 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 N3 ? B A1AAZ 6 ? B A1AAZ 6 ? 1_555 79.1 ? 28 N3 ? A BRU 8 ? A BRU 8 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 S1 ? B A1AAZ 6 ? B A1AAZ 6 ? 1_555 160.7 ? 29 O2 ? A BRU 8 ? A BRU 8 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 S1 ? B A1AAZ 6 ? B A1AAZ 6 ? 1_555 122.0 ? 30 O4 ? A BRU 8 ? A BRU 8 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 S1 ? B A1AAZ 6 ? B A1AAZ 6 ? 1_555 137.7 ? 31 N3 ? B A1AAZ 6 ? B A1AAZ 6 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 S1 ? B A1AAZ 6 ? B A1AAZ 6 ? 1_555 64.0 ? 32 N3 ? A BRU 8 ? A BRU 8 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 S1 ? B A1AAZ 7 ? B A1AAZ 7 ? 1_555 87.1 ? 33 O2 ? A BRU 8 ? A BRU 8 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 S1 ? B A1AAZ 7 ? B A1AAZ 7 ? 1_555 82.8 ? 34 O4 ? A BRU 8 ? A BRU 8 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 S1 ? B A1AAZ 7 ? B A1AAZ 7 ? 1_555 92.5 ? 35 N3 ? B A1AAZ 6 ? B A1AAZ 6 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 S1 ? B A1AAZ 7 ? B A1AAZ 7 ? 1_555 92.0 ? 36 S1 ? B A1AAZ 6 ? B A1AAZ 6 ? 1_555 HG ? E HG . ? A HG 101 ? 1_555 S1 ? B A1AAZ 7 ? B A1AAZ 7 ? 1_555 108.1 ? 37 N3 ? C A1AAZ 6 ? C A1AAZ 6 ? 1_555 HG ? I HG . ? D HG 101 ? 1_555 S1 ? C A1AAZ 6 ? C A1AAZ 6 ? 1_555 63.5 ? 38 N3 ? C A1AAZ 6 ? C A1AAZ 6 ? 1_555 HG ? I HG . ? D HG 101 ? 1_555 S1 ? C A1AAZ 7 ? C A1AAZ 7 ? 1_555 91.5 ? 39 S1 ? C A1AAZ 6 ? C A1AAZ 6 ? 1_555 HG ? I HG . ? D HG 101 ? 1_555 S1 ? C A1AAZ 7 ? C A1AAZ 7 ? 1_555 109.2 ? 40 N3 ? C A1AAZ 6 ? C A1AAZ 6 ? 1_555 HG ? I HG . ? D HG 101 ? 1_555 O2 ? D BRU 8 ? D BRU 8 ? 1_555 172.6 ? 41 S1 ? C A1AAZ 6 ? C A1AAZ 6 ? 1_555 HG ? I HG . ? D HG 101 ? 1_555 O2 ? D BRU 8 ? D BRU 8 ? 1_555 123.2 ? 42 S1 ? C A1AAZ 7 ? C A1AAZ 7 ? 1_555 HG ? I HG . ? D HG 101 ? 1_555 O2 ? D BRU 8 ? D BRU 8 ? 1_555 83.2 ? 43 N3 ? C A1AAZ 6 ? C A1AAZ 6 ? 1_555 HG ? I HG . ? D HG 101 ? 1_555 O4 ? D BRU 8 ? D BRU 8 ? 1_555 78.5 ? 44 S1 ? C A1AAZ 6 ? C A1AAZ 6 ? 1_555 HG ? I HG . ? D HG 101 ? 1_555 O4 ? D BRU 8 ? D BRU 8 ? 1_555 137.5 ? 45 S1 ? C A1AAZ 7 ? C A1AAZ 7 ? 1_555 HG ? I HG . ? D HG 101 ? 1_555 O4 ? D BRU 8 ? D BRU 8 ? 1_555 89.2 ? 46 O2 ? D BRU 8 ? D BRU 8 ? 1_555 HG ? I HG . ? D HG 101 ? 1_555 O4 ? D BRU 8 ? D BRU 8 ? 1_555 96.2 ? 47 N3 ? C A1AAZ 7 ? C A1AAZ 7 ? 1_555 HG ? J HG . ? D HG 102 ? 