data_4R8J # _entry.id 4R8J # _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 4R8J pdb_00004r8j 10.2210/pdb4r8j/pdb NDB NA3215 ? ? RCSB RCSB087033 ? ? WWPDB D_1000087033 ? ? # 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 2015-10-28 2 'Structure model' 1 1 2015-12-02 3 'Structure model' 1 2 2017-11-22 4 'Structure model' 1 3 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Refinement description' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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 3 'Structure model' software 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_conn_type 8 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 4 'Structure model' '_database_2.pdbx_DOI' 4 4 'Structure model' '_database_2.pdbx_database_accession' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.value' 18 4 'Structure model' '_struct_conn.conn_type_id' 19 4 'Structure model' '_struct_conn.id' 20 4 'Structure model' '_struct_conn.pdbx_dist_value' 21 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 22 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 23 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 25 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 26 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 27 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 28 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 29 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 31 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 32 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 33 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 34 4 'Structure model' '_struct_conn_type.id' 35 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 36 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 37 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4R8J _pdbx_database_status.recvd_initial_deposition_date 2014-09-02 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _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 ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3QRN _pdbx_database_related.details 'Structure of the same system in H2O' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hall, J.P.' 1 'Gurung, S.P.' 2 'Winter, G.W.' 3 'Cardin, C.J.' 4 # _citation.id primary _citation.title 'Monitoring one-electron photo-oxidation of guanine in DNA crystals using ultrafast infrared spectroscopy.' _citation.journal_abbrev 'Nat Chem' _citation.journal_volume 7 _citation.page_first 961 _citation.page_last 967 _citation.year 2015 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 1755-4349 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 26587711 _citation.pdbx_database_id_DOI 10.1038/nchem.2369 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hall, J.P.' 1 ? primary 'Poynton, F.E.' 2 ? primary 'Keane, P.M.' 3 ? primary 'Gurung, S.P.' 4 ? primary 'Brazier, J.A.' 5 ? primary 'Cardin, D.J.' 6 ? primary 'Winter, G.' 7 ? primary 'Gunnlaugsson, T.' 8 ? primary 'Sazanovich, I.V.' 9 ? primary 'Towrie, M.' 10 ? primary 'Cardin, C.J.' 11 ? primary 'Kelly, J.M.' 12 ? primary 'Quinn, S.J.' 13 ? # 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(*(THM)P*CP*GP*GP*CP*GP*CP*CP*GP*A)-3') ; 2966.013 1 ? ? ? ? 2 non-polymer syn 'BARIUM ION' 137.327 1 ? ? ? ? 3 non-polymer syn 'Ru(tap)2(dppz) complex' 747.732 1 ? ? ? ? 