data_1Y95 # _entry.id 1Y95 # _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 1Y95 pdb_00001y95 10.2210/pdb1y95/pdb NDB AR0054 ? ? RCSB RCSB031272 ? ? WWPDB D_1000031272 ? ? # 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 2004-12-21 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.value' 14 4 'Structure model' '_struct_conn.pdbx_dist_value' 15 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 16 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 17 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 18 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 19 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 20 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 22 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 23 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 24 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 25 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 26 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 27 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 29 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 30 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 31 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1Y95 _pdbx_database_status.recvd_initial_deposition_date 2004-12-14 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1Y6S 'HIV-1 Dis(Mal) Duplex Ba-Soaked' unspecified PDB 1Y6T 'HIV-1 Dis(Mal) Duplex CoHexa-Soaked' unspecified PDB 1NLC 'HIV-1 Dis(Mal) Duplex Zn-Soaked' unspecified PDB 1Y73 'HIV-1 Dis(Mal) Duplex PtCl4-Soaked' unspecified PDB 1XP7 'HIV-1 Dis(Mal) Duplex RuHexa-Soaked' unspecified PDB 1O3Z 'HIV-1 Dis(Mal) Duplex RU HEXAMINE--Soaked' unspecified PDB 1Y90 'HIV-1 Dis(Mal) Duplex Mn-Soaked' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ennifar, E.' 1 'Walter, P.' 2 'Dumas, P.' 3 # _citation.id primary _citation.title 'A crystallographic study of the binding of 13 metal ions to two related RNA duplexes' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 31 _citation.page_first 2671 _citation.page_last 2682 _citation.year 2003 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12736317 _citation.pdbx_database_id_DOI 10.1093/nar/gkg350 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ennifar, E.' 1 ? primary 'Walter, P.' 2 ? primary 'Dumas, P.' 3 ? # 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 "5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3'" 7402.472 2 ? ? ? 'HIV-1 DIS RNA' 2 non-polymer syn 'MAGNESIUM ION' 24.305 10 ? ? ? ? 3 non-polymer syn 'LEAD (II) ION' 207.200 3 ? ? ? ? 4 water nat water 18.015 44 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code CUUGCUGAGGUGCACACAGCAAG _entity_poly.pdbx_seq_one_letter_code_can CUUGCUGAGGUGCACACAGCAAG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 'LEAD (II) ION' PB 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 U n 1 3 U n 1 4 G n 1 5 C n 1 6 U n 1 7 G n 1 8 A n 1 9 G n 1 10 G n 1 11 U n 1 12 G n 1 13 C n 1 14 A n 1 15 C n 1 16 A n 1 17 C n 1 18 A n 1 19 G n 1 20 C n 1 21 A n 1 22 A n 1 23 G n # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 PB non-polymer . 'LEAD (II) ION' ? 