1_555 S1 ? C A1AAZ 7 ? C A1AAZ 7 ? 1_555 59.4 ? 48 N3 ? C A1AAZ 7 ? C A1AAZ 7 ? 1_555 HG ? J HG . ? D HG 102 ? 1_555 O4 ? D A1AAZ 6 ? D A1AAZ 6 ? 1_555 102.7 ? 49 S1 ? C A1AAZ 7 ? C A1AAZ 7 ? 1_555 HG ? J HG . ? D HG 102 ? 1_555 O4 ? D A1AAZ 6 ? D A1AAZ 6 ? 1_555 154.9 ? 50 N3 ? C A1AAZ 7 ? C A1AAZ 7 ? 1_555 HG ? J HG . ? D HG 102 ? 1_555 N3 ? D A1AAZ 7 ? D A1AAZ 7 ? 1_555 178.1 ? 51 S1 ? C A1AAZ 7 ? C A1AAZ 7 ? 1_555 HG ? J HG . ? D HG 102 ? 1_555 N3 ? D A1AAZ 7 ? D A1AAZ 7 ? 1_555 120.8 ? 52 O4 ? D A1AAZ 6 ? D A1AAZ 6 ? 1_555 HG ? J HG . ? D HG 102 ? 1_555 N3 ? D A1AAZ 7 ? D A1AAZ 7 ? 1_555 76.5 ? 53 N3 ? C A1AAZ 7 ? C A1AAZ 7 ? 1_555 HG ? J HG . ? D HG 102 ? 1_555 S1 ? D A1AAZ 7 ? D A1AAZ 7 ? 1_555 120.3 ? 54 S1 ? C A1AAZ 7 ? C A1AAZ 7 ? 1_555 HG ? J HG . ? D HG 102 ? 1_555 S1 ? D A1AAZ 7 ? D A1AAZ 7 ? 1_555 74.6 ? 55 O4 ? D A1AAZ 6 ? D A1AAZ 6 ? 1_555 HG ? J HG . ? D HG 102 ? 1_555 S1 ? D A1AAZ 7 ? D A1AAZ 7 ? 1_555 104.7 ? 56 N3 ? D A1AAZ 7 ? D A1AAZ 7 ? 1_555 HG ? J HG . ? D HG 102 ? 1_555 S1 ? D A1AAZ 7 ? D A1AAZ 7 ? 1_555 58.5 ? 57 O2 ? C BRU 8 ? C BRU 8 ? 1_555 HG ? H HG . ? C HG 101 ? 1_555 O4 ? C BRU 8 ? C BRU 8 ? 1_555 96.3 ? 58 O2 ? C BRU 8 ? C BRU 8 ? 1_555 HG ? H HG . ? C HG 101 ? 1_555 N3 ? D A1AAZ 6 ? D A1AAZ 6 ? 1_555 174.2 ? 59 O4 ? C BRU 8 ? C BRU 8 ? 1_555 HG ? H HG . ? C HG 101 ? 1_555 N3 ? D A1AAZ 6 ? D A1AAZ 6 ? 1_555 78.2 ? 60 O2 ? C BRU 8 ? C BRU 8 ? 1_555 HG ? H HG . ? C HG 101 ? 1_555 S1 ? D A1AAZ 6 ? D A1AAZ 6 ? 1_555 118.3 ? 61 O4 ? C BRU 8 ? C BRU 8 ? 1_555 HG ? H HG . ? C HG 101 ? 1_555 S1 ? D A1AAZ 6 ? D A1AAZ 6 ? 1_555 139.8 ? 62 N3 ? D A1AAZ 6 ? D A1AAZ 6 ? 1_555 HG ? H HG . ? C HG 101 ? 1_555 S1 ? D A1AAZ 6 ? D A1AAZ 6 ? 1_555 67.5 ? 63 O2 ? C BRU 8 ? C BRU 8 ? 1_555 HG ? H HG . ? C HG 101 ? 1_555 S1 ? D A1AAZ 7 ? D A1AAZ 7 ? 1_555 84.0 ? 64 O4 ? C BRU 8 ? C BRU 8 ? 1_555 HG ? H HG . ? C HG 101 ? 1_555 S1 ? D A1AAZ 7 ? D A1AAZ 7 ? 1_555 91.1 ? 65 N3 ? D A1AAZ 6 ? D A1AAZ 6 ? 1_555 HG ? H HG . ? C HG 101 ? 1_555 S1 ? D A1AAZ 7 ? D A1AAZ 7 ? 1_555 94.0 ? 66 S1 ? D A1AAZ 6 ? D A1AAZ 6 ? 1_555 HG ? H HG . ? C HG 101 ? 1_555 S1 ? D A1AAZ 7 ? D A1AAZ 7 ? 