4 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 5 water nat water 18.015 73 ? ? ? ? # _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 '(THM)(DC)(DG)(DG)(DC)(DG)(DC)(DC)(DG)(DA)' _entity_poly.pdbx_seq_one_letter_code_can XCGGCGCCGA _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'BARIUM ION' BA 3 'Ru(tap)2(dppz) complex' RKL 4 'CHLORIDE ION' CL 5 water DOD # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 THM n 1 2 DC n 1 3 DG n 1 4 DG n 1 5 DC n 1 6 DG n 1 7 DC n 1 8 DC n 1 9 DG n 1 10 DA 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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _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 'DNA was synthesised by ATDBio in Southampton, UK' # 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 BA non-polymer . 'BARIUM ION' ? 'Ba 2' 137.327 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 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 DOD non-polymer . 'DEUTERATED WATER' ? 'D2 O' 20.028 RKL non-polymer . 'Ru(tap)2(dppz) complex' ? 'C38 H22 N12 Ru 2' 747.732 THM 'DNA OH 5 prime terminus' . THYMIDINE ;DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE ; 'C10 H14 N2 O5' 242.229 # 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 THM 1 1 1 THM DT A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DC 7 7 7 DC DC A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DA 10 10 10 DA DA A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 BA 1 101 101 BA BA A . C 3 RKL 1 102 102 RKL RKL A . D 4 CL 1 103 103 CL CL A . E 5 DOD 1 201 201 DOD DOD A . E 5 DOD 2 202 202 DOD DOD A . E 5 DOD 3 203 203 DOD DOD A . E 5 DOD 4 204 204 DOD DOD A . E 5 DOD 5 205 205 DOD DOD A . E 5 DOD 6 206 206 DOD DOD A . E 5 DOD 7 207 207 DOD DOD A . E 5 DOD 8 208 208 DOD DOD A . E 5 DOD 9 209 209 DOD DOD A . E 5 DOD 10 210 210 DOD DOD A . E 5 DOD 11 211 211 DOD DOD A . E 5 DOD 12 212 212 DOD DOD A . E 5 DOD 13 213 213 DOD DOD A . E 5 DOD 14 214 214 DOD DOD A . E 5 DOD 15 215 215 DOD DOD A . E 5 DOD 16 216 216 DOD DOD A . E 5 DOD 17 217 217 DOD DOD A . E 5 DOD 18 218 218 DOD DOD A . E 5 DOD 19 219 219 DOD DOD A . E 5 DOD 20 220 220 DOD DOD A . E 5 DOD 21 221 221 DOD DOD A . E 5 DOD 22 222 222 DOD DOD A . E 5 DOD 23 223 223 DOD DOD A . E 5 DOD 24 224 224 DOD DOD A . E 5 DOD 25 225 225 DOD DOD A . E 5 DOD 26 226 226 DOD DOD A . E 5 DOD 27 227 227 DOD DOD A . E 5 DOD 28 228 228 DOD DOD A . E 5 DOD 29 229 229 DOD DOD A . E 5 DOD 30 230 230 DOD DOD A . E 5 DOD 31 231 231 DOD DOD A . E 5 DOD 32 232 232 DOD DOD A . E 5 DOD 33 233 233 DOD DOD A . E 5 DOD 34 234 234 DOD DOD A . E 5 DOD 35 235 235 DOD DOD A . E 5 DOD 36 236 236 DOD DOD A . E 5 DOD 37 237 237 DOD DOD A . E 5 DOD 38 238 238 DOD DOD A . E 5 DOD 39 239 239 DOD DOD A . E 5 DOD 40 240 240 DOD DOD A . E 5 DOD 41 241 241 DOD DOD A . E 5 DOD 42 242 242 DOD DOD A . E 5 DOD 43 243 243 DOD DOD A . E 5 DOD 44 244 244 DOD DOD A . E 5 DOD 45 245 245 DOD DOD A . E 5 DOD 46 246 246 DOD DOD A . E 5 DOD 47 247 247 DOD DOD A . E 5 DOD 48 248 248 DOD DOD A . E 5 DOD 49 249 249 DOD DOD A . E 5 DOD 50 250 250 DOD DOD A . E 5 DOD 51 251 251 DOD DOD A . E 5 DOD 52 252 252 DOD DOD A . E 5 DOD 53 253 253 DOD DOD A . E 5 DOD 54 254 254 DOD DOD A . E 5 DOD 55 255 255 DOD DOD A . E 5 DOD 56 256 256 DOD DOD A . E 5 DOD 57 257 257 DOD DOD A . E 5 DOD 58 258 258 DOD DOD A . E 5 DOD 59 259 259 DOD DOD A . E 5 DOD 60 260 260 DOD DOD A . E 5 DOD 61 261 261 DOD DOD A . E 5 DOD 62 262 262 DOD DOD A . E 5 DOD 63 263 263 DOD DOD A . E 5 DOD 64 264 264 DOD DOD A . E 5 DOD 65 265 265 DOD DOD A . E 5 DOD 66 266 266 DOD DOD A . E 5 DOD 67 267 267 DOD DOD A . E 5 DOD 68 268 268 DOD DOD A . E 5 DOD 69 269 269 DOD DOD A . E 5 DOD 70 270 270 DOD DOD A . E 5 DOD 71 271 271 DOD DOD A . E 5 DOD 72 272 272 DOD DOD A . E 5 DOD 73 273 273 DOD DOD A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal GDA 'data collection' . ? 