'Pb 2' 207.200 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 C 1 1 1 C CYT A . n A 1 2 U 2 2 2 U URI A . n A 1 3 U 3 3 3 U URI A . n A 1 4 G 4 4 4 G GUA A . n A 1 5 C 5 5 5 C CYT A . n A 1 6 U 6 6 6 U URI A . n A 1 7 G 7 7 7 G GUA A . n A 1 8 A 8 8 8 A ADE A . n A 1 9 G 9 9 9 G GUA A . n A 1 10 G 10 10 10 G GUA A . n A 1 11 U 11 11 11 U URI A . n A 1 12 G 12 12 12 G GUA A . n A 1 13 C 13 13 13 C CYT A . n A 1 14 A 14 14 14 A ADE A . n A 1 15 C 15 15 15 C CYT A . n A 1 16 A 16 16 16 A ADE A . n A 1 17 C 17 17 17 C CYT A . n A 1 18 A 18 18 18 A ADE A . n A 1 19 G 19 19 19 G GUA A . n A 1 20 C 20 20 20 C CYT A . n A 1 21 A 21 21 21 A ADE A . n A 1 22 A 22 22 22 A ADE A . n A 1 23 G 23 23 23 G GUA A . n B 1 1 C 1 1 1 C CYT B . n B 1 2 U 2 2 2 U URI B . n B 1 3 U 3 3 3 U URI B . n B 1 4 G 4 4 4 G GUA B . n B 1 5 C 5 5 5 C CYT B . n B 1 6 U 6 6 6 U URI B . n B 1 7 G 7 7 7 G GUA B . n B 1 8 A 8 8 8 A ADE B . n B 1 9 G 9 9 9 G GUA B . n B 1 10 G 10 10 10 G GUA B . n B 1 11 U 11 11 11 U URI B . n B 1 12 G 12 12 12 G GUA B . n B 1 13 C 13 13 13 C CYT B . n B 1 14 A 14 14 14 A ADE B . n B 1 15 C 15 15 15 C CYT B . n B 1 16 A 16 16 16 A ADE B . n B 1 17 C 17 17 17 C CYT B . n B 1 18 A 18 18 18 A ADE B . n B 1 19 G 19 19 19 G GUA B . n B 1 20 C 20 20 20 C CYT B . n B 1 21 A 21 21 21 A ADE B . n B 1 22 A 22 22 22 A ADE B . n B 1 23 G 23 23 23 G GUA B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 MG 1 30 30 MG MG A . D 2 MG 1 32 32 MG MG A . E 3 PB 1 36 36 PB PB A . F 2 MG 1 37 37 MG MG A . G 2 MG 1 38 38 MG MG A . H 2 MG 1 40 40 MG MG A . I 2 MG 1 43 43 MG MG A . J 3 PB 1 31 31 PB PB B . K 2 MG 1 33 33 MG MG B . L 2 MG 1 34 34 MG MG B . M 3 PB 1 35 35 PB PB B . N 2 MG 1 41 41 MG MG B . O 2 MG 1 42 42 MG MG B . P 4 HOH 1 100 100 HOH WAT A . P 4 HOH 2 105 105 HOH WAT A . P 4 HOH 3 106 106 HOH WAT A . P 4 HOH 4 108 108 HOH WAT A . P 4 HOH 5 110 110 HOH WAT A . P 4 HOH 6 111 111 HOH WAT A . P 4 HOH 7 112 112 HOH WAT A . P 4 HOH 8 113 113 HOH WAT A . P 4 HOH 9 114 114 HOH WAT A . P 4 HOH 10 115 115 HOH WAT A . P 4 HOH 11 120 120 HOH WAT A . P 4 HOH 12 121 121 HOH WAT A . P 4 HOH 13 124 124 HOH WAT A . P 4 HOH 14 125 125 HOH WAT A . P 4 HOH 15 129 129 HOH WAT A . P 4 HOH 16 132 132 HOH WAT A . P 4 HOH 17 134 134 HOH WAT A . P 4 HOH 18 135 135 HOH WAT A . P 4 HOH 19 141 141 HOH WAT A . P 4 HOH 20 142 142 HOH WAT A . Q 4 HOH 1 101 101 HOH WAT B . Q 4 HOH 2 102 102 HOH WAT B . Q 4 HOH 3 103 103 HOH WAT B . Q 4 HOH 4 104 104 HOH WAT B . Q 4 HOH 5 107 107 HOH WAT B . Q 4 HOH 6 109 109 HOH WAT B . Q 4 HOH 7 116 116 HOH WAT B . Q 4 HOH 8 117 117 HOH WAT B . Q 4 HOH 9 118 118 HOH WAT B . Q 4 HOH 10 119 119 HOH WAT B . Q 4 HOH 11 122 122 HOH WAT B . Q 4 HOH 12 123 123 HOH WAT B . Q 4 HOH 13 126 126 HOH WAT B . Q 4 HOH 14 127 127 HOH WAT B . Q 4 HOH 15 128 128 HOH WAT B . Q 4 HOH 16 130 130 HOH WAT B . Q 4 HOH 17 131 131 HOH WAT B . Q 4 HOH 18 133 133 HOH WAT B . Q 4 HOH 19 136 136 HOH WAT B . Q 4 HOH 20 137 137 HOH WAT B . Q 4 HOH 21 138 138 HOH WAT B . Q 4 HOH 22 139 139 HOH WAT B . Q 4 HOH 23 140 140 HOH WAT B . Q 4 HOH 24 143 143 HOH WAT B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 CNS phasing . ? 4 # _cell.entry_id 1Y95 _cell.length_a 59.200 _cell.length_b 59.200 _cell.length_c 65.800 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y95 _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1Y95 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.25 _exptl_crystal.density_percent_sol 50 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 310 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details 'MPD, spermine, KCl, MgCl2, Na Cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 310K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 spermine ? ? ? 