1_555 111.0 ? # _pdbx_entry_details.entry_id 9VGY _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.has_protein_modification N # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DG _pdbx_validate_rmsd_bond.auth_seq_id_1 10 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C3'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DG _pdbx_validate_rmsd_bond.auth_seq_id_2 10 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.382 _pdbx_validate_rmsd_bond.bond_target_value 1.419 _pdbx_validate_rmsd_bond.bond_deviation -0.037 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.006 _pdbx_validate_rmsd_bond.linker_flag 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 "C3'" B DG 10 ? ? "C2'" B DG 10 ? ? "C1'" B DG 10 ? ? 96.75 102.40 -5.65 0.80 N 2 1 "O4'" B DG 10 ? ? "C1'" B DG 10 ? ? N9 B DG 10 ? ? 110.50 108.30 2.20 0.30 N 3 1 "O4'" C DG 12 ? ? "C1'" C DG 12 ? ? N9 C DG 12 ? ? 110.14 108.30 1.84 0.30 N 4 1 "O4'" D DG 10 ? ? "C1'" D DG 10 ? ? N9 D DG 10 ? ? 111.81 108.30 3.51 0.30 N # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A DC 1 ? A DC 1 2 1 Y 1 C DC 1 ? C DC 1 # 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 A1AAZ "C1'" C N R 1 A1AAZ C2 C N N 2 A1AAZ "C2'" C N N 3 A1AAZ "C3'" C N S 4 A1AAZ C4 C N N 5 A1AAZ "C4'" C N R 6 A1AAZ C5 C N N 7 A1AAZ "C5'" C N N 8 A1AAZ C6 C N N 9 A1AAZ C7 C N N 10 A1AAZ N1 N N N 11 A1AAZ N3 N N N 12 A1AAZ "O3'" O N N 13 A1AAZ O4 O N N 14 A1AAZ "O4'" O N N 15 A1AAZ "O5'" O N N 16 A1AAZ OP1 O N N 17 A1AAZ OP2 O N N 18 A1AAZ P P N N 19 A1AAZ S1 S N N 20 A1AAZ H1 H N N 21 A1AAZ H2 H N N 22 A1AAZ H3 H N N 23 A1AAZ H4 H N N 24 A1AAZ H5 H N N 25 A1AAZ H6 H N N 26 A1AAZ H7 H N N 27 A1AAZ H8 H N N 28 A1AAZ H9 H N N 29 A1AAZ H10 H N N 30 A1AAZ H11 H N N 31 A1AAZ H12 H N N 32 A1AAZ H15 H N N 33 A1AAZ OP3 O N N 34 A1AAZ H17 H N N 35 A1AAZ H13 H N N 36 BRU N1 N N N 37 BRU C2 C N N 38 BRU N3 N N N 39 BRU C4 C N N 40 BRU C5 C N N 41 BRU C6 C N N 42 BRU O2 O N N 43 BRU O4 O N N 44 BRU BR BR N N 45 BRU "C1'" C N R 46 BRU "C2'" C N N 47 BRU "C3'" C N S 48 BRU "C4'" C N R 49 BRU "O3'" O N N 50 BRU "O4'" O N N 51 BRU "C5'" C N N 52 BRU "O5'" O N N 53 BRU P P N N 54 BRU OP1 O N N 55 BRU OP2 O N N 56 BRU OP3 O N N 57 BRU HN3 H N N 58 BRU H6 H N N 59 BRU "H1'" H N N 60 BRU "H2'" H N N 61 BRU "H2''" H N N 62 BRU "H3'" H N N 63 BRU "H4'" H N N 64 BRU "HO3'" H N N 65 BRU "H5'" H N N 66 BRU "H5''" H N N 67 BRU HOP2 H N N 68 BRU HOP3 H N N 69 DA OP3 O N N 70 DA P P N N 71 DA OP1 O N N 72 DA OP2 O N N 73 DA "O5'" O N N 74 DA "C5'" C N N 75 DA "C4'" C N R 76 DA "O4'" O N N 77 DA "C3'" C N S 78 DA "O3'" O N N 79 DA "C2'" C