1 SHELXCD phasing . ? 2 REFMAC refinement 5.8.0073 ? 3 XDS 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 SHELXE 'model building' . ? 6 # _cell.entry_id 4R8J _cell.length_a 42.370 _cell.length_b 42.370 _cell.length_c 39.420 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 4R8J _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4R8J _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.90 _exptl_crystal.density_percent_sol 57.65 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;The drops contained 1 l of 2mM oligonuclotide, 1 l of 4mM rac [Ru(TAP)2(dppz)]Cl2 and 6 l of the following solution; 10% (vol/vol) MPD, 40 mM sodium cacodylate (pH 6.0), 12mM spermine tetra-HCl, 80mM sodium chloride and 20 mM barium chloride. The drop was equilibrated against 1ml of 35% (vol/vol) 2-methyl-2,4-pentanediol (MPD) in H2O , VAPOR DIFFUSION, SITTING DROP, temperature 291K ; # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'PSI PILATUS 6M' _diffrn_detector.pdbx_collection_date 2014-08-14 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'DUAL SI(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.8266 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I03' _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I03 _diffrn_source.pdbx_wavelength 0.8266 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4R8J _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 18.660 _reflns.d_resolution_high 1.210 _reflns.number_obs 11471 _reflns.number_all ? _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4R8J _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 10864 _refine.ls_number_reflns_all 11471 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 18.66 _refine.ls_d_res_high 1.21 _refine.ls_percent_reflns_obs 99.9 _refine.ls_R_factor_obs 0.110 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.109 _refine.ls_R_factor_R_free 0.125 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 568 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.987 _refine.correlation_coeff_Fo_to_Fc_free 0.984 _refine.B_iso_mean 22.51 _refine.aniso_B[1][1] -0.41000 _refine.aniso_B[2][2] -0.41000 _refine.aniso_B[3][3] 0.82000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] -0.00000 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _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_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.027 _refine.pdbx_overall_ESU_R_Free 0.027 _refine.overall_SU_ML 0.021 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 1.042 _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.ls_redundancy_reflns_obs ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? # _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 202 _refine_hist.pdbx_number_atoms_ligand 53 _refine_hist.number_atoms_solvent 73 _refine_hist.number_atoms_total 328 _refine_hist.d_res_high 1.21 _refine_hist.d_res_low 18.66 # 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 r_bond_refined_d 0.016 0.013 ? 290 'X-RAY DIFFRACTION' ? r_bond_other_d 0.006 0.020 ? 134 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.592 1.598 ? 456 'X-RAY DIFFRACTION' ? r_angle_other_deg 3.753 3.000 ? 308 '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' ? r_chiral_restr 0.103 0.200 ? 30 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.032 0.020 ? 176 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.005 0.020 ? 78 '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' ? r_scbond_it 2.514 2.002 ? 290 'X-RAY DIFFRACTION' ? r_scbond_other 2.510 8.549 ? 