1 3 1 KCl ? ? ? 1 4 1 MgCl2 ? ? ? 1 5 1 'Na Cacodylate' ? ? ? 1 6 1 H2O ? ? ? 1 7 2 MPD ? ? ? 1 8 2 KCl ? ? ? 1 9 2 MgCl2 ? ? ? 1 10 2 'Na Cacodylate' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 293 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MACSCIENCE _diffrn_detector.pdbx_collection_date 1999-04-23 _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 mirror _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.54 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type ENRAF-NONIUS _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.54 # _reflns.entry_id 1Y95 _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 8 _reflns.d_resolution_high 2.8 _reflns.number_obs 3213 _reflns.number_all ? _reflns.percent_possible_obs 96.3 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.045 _reflns.pdbx_netI_over_sigmaI 12.6 _reflns.B_iso_Wilson_estimate 57.0 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.8 _reflns_shell.d_res_low 2.97 _reflns_shell.percent_possible_all 94.5 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.299 _reflns_shell.meanI_over_sigI_obs 3.2 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1Y95 _refine.ls_number_reflns_obs 3213 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 191670.41 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 7.97 _refine.ls_d_res_high 2.80 _refine.ls_percent_reflns_obs 96.3 _refine.ls_R_factor_obs 0.226 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.226 _refine.ls_R_factor_R_free 0.253 _refine.ls_R_factor_R_free_error 0.014 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.0 _refine.ls_number_reflns_R_free 320 _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 52.2 _refine.aniso_B[1][1] 0.53 _refine.aniso_B[2][2] 0.53 _refine.aniso_B[3][3] -1.06 _refine.aniso_B[1][2] 7.58 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.225376 _refine.solvent_model_param_bsol 19.9963 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'FOURIER SYNTHESIS' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _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.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1Y95 _refine_analyze.Luzzati_coordinate_error_obs 0.38 _refine_analyze.Luzzati_sigma_a_obs 0.84 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.42 _refine_analyze.Luzzati_sigma_a_free 0.68 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 1048 _refine_hist.pdbx_number_atoms_ligand 13 _refine_hist.number_atoms_solvent 44 _refine_hist.number_atoms_total 1105 _refine_hist.d_res_high 2.80 _refine_hist.d_res_low 7.97 # 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 c_bond_d 0.004 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 0.8 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 12.4 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.31 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 1.10 1.50 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 1.77 2.00 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.80 _refine_ls_shell.d_res_low 2.97 _refine_ls_shell.number_reflns_R_work 463 _refine_ls_shell.R_factor_R_work 0.395 _refine_ls_shell.percent_reflns_obs 94.6 _refine_ls_shell.R_factor_R_free 0.399 _refine_ls_shell.R_factor_R_free_error 0.052 _refine_ls_shell.percent_reflns_R_free 11.1 _refine_ls_shell.number_reflns_R_free 58 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 WATER_REP.PARAM WATER.TOP 'X-RAY DIFFRACTION' 2 DNA-RNA.PARAM DNA-RNA.TOP 'X-RAY DIFFRACTION' 3 ION2.PARAM ION2.TOP 'X-RAY DIFFRACTION' 4 BRU_REP.PARAM ? 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 1Y95 _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 1Y95 _struct.title 'HIV-1 Dis(Mal) Duplex Pb-Soaked' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1Y95 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, HIV-1, metal ions, bulge' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 3 ? K N N 2 ? L N N 2 ? M N N 3 ? N N N 2 ? O N N 2 ? P N N 4 ? Q N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1Y95 _struct_ref.pdbx_db_accession 1Y95 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1Y95 A 1 ? 23 ? 1Y95 1 ? 23 ? 1 23 2 1 1Y95 B 1 ? 23 ? 1Y95 1 ? 23 ? 1 23 # _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 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q # _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 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A U 3 O4 ? ? ? 1_555 D MG . MG ? ? A U 3 A MG 32 1_555 ? ? ? ? ? ? ? 3.118 ? ? metalc2 metalc ? ? A G 4 O6 ? ? ? 1_555 D MG . MG ? ? A G 4 A MG 32 1_555 ? ? ? ? ? ? ? 2.920 ? ? metalc3 metalc ? ? A A 8 OP2 ? ? ? 1_555 E PB . PB ? ? A A 8 A PB 36 1_555 ? ? ? ? ? ? ? 2.630 ? ? metalc4 metalc ? ? A G 9 N7 ? ? ? 1_555 E PB . PB ? ? A G 9 A PB 36 1_555 ? ? ? ? ? ? ? 2.923 ? ? metalc5 metalc ? ? A G 9 OP1 ? ? ? 1_555 J PB . PB ? ? A G 9 B PB 31 1_555 ? ? ? ? ? ? ? 2.820 ? ? metalc6 metalc ? ? A G 10 OP2 ? ? ? 1_555 J PB . PB ? ? A G 10 B PB 31 1_555 ? ? ? ? ? ? ? 3.439 ? ? metalc7 metalc ? ? D MG . MG ? ? ? 1_555 N MG . MG ? ? A MG 32 B MG 41 1_555 ? ? ? ? ? ? ? 2.106 ? ? metalc8 metalc ? ? L MG . MG ? ? ? 1_555 Q HOH . O ? ? B MG 34 B HOH 116 1_555 ? ? ? ? ? ? ? 2.493 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 23 N1 ? ? A C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 23 O6 ? ? A C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 23 N2 ? ? A C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 B A 22 N1 ? ? A U 2 B A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 B A 22 N6 ? ? A U 2 B A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 3 N3 ? ? ? 1_555 B A 21 N1 ? ? A U 3 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A U 3 O4 ? ? ? 1_555 B A 21 N6 ? ? A U 3 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 20 N3 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 20 O2 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 20 N4 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 6 N3 ? ? ? 1_555 B A 18 N1 ? ? A U 6 B A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 6 O4 ? ? ? 1_555 B A 18 N6 ? ? A U 6 B A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 17 N3 ? ? A G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 17 O2 ? ? A G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 17 N4 ? ? A G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 9 N1 ? ? ? 1_555 B A 16 N1 ? ? A G 9 B A 16 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog20 hydrog ? ? A G 10 N1 ? ? ? 1_555 B C 15 N3 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 10 N2 ? ? ? 1_555 B C 15 O2 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 10 O6 ? ? ? 