N N 80 DA "C1'" C N R 81 DA N9 N Y N 82 DA C8 C Y N 83 DA N7 N Y N 84 DA C5 C Y N 85 DA C6 C Y N 86 DA N6 N N N 87 DA N1 N Y N 88 DA C2 C Y N 89 DA N3 N Y N 90 DA C4 C Y N 91 DA HOP3 H N N 92 DA HOP2 H N N 93 DA "H5'" H N N 94 DA "H5''" H N N 95 DA "H4'" H N N 96 DA "H3'" H N N 97 DA "HO3'" H N N 98 DA "H2'" H N N 99 DA "H2''" H N N 100 DA "H1'" H N N 101 DA H8 H N N 102 DA H61 H N N 103 DA H62 H N N 104 DA H2 H N N 105 DC OP3 O N N 106 DC P P N N 107 DC OP1 O N N 108 DC OP2 O N N 109 DC "O5'" O N N 110 DC "C5'" C N N 111 DC "C4'" C N R 112 DC "O4'" O N N 113 DC "C3'" C N S 114 DC "O3'" O N N 115 DC "C2'" C N N 116 DC "C1'" C N R 117 DC N1 N N N 118 DC C2 C N N 119 DC O2 O N N 120 DC N3 N N N 121 DC C4 C N N 122 DC N4 N N N 123 DC C5 C N N 124 DC C6 C N N 125 DC HOP3 H N N 126 DC HOP2 H N N 127 DC "H5'" H N N 128 DC "H5''" H N N 129 DC "H4'" H N N 130 DC "H3'" H N N 131 DC "HO3'" H N N 132 DC "H2'" H N N 133 DC "H2''" H N N 134 DC "H1'" H N N 135 DC H41 H N N 136 DC H42 H N N 137 DC H5 H N N 138 DC H6 H N N 139 DG OP3 O N N 140 DG P P N N 141 DG OP1 O N N 142 DG OP2 O N N 143 DG "O5'" O N N 144 DG "C5'" C N N 145 DG "C4'" C N R 146 DG "O4'" O N N 147 DG "C3'" C N S 148 DG "O3'" O N N 149 DG "C2'" C N N 150 DG "C1'" C N R 151 DG N9 N Y N 152 DG C8 C Y N 153 DG N7 N Y N 154 DG C5 C Y N 155 DG C6 C N N 156 DG O6 O N N 157 DG N1 N N N 158 DG C2 C N N 159 DG N2 N N N 160 DG N3 N N N 161 DG C4 C Y N 162 DG HOP3 H N N 163 DG HOP2 H N N 164 DG "H5'" H N N 165 DG "H5''" H N N 166 DG "H4'" H N N 167 DG "H3'" H N N 168 DG "HO3'" H N N 169 DG "H2'" H N N 170 DG "H2''" H N N 171 DG "H1'" H N N 172 DG H8 H N N 173 DG H1 H N N 174 DG H21 H N N 175 DG H22 H N N 176 HG HG HG N N 177 HOH O O N N 178 HOH H1 H N N 179 HOH H2 H N N 180 # 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 A1AAZ "C1'" "C2'" sing N N 1 A1AAZ "C1'" N1 sing N N 2 A1AAZ "C1'" "O4'" sing N N 3 A1AAZ C2 N1 sing N N 4 A1AAZ C2 N3 sing N N 5 A1AAZ C2 S1 doub N N 6 A1AAZ "C2'" "C3'" sing N N 7 A1AAZ "C3'" "C4'" sing N N 8 A1AAZ "C3'" "O3'" sing N N 9 A1AAZ C4 C5 sing N N 10 A1AAZ C4 N3 sing N N 11 A1AAZ C4 O4 doub N N 12 A1AAZ "C4'" "C5'" sing N N 13 A1AAZ "C4'" "O4'" sing N N 14 A1AAZ C5 C6 doub N N 15 A1AAZ C5 C7 sing N N 16 A1AAZ "C5'" "O5'" sing N N 17 A1AAZ C6 N1 sing N N 18 A1AAZ "O5'" P sing N N 19 A1AAZ OP1 P doub N N 20 A1AAZ OP2 P sing N N 21 A1AAZ "C1'" H1 sing N N 22 A1AAZ "C2'" H2 sing N N 23 A1AAZ "C2'" H3 sing N N 24 A1AAZ "C3'" H4 sing N N 25 A1AAZ "C4'" H5 sing N N 26 A1AAZ "C5'" H6 sing N N 27 A1AAZ "C5'" H7 sing N N 28 A1AAZ C6 H8 sing N N 29 A1AAZ C7 H9 sing N N 30 A1AAZ C7 H10 sing N N 31 A1AAZ C7 H11 sing N N 32 A1AAZ "O3'" H12 sing N N 33 A1AAZ OP2 H15 sing N N 34 A1AAZ P OP3 sing N N 35 A1AAZ N3 H17 sing N N 36 A1AAZ OP3 H13 sing N N 37 BRU N1 C2 sing N N 38 BRU N1 C6 sing N N 39 BRU N1 "C1'" sing N N 40 BRU C2 N3 sing N N 41 BRU C2 O2 doub N N 42 BRU N3 C4 sing N N 43 BRU N3 HN3 sing N N 44 BRU C4 C5 sing N N 45 BRU C4 O4 doub N N 46 BRU C5 C6 doub N N 47 BRU C5 BR sing N N 48 BRU C6 H6 sing N N 49 BRU "C1'" "C2'" sing N N 50 BRU "C1'" "O4'" sing N N 51 BRU "C1'" "H1'" sing N N 52 BRU "C2'" "C3'" sing N N 53 BRU "C2'" "H2'" sing N N 54 BRU "C2'" "H2''" sing N N 55 BRU "C3'" "C4'" sing N N 56 BRU "C3'" "O3'" sing N N 57 BRU "C3'" "H3'" sing N N 58 BRU "C4'" "O4'" sing N N 59 BRU "C4'" "C5'" sing N N 60 BRU "C4'" "H4'" sing N N 61 BRU "O3'" "HO3'" sing N N 62 BRU "C5'" "O5'" sing N N 63 BRU "C5'" "H5'" sing N N 64 BRU "C5'" "H5''" sing N N 65 BRU "O5'" P sing N N 66 BRU P OP1 doub N N 67 BRU P OP2 sing N N 68 BRU P OP3 sing N N 69 BRU OP2 HOP2 sing N N 70 BRU OP3 HOP3 sing N N 71 DA OP3 P sing N N 72 DA OP3 HOP3 sing N N 73 DA P OP1 doub N N 74 DA P OP2 sing N N 75 DA P "O5'" sing N N 76 DA OP2 HOP2 sing N N 77 DA "O5'" "C5'" sing N N 78 DA "C5'" "C4'" sing N N 79 DA "C5'" "H5'" sing N N 80 DA "C5'" "H5''" sing N N 81 DA "C4'" "O4'" sing N N 82 DA "C4'" "C3'" sing N N 83 DA "C4'" "H4'" sing N N 84 DA "O4'" "C1'" sing N N 85 DA "C3'" "O3'" sing N N 86 DA "C3'" "C2'" sing N N 87 DA "C3'" "H3'" sing N N 88 DA "O3'" "HO3'" sing N N 89 DA "C2'" "C1'" sing N N 90 DA "C2'" "H2'" sing N N 91 DA "C2'" "H2''" sing N N 92 DA "C1'" N9 sing N N 93 DA "C1'" "H1'" sing N N 94 DA N9 C8 sing Y N 95 DA N9 C4 sing Y N 96 DA C8 N7 doub Y N 97 DA C8 H8 sing N N 98 DA N7 C5 sing Y N 99 DA C5 C6 sing Y N 100 DA C5 C4 doub Y N 101 DA C6 N6 sing N N 102 DA C6 N1 doub Y N 103 DA N6 H61 sing N N 104 DA N6 H62 sing N N 105 DA N1 C2 sing Y N 106 DA C2 N3 doub Y N 107 DA C2 H2 sing N N 108 DA N3 C4 sing Y N 109 DC OP3 P sing N N 110 DC OP3 HOP3 sing N N 111 DC P OP1 doub N N 112 DC P OP2 sing N N 113 DC P "O5'" sing N N 114 DC OP2 HOP2 sing N N 115 DC "O5'" "C5'" sing N N 