291 'X-RAY DIFFRACTION' ? r_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_other 3.408 34.236 ? 457 'X-RAY DIFFRACTION' ? r_long_range_B_refined 3.383 22.245 ? 685 'X-RAY DIFFRACTION' ? r_long_range_B_other 3.065 21.665 ? 649 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 5.669 3.000 ? 290 'X-RAY DIFFRACTION' ? r_sphericity_free 28.452 5.000 ? 14 'X-RAY DIFFRACTION' ? r_sphericity_bonded 14.099 5.000 ? 315 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.21 _refine_ls_shell.d_res_low 1.24 _refine_ls_shell.number_reflns_R_work 765 _refine_ls_shell.R_factor_R_work 0.2120 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.2160 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 49 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _database_PDB_matrix.entry_id 4R8J _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 4R8J _struct.title 'd(TCGGCGCCGA) with lambda-[Ru(TAP)2(dppz)]2+ soaked in D2O' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4R8J _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA kinking, Infra-red, Ruthenium, 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 2 ? C N N 3 ? D N N 4 ? E N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4R8J _struct_ref.pdbx_db_accession 4R8J _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code TCGGCGCCGA _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4R8J _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4R8J _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 10 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 7_555 y,x,-z 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale one ? A THM 1 "O3'" ? ? ? 1_555 A DC 2 P ? ? A THM 1 A DC 2 1_555 ? ? ? ? ? ? ? 1.607 ? ? metalc1 metalc ? ? A DG 4 O6 ? ? ? 1_555 B BA . BA ? ? A DG 4 A BA 101 1_555 ? ? ? ? ? ? ? 2.898 ? ? metalc2 metalc ? ? B BA . BA ? ? ? 1_555 E DOD . O ? ? A BA 101 A DOD 201 1_555 ? ? ? ? ? ? ? 2.815 ? ? metalc3 metalc ? ? B BA . BA ? ? ? 1_555 E DOD . O ? ? A BA 101 A DOD 202 1_555 ? ? ? ? ? ? ? 2.814 ? ? metalc4 metalc ? ? B BA . BA ? ? ? 1_555 E DOD . O ? ? A BA 101 A DOD 203 1_555 ? ? ? ? ? ? ? 2.736 ? ? metalc5 metalc ? ? B BA . BA ? ? ? 1_555 E DOD . O ? ? A BA 101 A DOD 204 1_555 ? ? ? ? ? ? ? 2.847 ? ? metalc6 metalc ? ? B BA . BA ? ? ? 1_555 E DOD . O ? ? A BA 101 A DOD 205 1_555 ? ? ? ? ? ? ? 2.874 ? ? metalc7 metalc ? ? B BA . BA ? ? ? 1_555 E DOD . O ? ? A BA 101 A DOD 206 1_555 ? ? ? ? ? ? ? 2.809 ? ? hydrog1 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 2 A DG 9 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 2 A DG 9 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 2 A DG 9 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 3 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 3 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 3 A DC 8 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DC 7 N3 ? ? A DG 4 A DC 7 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DC 7 O2 ? ? A DG 4 A DC 7 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DC 7 N4 ? ? A DG 4 A DC 7 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 N3 ? ? ? 1_555 A DG 6 N1 ? ? A DC 5 A DG 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N4 ? ? ? 1_555 A DG 6 O6 ? ? A DC 5 A DG 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 O2 ? ? ? 1_555 A DG 6 N2 ? ? A DC 5 A DG 6 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 N1 ? ? ? 1_555 A DC 5 N3 ? ? A DG 6 A DC 5 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N2 ? ? ? 1_555 A DC 5 O2 ? ? A DG 6 A DC 5 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 O6 ? ? ? 