1_555 B C 15 N4 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A U 11 N3 ? ? ? 1_555 B A 14 N1 ? ? A U 11 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A U 11 O4 ? ? ? 1_555 B A 14 N6 ? ? A U 11 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 13 N3 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 13 O2 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 13 N4 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 13 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 13 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 13 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 14 N1 ? ? ? 1_555 B U 11 N3 ? ? A A 14 B U 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A A 14 N6 ? ? ? 1_555 B U 11 O4 ? ? A A 14 B U 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 15 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 15 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 15 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A A 16 N1 ? ? ? 1_555 B G 9 N1 A ? A A 16 B G 9 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog37 hydrog ? ? A A 16 N6 ? ? ? 1_555 B G 9 O6 A ? A A 16 B G 9 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog38 hydrog ? ? A C 17 N3 ? ? ? 1_555 B G 7 N1 A ? A C 17 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 17 N4 ? ? ? 1_555 B G 7 O6 A ? A C 17 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 17 O2 ? ? ? 1_555 B G 7 N2 A ? A C 17 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A A 18 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 18 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A A 18 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 18 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 19 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 19 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 19 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 20 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 20 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 20 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A A 21 N1 ? ? ? 1_555 B U 3 N3 ? ? A A 21 B U 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A A 21 N6 ? ? ? 1_555 B U 3 O4 ? ? A A 21 B U 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A A 22 N1 ? ? ? 1_555 B U 2 N3 ? ? A A 22 B U 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A A 22 N6 ? ? ? 1_555 B U 2 O4 ? ? A A 22 B U 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A G 23 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 23 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A G 23 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 23 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A G 23 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 23 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O4 ? A U 3 ? A U 3 ? 1_555 MG ? D MG . ? A MG 32 ? 1_555 O6 ? A G 4 ? A G 4 ? 1_555 61.8 ? 2 O4 ? A U 3 ? A U 3 ? 1_555 MG ? D MG . ? A MG 32 ? 1_555 MG ? N MG . ? B MG 41 ? 1_555 133.8 ? 3 O6 ? A G 4 ? A G 4 ? 1_555 MG ? D MG . ? A MG 32 ? 1_555 MG ? N MG . ? B MG 41 ? 1_555 94.7 ? 4 OP2 ? A A 8 ? A A 8 ? 1_555 PB ? E PB . ? A PB 36 ? 1_555 N7 ? A G 9 ? A G 9 ? 1_555 73.3 ? 5 OP1 ? A G 9 ? A G 9 ? 1_555 PB ? J PB . ? B PB 31 ? 1_555 OP2 ? A G 10 ? A G 10 ? 1_555 63.8 ? # 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 B PB 31 ? 