116 DC "C5'" "C4'" sing N N 117 DC "C5'" "H5'" sing N N 118 DC "C5'" "H5''" sing N N 119 DC "C4'" "O4'" sing N N 120 DC "C4'" "C3'" sing N N 121 DC "C4'" "H4'" sing N N 122 DC "O4'" "C1'" sing N N 123 DC "C3'" "O3'" sing N N 124 DC "C3'" "C2'" sing N N 125 DC "C3'" "H3'" sing N N 126 DC "O3'" "HO3'" sing N N 127 DC "C2'" "C1'" sing N N 128 DC "C2'" "H2'" sing N N 129 DC "C2'" "H2''" sing N N 130 DC "C1'" N1 sing N N 131 DC "C1'" "H1'" sing N N 132 DC N1 C2 sing N N 133 DC N1 C6 sing N N 134 DC C2 O2 doub N N 135 DC C2 N3 sing N N 136 DC N3 C4 doub N N 137 DC C4 N4 sing N N 138 DC C4 C5 sing N N 139 DC N4 H41 sing N N 140 DC N4 H42 sing N N 141 DC C5 C6 doub N N 142 DC C5 H5 sing N N 143 DC C6 H6 sing N N 144 DG OP3 P sing N N 145 DG OP3 HOP3 sing N N 146 DG P OP1 doub N N 147 DG P OP2 sing N N 148 DG P "O5'" sing N N 149 DG OP2 HOP2 sing N N 150 DG "O5'" "C5'" sing N N 151 DG "C5'" "C4'" sing N N 152 DG "C5'" "H5'" sing N N 153 DG "C5'" "H5''" sing N N 154 DG "C4'" "O4'" sing N N 155 DG "C4'" "C3'" sing N N 156 DG "C4'" "H4'" sing N N 157 DG "O4'" "C1'" sing N N 158 DG "C3'" "O3'" sing N N 159 DG "C3'" "C2'" sing N N 160 DG "C3'" "H3'" sing N N 161 DG "O3'" "HO3'" sing N N 162 DG "C2'" "C1'" sing N N 163 DG "C2'" "H2'" sing N N 164 DG "C2'" "H2''" sing N N 165 DG "C1'" N9 sing N N 166 DG "C1'" "H1'" sing N N 167 DG N9 C8 sing Y N 168 DG N9 C4 sing Y N 169 DG C8 N7 doub Y N 170 DG C8 H8 sing N N 171 DG N7 C5 sing Y N 172 DG C5 C6 sing N N 173 DG C5 C4 doub Y N 174 DG C6 O6 doub N N 175 DG C6 N1 sing N N 176 DG N1 C2 sing N N 177 DG N1 H1 sing N N 178 DG C2 N2 sing N N 179 DG C2 N3 doub N N 180 DG N2 H21 sing N N 181 DG N2 H22 sing N N 182 DG N3 C4 sing N N 183 HOH O H1 sing N N 184 HOH O H2 sing N N 185 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9VGY 'double helix' 9VGY 'b-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 B DC 9 1_555 A DG 4 1_555 0.235 -0.147 0.057 -4.812 -21.999 2.030 1 B_DC9:DG4_A B 9 ? A 4 ? 19 1 1 B DG 10 1_555 A DC 3 1_555 -0.127 -0.313 0.157 1.028 -4.161 -3.707 2 B_DG10:DC3_A B 10 ? A 3 ? 19 1 1 B DC 11 1_555 A DG 2 1_555 0.198 -0.155 0.236 -0.976 -0.669 0.137 3 B_DC11:DG2_A B 11 ? A 2 ? 19 1 1 C DG 2 1_555 D DC 11 1_555 -0.241 -0.204 0.200 -3.306 -5.026 -0.140 4 C_DG2:DC11_D C 2 ? D 11 ? 19 1 1 C DC 3 1_555 D DG 10 1_555 0.088 -0.197 0.271 -5.220 -5.075 -2.354 5 C_DC3:DG10_D C 3 ? D 10 ? 