1_555 A DC 5 N4 ? ? A DG 6 A DC 5 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 N3 ? ? ? 1_555 A DG 4 N1 ? ? A DC 7 A DG 4 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 N4 ? ? ? 1_555 A DG 4 O6 ? ? A DC 7 A DG 4 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 7 O2 ? ? ? 1_555 A DG 4 N2 ? ? A DC 7 A DG 4 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 8 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 8 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 8 A DG 3 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 9 A DC 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 9 A DC 2 7_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 9 A DC 2 7_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 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 201 ? 1_555 126.6 ? 2 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 202 ? 1_555 136.9 ? 3 O ? E DOD . ? A DOD 201 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 202 ? 1_555 68.8 ? 4 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 203 ? 1_555 69.6 ? 5 O ? E DOD . ? A DOD 201 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 203 ? 1_555 139.2 ? 6 O ? E DOD . ? A DOD 202 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 203 ? 1_555 75.9 ? 7 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 204 ? 1_555 63.0 ? 8 O ? E DOD . ? A DOD 201 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 204 ? 1_555 135.1 ? 9 O ? E DOD . ? A DOD 202 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 204 ? 1_555 139.3 ? 10 O ? E DOD . ? A DOD 203 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 204 ? 1_555 85.4 ? 11 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 205 ? 1_555 111.8 ? 12 O ? E DOD . ? A DOD 201 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 205 ? 1_555 65.2 ? 13 O ? E DOD . ? A DOD 202 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 205 ? 1_555 111.0 ? 14 O ? E DOD . ? A DOD 203 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 205 ? 1_555 150.7 ? 15 O ? E DOD . ? A DOD 204 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 205 ? 1_555 70.9 ? 16 O6 ? A DG 4 ? A DG 4 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 206 ? 1_555 119.7 ? 17 O ? E DOD . ? A DOD 201 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 206 ? 1_555 112.6 ? 18 O ? E DOD . ? A DOD 202 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 206 ? 1_555 72.1 ? 19 O ? E DOD . ? A DOD 203 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 206 ? 1_555 73.7 ? 20 O ? E DOD . ? A DOD 204 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 206 ? 1_555 68.0 ? 21 O ? E DOD . ? A DOD 205 ? 1_555 BA ? B BA . ? A BA 101 ? 1_555 O ? E DOD . ? A DOD 206 ? 1_555 81.3 ? # 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 BA 101 ? 8 'BINDING SITE FOR RESIDUE BA A 101' AC2 Software A RKL 102 ? 13 'BINDING SITE FOR RESIDUE RKL A 102' AC3 Software A CL 103 ? 4 'BINDING SITE FOR RESIDUE CL A 103' # 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 8 DG A 3 ? DG A 3 . ? 1_555 ? 2 AC1 8 DG A 4 ? DG A 4 . ? 1_555 ? 3 AC1 8 DOD E . ? DOD A 201 . ? 1_555 ? 4 AC1 8 DOD E . ? DOD A 202 . ? 1_555 ? 5 AC1 8 DOD E . ? DOD A 203 . ? 1_555 ? 6 AC1 8 DOD E . ? DOD A 204 . ? 1_555 ? 7 AC1 8 DOD E . ? DOD A 205 . ? 1_555 ? 8 AC1 8 DOD E . ? DOD A 206 . ? 1_555 ? 9 AC2 13 THM A 1 ? THM A 1 . ? 7_555 ? 10 AC2 13 DC A 2 ? DC A 2 . ? 7_555 ? 11 AC2 13 DG A 3 ? DG A 3 . ? 5_554 ? 12 AC2 13 DG A 3 ? DG A 3 . ? 7_555 ? 13 AC2 13 DG A 4 ? DG A 4 . ? 5_554 ? 14 AC2 13 DC A 5 ? DC A 5 . ? 5_554 ? 15 AC2 13 DC A 7 ? DC A 7 . ? 3_554 ? 16 AC2 13 DC A 8 ? DC A 8 . ? 3_554 ? 