4 'BINDING SITE FOR RESIDUE PB B 31' AC2 Software A MG 32 ? 4 'BINDING SITE FOR RESIDUE MG A 32' AC3 Software B MG 33 ? 2 'BINDING SITE FOR RESIDUE MG B 33' AC4 Software B MG 34 ? 3 'BINDING SITE FOR RESIDUE MG B 34' AC5 Software B PB 35 ? 2 'BINDING SITE FOR RESIDUE PB B 35' AC6 Software A PB 36 ? 2 'BINDING SITE FOR RESIDUE PB A 36' AC7 Software A MG 37 ? 1 'BINDING SITE FOR RESIDUE MG A 37' AC8 Software A MG 38 ? 1 'BINDING SITE FOR RESIDUE MG A 38' AC9 Software A MG 40 ? 2 'BINDING SITE FOR RESIDUE MG A 40' BC1 Software B MG 41 ? 1 'BINDING SITE FOR RESIDUE MG B 41' BC2 Software A MG 43 ? 1 'BINDING SITE FOR RESIDUE MG A 43' # 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 4 G A 9 ? G A 9 . ? 1_555 ? 2 AC1 4 G A 10 ? G A 10 . ? 1_555 ? 3 AC1 4 A B 8 ? A B 8 . ? 1_555 ? 4 AC1 4 G B 9 ? G B 9 . ? 1_555 ? 5 AC2 4 U A 3 ? U A 3 . ? 1_555 ? 6 AC2 4 G A 4 ? G A 4 . ? 1_555 ? 7 AC2 4 MG H . ? MG A 40 . ? 1_555 ? 8 AC2 4 MG N . ? MG B 41 . ? 1_555 ? 9 AC3 2 U B 3 ? U B 3 . ? 1_555 ? 10 AC3 2 G B 4 ? G B 4 . ? 1_555 ? 11 AC4 3 U B 6 ? U B 6 . ? 1_555 ? 12 AC4 3 G B 7 ? G B 7 . ? 1_555 ? 13 AC4 3 HOH Q . ? HOH B 116 . ? 1_555 ? 14 AC5 2 A B 8 ? A B 8 . ? 1_555 ? 15 AC5 2 G B 9 ? G B 9 . ? 1_555 ? 16 AC6 2 A A 8 ? A A 8 . ? 1_555 ? 17 AC6 2 G A 9 ? G A 9 . ? 1_555 ? 18 AC7 1 G A 12 ? G A 12 . ? 1_555 ? 19 AC8 1 C A 1 ? C A 1 . ? 1_455 ? 20 AC9 2 G A 4 ? G A 4 . ? 1_555 ? 21 AC9 2 MG D . ? MG A 32 . ? 1_555 ? 22 BC1 1 MG D . ? MG A 32 . ? 1_555 ? 23 BC2 1 G A 19 ? G A 19 . ? 1_555 ? # loop_ _pdbx_validate_polymer_linkage.id _pdbx_validate_polymer_linkage.PDB_model_num _pdbx_validate_polymer_linkage.auth_atom_id_1 _pdbx_validate_polymer_linkage.auth_asym_id_1 _pdbx_validate_polymer_linkage.auth_comp_id_1 _pdbx_validate_polymer_linkage.auth_seq_id_1 _pdbx_validate_polymer_linkage.PDB_ins_code_1 _pdbx_validate_polymer_linkage.label_alt_id_1 _pdbx_validate_polymer_linkage.auth_atom_id_2 _pdbx_validate_polymer_linkage.auth_asym_id_2 _pdbx_validate_polymer_linkage.auth_comp_id_2 _pdbx_validate_polymer_linkage.auth_seq_id_2 _pdbx_validate_polymer_linkage.PDB_ins_code_2 _pdbx_validate_polymer_linkage.label_alt_id_2 _pdbx_validate_polymer_linkage.dist 1 1 "O3'" B U 6 ? ? P B G 7 ? B 2.88 2 1 "O3'" B G 9 ? A P B G 10 ? ? 2.71 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 117 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id Q _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 MG MG MG N N 114 PB PB PB N N 115 U OP3 O N N 116 U P P N N 117 U OP1 O N N 118 U OP2 O N N 119 U "O5'" O N N 120 U "C5'" C N N 121 U "C4'" C N R 122 U "O4'" O N N 123 U "C3'" C N S 124 U "O3'" O N N 125 U "C2'" C N R 126 U "O2'" O N N 127 U "C1'" C N R 128 U N1 N N N 129 U C2 C N N 130 U O2 O N N 131 U N3 N N N 132 U C4 C N N 133 U O4 O N N 134 U C5 C N N 135 U C6 C N N 136 U HOP3 H N N 137 U HOP2 H N N 138 U "H5'" H N N 139 U "H5''" H N N 140 U "H4'" H N N 141 U "H3'" H N N 142 U "HO3'" H N N 143 U "H2'" H N N 144 U "HO2'" H N N 145 U "H1'" H N N 146 U H3 H N N 147 U H5 H N N 148 U H6 H N N 149 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1Y95 'double helix' 1Y95 'a-form double helix' 1Y95 'bulge loop' 1Y95 'mismatched base pair' # 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 C 1 1_555 B G 23 1_555 0.605 -0.438 0.598 2.483 -20.286 -2.191 1 A_C1:G23_B A 1 ? B 23 ? 