19 1 1 C DG 4 1_555 D DC 9 1_555 -0.227 -0.140 0.170 2.460 -18.831 0.407 6 C_DG4:DC9_D C 4 ? D 9 ? 19 1 1 C A1AAZ 6 1_555 D BRU 8 1_555 1.526 -0.756 0.199 -3.760 -17.148 -9.339 7 C_A1AAZ6:BRU8_D C 6 ? D 8 ? ? ? 1 C BRU 8 1_555 D A1AAZ 6 1_555 -1.349 -0.905 0.217 3.659 -16.949 -8.235 8 C_BRU8:A1AAZ6_D C 8 ? D 6 ? ? ? 1 C DC 9 1_555 D DG 4 1_555 0.371 -0.152 0.029 1.146 -20.743 0.690 9 C_DC9:DG4_D C 9 ? D 4 ? 19 1 1 C DG 10 1_555 D DC 3 1_555 -0.370 -0.147 0.119 2.457 -4.409 0.991 10 C_DG10:DC3_D C 10 ? D 3 ? 19 1 1 C DC 11 1_555 D DG 2 1_555 0.238 -0.197 0.207 5.150 -13.807 -2.663 11 C_DC11:DG2_D C 11 ? D 2 ? 19 1 1 C DG 12 1_555 D DC 1 1_555 -0.282 -0.263 0.097 15.417 6.986 -1.580 12 C_DG12:DC1_D C 12 ? D 1 ? 19 1 1 A BRU 8 1_555 B A1AAZ 6 1_555 -1.678 -0.747 0.400 3.920 -17.769 -11.309 13 A_BRU8:A1AAZ6_B A 8 ? B 6 ? ? ? 1 A DC 9 1_555 B DG 4 1_555 0.284 -0.151 0.365 -2.793 -19.014 -0.540 14 A_DC9:DG4_B A 9 ? B 4 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.354 -0.184 0.351 1.613 -10.633 -0.203 15 A_DG10:DC3_B A 10 ? B 3 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.334 -0.339 0.019 1.509 5.792 -0.873 16 A_DC11:DG2_B A 11 ? B 2 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.077 -0.019 0.522 33.869 2.036 -2.820 17 A_DG12:DC1_B A 12 ? B 1 ? 19 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 B DC 9 1_555 A DG 4 1_555 B DG 10 1_555 A DC 3 1_555 0.626 0.899 3.268 -0.063 9.237 29.122 -0.207 -1.202 3.386 17.813 0.122 30.522 1 BB_DC9DG10:DC3DG4_AA B 9 ? A 4 ? B 10 ? A 3 ? 1 B DG 10 1_555 A DC 3 1_555 B DC 11 1_555 A DG 2 1_555 -0.319 0.308 3.455 -1.955 -2.986 38.824 0.843 0.229 3.434 -4.481 2.933 38.982 2 BB_DG10DC11:DG2DC3_AA B 10 ? A 3 ? B 11 ? A 2 ? 1 B DC 11 1_555 A DG 2 1_555 C DG 2 1_555 D DC 11 1_555 0.134 1.268 3.549 0.210 -2.188 -70.175 -1.019 0.124 3.582 1.903 0.182 -70.205 3 BC_DC11DG2:DC11DG2_DA B 11 ? A 2 ? C 2 ? D 11 ? 1 C DG 2 1_555 D DC 11 1_555 C DC 3 1_555 D DG 10 1_555 0.507 0.430 3.476 0.901 -3.916 39.371 1.121 -0.638 3.429 -5.795 -1.333 39.568 4 CC_DG2DC3:DG10DC11_DD C 2 ? D 11 ? C 3 ? D 10 ? 1 C DC 3 1_555 D DG 10 1_555 C DG 4 1_555 D DC 9 1_555 -0.615 0.848 3.229 0.235 9.328 27.476 -0.426 1.282 3.326 18.958 -0.479 28.988 5 CC_DC3DG4:DC9DG10_DD C 3 ? D 10 ? C 4 ? D 9 ? 