17 AC2 13 DG A 9 ? DG A 9 . ? 1_555 ? 18 AC2 13 DA A 10 ? DA A 10 . ? 3_554 ? 19 AC2 13 CL D . ? CL A 103 . ? 1_555 ? 20 AC2 13 DOD E . ? DOD A 207 . ? 3_554 ? 21 AC2 13 DOD E . ? DOD A 239 . ? 4_455 ? 22 AC3 4 DG A 4 ? DG A 4 . ? 5_554 ? 23 AC3 4 DC A 5 ? DC A 5 . ? 5_554 ? 24 AC3 4 RKL C . ? RKL A 102 . ? 1_555 ? 25 AC3 4 DOD E . ? DOD A 212 . ? 1_555 ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O5'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 DG _pdbx_validate_rmsd_angle.auth_seq_id_1 4 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 P _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 DG _pdbx_validate_rmsd_angle.auth_seq_id_2 4 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 OP2 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 DG _pdbx_validate_rmsd_angle.auth_seq_id_3 4 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 99.32 _pdbx_validate_rmsd_angle.angle_target_value 105.70 _pdbx_validate_rmsd_angle.angle_deviation -6.38 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.90 _pdbx_validate_rmsd_angle.linker_flag N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id DC _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 5 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.072 _pdbx_validate_planes.type 'SIDE CHAIN' # 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 BA BA BA N N 1 CL CL CL N N 2 DA OP3 O N N 3 DA P P N N 4 DA OP1 O N N 5 DA OP2 O N N 6 DA "O5'" O N N 7 DA "C5'" C N N 8 DA "C4'" C N R 9 DA "O4'" O N N 10 DA "C3'" C N S 11 DA "O3'" O N N 12 DA "C2'" C N N 13 DA "C1'" C N R 14 DA N9 N Y N 15 DA C8 C Y N 16 DA N7 N Y N 17 DA C5 C Y N 18 DA C6 C Y N 19 DA N6 N N N 20 DA N1 N Y N 21 DA C2 C Y N 22 DA N3 N Y N 23 DA C4 C Y N 24 DA HOP3 H N N 25 DA HOP2 H N N 26 DA "H5'" H N N 27 DA "H5''" H N N 28 DA "H4'" H N N 29 DA "H3'" H N N 30 DA "HO3'" H N N 31 DA "H2'" H N N 32 DA "H2''" H N N 33 DA "H1'" H N N 34 DA H8 H N N 35 DA H61 H N N 36 DA H62 H N N 37 DA H2 H N N 38 DC OP3 O N N 39 DC P P N N 40 DC OP1 O N N 41 DC OP2 O N N 42 DC "O5'" O N N 43 DC "C5'" C N N 44 DC "C4'" C N R 45 DC "O4'" O N N 46 DC "C3'" C N S 47 DC "O3'" O N N 48 DC "C2'" C N N 49 DC "C1'" C N R 50 DC N1 N N N 51 DC C2 C N N 52 DC O2 O N N 53 DC N3 N N N 54 DC C4 C N N 55 DC N4 N N N 56 DC C5 C N N 57 DC C6 C N N 58 DC HOP3 H N N 59 DC HOP2 H N N 60 DC "H5'" H N N 61 DC "H5''" H N N 62 DC "H4'" H N N 63 DC "H3'" H N N 64 DC "HO3'" H N N 65 DC "H2'" H N N 66 DC "H2''" H N N 67 DC "H1'" H N N 68 DC H41 H N N 69 DC H42 H N N 70 DC H5 H N N 71 DC H6 H N N 72 DG OP3 O N N 73 DG P P N N 74 DG OP1 O N N 75 DG OP2 O N N 76 DG "O5'" O N N 77 DG "C5'" C N N 78 DG "C4'" C N R 79 DG "O4'" O N N 80 DG "C3'" C N S 81 DG "O3'" O N N 82 DG "C2'" C N N 83 DG "C1'" C N R 84 DG N9 N Y N 85 DG C8 C Y N 86 DG N7 N Y N 87 DG C5 C Y N 88 DG C6 C N N 89 DG O6 O N N 90 DG N1 N N N 91 DG C2 C N N 92 DG N2 N N N 93 DG N3 N N N 94 DG C4 C Y N 95 DG HOP3 H N N 96 DG HOP2 H N N 97 DG "H5'" H N N 98 DG "H5''" H N N 99 DG "H4'" H N N 100 DG "H3'" H N N 101 DG "HO3'" H N N 102 DG "H2'" H N N 103 DG "H2''" H N N 104 DG "H1'" H N N 105 DG H8 H N N 106 DG H1 H N N 107 DG H21 H N N 108 DG H22 H N N 109 DOD O O N N 110 DOD D1 D N N 111 DOD D2 D N N 112 RKL RU RU N N 113 RKL C1 C Y N 114 RKL N1 N Y N 115 RKL C2 C Y N 116 RKL N2 N Y N 117 RKL C3 C Y N 118 RKL N3 N Y N 119 RKL C4 C Y N 120 RKL N4 N Y N 121 RKL C5 C Y N 122 RKL N5 N Y N 123 RKL C6 C Y N 124 RKL N6 N Y N 125 RKL C7 C Y N 126 RKL N7 N Y N 127 RKL C8 C Y N 128 RKL N8 N Y N 129 RKL C9 C Y N 130 RKL N9 N Y N 131 RKL C10 C Y N 132 RKL N10 N Y N 133 RKL C11 C Y N 134 RKL N11 N Y N 135 RKL C12 C Y N 136 RKL N12 N Y N 137 RKL C13 C Y N 138 RKL C14 C Y N 139 RKL C15 C Y N 140 RKL C16 C Y N 141 RKL C17 C Y N 142 RKL C18 C Y N 143 RKL C19 C Y N 144 RKL C20 C Y N 145 RKL C21 C Y N 146 RKL C22 C Y N 147 RKL C23 C Y N 148 RKL C24 C Y N 149 RKL C25 C Y N 150 RKL C26 C Y N 151 RKL C27 C Y N 152 RKL C28 C Y N 153 RKL C29 C Y N 154 RKL C30 C Y N 155 RKL C31 C Y N 156 RKL C32 C Y N 157 RKL C33 C Y N 158 RKL C34 C Y N 159 RKL C35 C Y N 160 RKL C36 C Y N 161 RKL C37 C Y N 162 RKL C38 C Y N 163 RKL H2 H N N 164 RKL H3 H N N 165 RKL H4 H N N 166 RKL H9 H N N 167 RKL H11 H N N 168 RKL H12 H N N 169 RKL H14 H N N 170 RKL H16 H N N 171 RKL H17 H N N 172 RKL H18 H N N 173 RKL H20 H N N 174 RKL H21 H N N 175 RKL H23 H N N 176 RKL H24 H N N 177 RKL H27 H N N 178 RKL H28 H N N 179 RKL H30 H N N 180 RKL H31 H N N 181 RKL H33 H N N 182 RKL H34 H N N 183 RKL H37 H N N 184 RKL H38 H N N 185 THM "O5'" O N N 186 THM "C5'" C N N 187 THM "C4'" C N R 188 THM "O4'" O N N 189 THM "C3'" C N S 190 THM "O3'" O N N 191 THM "C2'" C N N 192 THM "C1'" C N R 193 THM N1 N N N 194 THM C2 C N N 195 THM O2 O N N 196 THM N3 N N N 197 THM C4 C N N 198 THM O4 O N N 199 THM C5 C N N 200 THM C5M C N N 201 THM C6 C N N 202 THM "HO5'" H N N 203 THM "H5'1" H N N 204 THM "H5'2" H N N 205 THM "H4'" H N N 206 THM "H3'" H N N 207 THM "HO3'" H N N 208 THM "H2'1" H N N 209 THM "H2'2" H N N 210 THM "H1'" H N N 211 THM HN3 H N N 212 THM HM51 H N N 213 THM HM52 H N N 214 THM HM53 H N N 215 THM H6 H N N 216 # 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 DOD O D1 sing N N 113 DOD O D2 sing N N 114 RKL RU N1 sing N N 115 RKL RU N2 sing N N 116 RKL RU N5 sing N N 117 RKL RU N8 sing N N 118 RKL RU N9 sing N N 119 RKL RU N12 sing N N 120 RKL C1 N2 doub Y N 121 RKL C1 C5 sing Y N 122 RKL C1 C10 sing Y N 123 RKL N1 C10 doub Y N 124 RKL N1 C12 sing Y N 125 RKL C2 N2 sing Y N 126 RKL C2 C3 doub Y N 127 RKL C2 H2 sing N N 128 RKL C3 C4 sing Y N 129 RKL C3 H3 sing N N 130 RKL N3 C6 doub Y N 131 RKL N3 C15 sing Y N 132 RKL C4 C5 doub Y N 133 RKL C4 H4 sing N N 134 RKL N4 C7 doub Y N 135 RKL N4 C13 sing Y N 136 RKL C5 C6 sing Y N 137 RKL N5 C19 doub Y N 138 RKL N5 C20 sing Y N 139 RKL C6 C7 sing Y N 140 RKL N6 C21 sing Y N 141 RKL N6 C22 doub Y N 142 RKL C7 C8 sing Y N 143 RKL N7 C25 doub Y N 144 RKL N7 C27 sing Y N 145 RKL C8 C9 doub Y N 146 RKL C8 C10 sing Y N 147 RKL N8 C26 doub Y N 148 RKL N8 C28 sing Y N 149 RKL C9 C11 sing Y N 150 RKL C9 H9 sing N N 151 RKL N9 C29 doub Y N 152 RKL N9 C30 sing Y N 153 RKL N10 C31 sing Y N 154 RKL N10 C32 doub Y N 155 RKL C11 C12 doub Y N 156 RKL C11 H11 sing N N 157 RKL N11 C35 doub Y N 158 RKL N11 C37 sing Y N 159 RKL C12 H12 sing N N 160 RKL N12 C36 doub Y N 161 RKL N12 C38 sing Y N 162 RKL C13 C14 sing Y N 163 RKL C13 C15 doub Y N 164 RKL C14 C18 doub Y N 165 RKL C14 H14 sing N N 166 RKL C15 C16 sing Y N 167 RKL C16 C17 doub Y N 168 RKL C16 H16 sing N N 169 RKL C17 C18 sing Y N 170 RKL C17 H17 sing N N 171 RKL C18 H18 sing N N 172 RKL C19 C22 sing Y N 173 RKL C19 C26 sing Y N 174 RKL C20 C21 doub Y N 175 RKL C20 H20 sing N N 176 RKL C21 H21 sing N N 177 RKL C22 C23 sing Y N 178 RKL C23 C24 doub Y N 179 RKL C23 H23 sing N N 180 RKL C24 C25 sing Y N 181 RKL C24 H24 sing N N 182 RKL C25 C26 sing Y N 183 RKL C27 C28 doub Y N 184 RKL C27 H27 sing N N 185 RKL C28 H28 sing N N 186 RKL C29 C32 sing Y N 187 RKL C29 C36 sing Y N 188 RKL C30 C31 doub Y N 189 RKL C30 H30 sing N N 190 RKL C31 H31 sing N N 191 RKL C32 C33 sing Y N 192 RKL C33 C34 doub Y N 193 RKL C33 H33 sing N N 194 RKL C34 C35 sing Y N 195 RKL C34 