1 C DG 4 1_555 D DC 9 1_555 C A1AAZ 6 1_555 D BRU 8 1_555 -0.065 -0.386 3.485 -1.198 4.473 35.521 -1.308 -0.076 3.414 7.294 1.954 35.812 6 CC_DG4A1AAZ6:BRU8DC9_DD C 4 ? D 9 ? C 6 ? D 8 ? 1 C A1AAZ 6 1_555 D BRU 8 1_555 C BRU 8 1_555 D A1AAZ 6 1_555 -0.126 -2.982 6.162 0.294 31.282 66.910 -4.273 0.123 4.578 26.924 -0.253 73.084 7 CC_A1AAZ6BRU8:A1AAZ6BRU8_DD C 6 ? D 8 ? C 8 ? D 6 ? 1 C BRU 8 1_555 D A1AAZ 6 1_555 C DC 9 1_555 D DG 4 1_555 0.155 -0.329 3.391 2.455 2.064 35.932 -0.834 0.110 3.370 3.338 -3.969 36.071 8 CC_BRU8DC9:DG4A1AAZ6_DD C 8 ? D 6 ? C 9 ? D 4 ? 1 C DC 9 1_555 D DG 4 1_555 C DG 10 1_555 D DC 3 1_555 1.302 1.119 3.260 3.691 6.149 32.306 0.874 -1.632 3.530 10.884 -6.534 33.072 9 CC_DC9DG10:DC3DG4_DD C 9 ? D 4 ? C 10 ? D 3 ? 1 C DG 10 1_555 D DC 3 1_555 C DC 11 1_555 D DG 2 1_555 -0.943 0.659 3.269 -1.148 -2.717 40.299 1.259 1.236 3.244 -3.937 1.663 40.402 10 CC_DG10DC11:DG2DC3_DD C 10 ? D 3 ? C 11 ? D 2 ? 1 C DC 11 1_555 D DG 2 1_555 C DG 12 1_555 D DC 1 1_555 1.720 1.174 3.130 4.871 -3.481 33.213 2.575 -2.193 3.207 -6.029 -8.436 33.734 11 CC_DC11DG12:DC1DG2_DD C 11 ? D 2 ? C 12 ? D 1 ? 1 A BRU 8 1_555 B A1AAZ 6 1_555 A DC 9 1_555 B DG 4 1_555 -0.081 -0.592 3.422 0.497 4.124 35.681 -1.570 0.204 3.333 6.702 -0.808 35.915 12 AA_BRU8DC9:DG4A1AAZ6_BB A 8 ? B 6 ? A 9 ? B 4 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 -0.466 0.675 3.257 0.750 8.890 30.343 -0.448 0.999 3.306 16.540 -1.395 31.598 13 AA_DC9DG10:DC3DG4_BB A 9 ? B 4 ? A 10 ? B 3 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 1.319 0.807 3.422 3.716 -2.399 39.690 1.474 -1.480 3.474 -3.520 -5.452 39.926 14 AA_DG10DC11:DG2DC3_BB A 10 ? B 3 ? A 11 ? B 2 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 -0.023 0.516 2.756 -0.484 -2.807 29.900 1.477 -0.039 2.697 -5.424 0.936 30.032 15 AA_DC11DG12:DC1DG2_BB A 11 ? B 2 ? A 12 ? B 1 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Ministry of Education, Culture, Sports, Science and Technology (Japan)' Japan 17H03033 1 'Ministry of Education, Culture, Sports, Science and Technology (Japan)' Japan 21H01956 2 'Japan Agency for Medical Research and Development (AMED)' Japan JP23ama121014 3 # _atom_sites.entry_id 9VGY _atom_sites.fract_transf_matrix[1][1] 0.025786 _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] 0.021149 _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] 0.015025 _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 BR C HG N O P S # loop_ #