H34 sing N N 196 RKL C35 C36 sing Y N 197 RKL C37 C38 doub Y N 198 RKL C37 H37 sing N N 199 RKL C38 H38 sing N N 200 THM "O5'" "C5'" sing N N 201 THM "O5'" "HO5'" sing N N 202 THM "C5'" "C4'" sing N N 203 THM "C5'" "H5'1" sing N N 204 THM "C5'" "H5'2" sing N N 205 THM "C4'" "O4'" sing N N 206 THM "C4'" "C3'" sing N N 207 THM "C4'" "H4'" sing N N 208 THM "O4'" "C1'" sing N N 209 THM "C3'" "O3'" sing N N 210 THM "C3'" "C2'" sing N N 211 THM "C3'" "H3'" sing N N 212 THM "O3'" "HO3'" sing N N 213 THM "C2'" "C1'" sing N N 214 THM "C2'" "H2'1" sing N N 215 THM "C2'" "H2'2" sing N N 216 THM "C1'" N1 sing N N 217 THM "C1'" "H1'" sing N N 218 THM N1 C2 sing N N 219 THM N1 C6 sing N N 220 THM C2 O2 doub N N 221 THM C2 N3 sing N N 222 THM N3 C4 sing N N 223 THM N3 HN3 sing N N 224 THM C4 O4 doub N N 225 THM C4 C5 sing N N 226 THM C5 C5M sing N N 227 THM C5 C6 doub N N 228 THM C5M HM51 sing N N 229 THM C5M HM52 sing N N 230 THM C5M HM53 sing N N 231 THM C6 H6 sing N N 232 # _ndb_struct_conf_na.entry_id 4R8J _ndb_struct_conf_na.feature '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 A DC 2 1_555 A DG 9 7_555 0.126 -0.080 0.238 -11.206 6.225 1.984 1 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DG 3 1_555 A DC 8 7_555 -0.208 -0.030 0.177 24.280 -5.095 -0.544 2 A_DG3:DC8_A A 3 ? A 8 ? 19 1 1 A DG 4 1_555 A DC 7 7_555 -0.193 -0.169 -0.043 -6.558 1.887 -1.550 3 A_DG4:DC7_A A 4 ? A 7 ? 19 1 1 A DC 5 1_555 A DG 6 7_555 0.247 -0.093 0.128 0.985 -5.117 -1.288 4 A_DC5:DG6_A A 5 ? A 6 ? 19 1 1 A DG 6 1_555 A DC 5 7_555 -0.247 -0.093 0.128 -0.985 -5.117 -1.288 5 A_DG6:DC5_A A 6 ? A 5 ? 19 1 1 A DC 7 1_555 A DG 4 7_555 0.193 -0.169 -0.043 6.558 1.887 -1.550 6 A_DC7:DG4_A A 7 ? A 4 ? 19 1 1 A DC 8 1_555 A DG 3 7_555 0.208 -0.030 0.177 -24.280 -5.095 -0.544 7 A_DC8:DG3_A A 8 ? A 3 ? 19 1 1 A DG 9 1_555 A DC 2 7_555 -0.126 -0.080 0.238 11.206 6.225 1.984 8 A_DG9:DC2_A A 9 ? A 2 ? 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 A DC 2 1_555 A DG 9 7_555 A DG 3 1_555 A DC 8 7_555 -0.528 1.674 2.615 2.222 3.362 19.912 3.481 2.335 2.781 9.595 -6.342 20.311 1 AA_DC2DG3:DC8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DG 3 1_555 A DC 8 7_555 A DG 4 1_555 A DC 7 7_555 -0.103 0.837 5.152 -1.932 49.764 14.724 -5.355 -0.127 2.314 74.512 2.892 51.800 2 AA_DG3DG4:DC7DC8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DG 4 1_555 A DC 7 7_555 A DC 5 1_555 A DG 6 7_555 -0.847 0.255 3.143 -1.797 -3.744 40.730 0.760 1.022 3.141 -5.363 2.574 40.933 3 AA_DG4DC5:DG6DC7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DC 5 1_555 A DG 6 7_555 A DG 6 1_555 A DC 5 7_555 0.000 1.179 3.801 0.000 29.050 23.383 -3.426 0.000 3.328 51.969 0.000 37.134 4 AA_DC5DG6:DC5DG6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DG 6 1_555 A DC 5 7_555 A DC 7 1_555 A DG 4 7_555 0.847 0.255 3.143 1.797 -3.744 40.730 0.760 -1.022 3.141 -5.363 -2.574 40.933 5 AA_DG6DC7:DG4DC5_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A DC 7 1_555 A DG 4 7_555 A DC 8 1_555 A DG 3 7_555 0.103 0.837 5.152 1.932 49.764 14.724 -5.355 0.127 2.314 74.512 -2.892 51.800 6 AA_DC7DC8:DG3DG4_AA A 7 ? A 4 ? A 8 ? A 3 ? 1 A DC 8 1_555 A DG 3 7_555 A DG 9 1_555 A DC 2 7_555 0.528 1.674 2.615 -2.222 3.362 19.912 3.481 -2.335 2.781 9.595 6.342 20.311 7 AA_DC8DG9:DC2DG3_AA A 8 ? A 3 ? A 9 ? A 2 ? # _atom_sites.entry_id 4R8J _atom_sites.fract_transf_matrix[1][1] 0.023602 _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] 0.023602 _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] 0.025368 _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 BA C CL D H N O P RU # loop_