19 1 1 A U 2 1_555 B A 22 1_555 -0.119 -0.435 0.289 -3.680 -17.990 4.264 2 A_U2:A22_B A 2 ? B 22 ? 20 1 1 A U 3 1_555 B A 21 1_555 -0.130 -0.322 0.240 3.495 -8.648 6.003 3 A_U3:A21_B A 3 ? B 21 ? 20 1 1 A G 4 1_555 B C 20 1_555 0.050 0.169 0.129 1.420 -7.589 8.420 4 A_G4:C20_B A 4 ? B 20 ? 19 1 1 A C 5 1_555 B G 19 1_555 0.630 -0.347 0.083 4.213 -12.985 -3.399 5 A_C5:G19_B A 5 ? B 19 ? 19 1 1 A U 6 1_555 B A 18 1_555 -0.084 -0.203 0.175 -6.681 -16.534 -1.471 6 A_U6:A18_B A 6 ? B 18 ? 20 1 1 A G 7 1_555 B C 17 1_555 0.168 -0.161 0.133 -0.555 -8.341 -1.252 7 A_G7:C17_B A 7 ? B 17 ? 19 1 1 A G 9 1_555 B A 16 1_555 -0.156 1.673 -0.482 21.719 -9.779 3.537 8 A_G9:A16_B A 9 ? B 16 ? ? 1 1 A G 10 1_555 B C 15 1_555 -0.155 -0.141 -0.023 -11.556 -14.358 1.298 9 A_G10:C15_B A 10 ? B 15 ? 19 1 1 A U 11 1_555 B A 14 1_555 0.337 -0.522 0.348 -9.511 -3.178 0.533 10 A_U11:A14_B A 11 ? B 14 ? 20 1 1 A G 12 1_555 B C 13 1_555 -0.223 -0.279 0.139 -4.629 -24.165 3.897 11 A_G12:C13_B A 12 ? B 13 ? 19 1 1 A C 13 1_555 B G 12 1_555 -0.087 -0.148 0.411 -1.823 -12.618 -0.263 12 A_C13:G12_B A 13 ? B 12 ? 19 1 1 A A 14 1_555 B U 11 1_555 -0.027 -0.389 1.107 19.196 -2.241 1.944 13 A_A14:U11_B A 14 ? B 11 ? 20 1 1 A C 15 1_555 B G 10 1_555 -0.390 -0.258 0.478 2.494 -10.268 -2.836 14 A_C15:G10_B A 15 ? B 10 ? 19 1 1 A A 16 1_555 B G 9 1_555 -0.353 1.287 -0.359 -12.805 -23.275 -6.272 15 A_A16:G9_B A 16 ? B 9 ? 8 1 1 A C 17 1_555 B G 7 1_555 0.543 -0.056 0.055 -0.284 -0.435 4.112 16 A_C17:G7_B A 17 ? B 7 ? 19 1 1 A A 18 1_555 B U 6 1_555 -0.265 -0.180 0.315 6.141 -2.629 2.043 17 A_A18:U6_B A 18 ? B 6 ? 20 1 1 A G 19 1_555 B C 5 1_555 -0.433 -0.540 0.289 8.248 -13.567 -2.400 18 A_G19:C5_B A 19 ? B 5 ? 19 1 1 A C 20 1_555 B G 4 1_555 0.083 -0.233 0.149 -3.900 -8.045 5.092 19 A_C20:G4_B A 20 ? B 4 ? 19 1 1 A A 21 1_555 B U 3 1_555 0.071 -0.103 0.362 4.668 -13.944 10.046 20 A_A21:U3_B A 21 ? B 3 ? 20 1 1 A A 22 1_555 B U 2 1_555 -0.016 -0.326 0.280 14.607 -11.582 0.079 21 A_A22:U2_B A 22 ? B 2 ? 20 1 1 A G 23 1_555 B C 1 1_555 -0.445 -0.383 -0.187 -1.758 -14.181 2.320 22 A_G23:C1_B A 23 ? 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 A C 1 1_555 B G 23 1_555 A U 2 1_555 B A 22 1_555 -0.251 -1.872 3.210 -3.758 13.263 33.009 -4.747 -0.071 2.325 22.177 6.283 35.698 1 AA_C1U2:A22G23_BB A 1 ? B 23 ? A 2 ? B 22 ? 1 A U 2 1_555 B A 22 1_555 A U 3 1_555 B A 21 1_555 -0.109 -1.231 3.102 -2.229 4.339 33.473 -2.765 -0.147 2.924 7.485 3.844 33.817 2 AA_U2U3:A21A22_BB A 2 ? B 22 ? A 3 ? B 21 ? 1 A U 3 1_555 B A 21 1_555 A G 4 1_555 B C 20 1_555 0.150 -1.635 3.011 2.192 12.385 30.793 -4.585 0.042 2.212 22.197 -3.928 33.205 3 AA_U3G4:C20A21_BB A 3 ? B 21 ? A 4 ? B 20 ? 1 A G 4 1_555 B C 20 1_555 A C 5 1_555 B G 19 1_555 -0.644 -1.140 3.302 0.183 5.727 34.700 -2.727 1.093 3.078 9.521 -0.305 35.155 4 AA_G4C5:G19C20_BB A 4 ? B 20 ? A 5 ? B 19 ? 1 A C 5 1_555 B G 19 1_555 A U 6 1_555 B A 18 1_555 0.205 -1.517 3.435 3.035 14.125 27.555 -5.408 0.171 2.400 27.397 -5.887 31.047 5 AA_C5U6:A18G19_BB A 5 ? B 19 ? A 6 ? B 18 ? 1 A U 6 1_555 B A 18 1_555 A G 7 1_555 B C 17 1_555 0.616 -1.650 2.956 0.894 16.145 31.515 -4.610 -0.911 1.926 27.572 -1.527 35.327 6 AA_U6G7:C17A18_BB A 6 ? B 18 ? A 7 ? B 17 ? 1 A G 7 1_555 B C 17 1_555 A G 9 1_555 B A 16 1_555 -1.311 0.045 2.940 4.621 4.336 38.957 -0.382 2.421 2.762 6.449 -6.873 39.450 7 AA_G7G9:A16C17_BB A 7 ? B 17 ? A 9 ? B 16 ? 1 A G 9 1_555 B A 16 1_555 A G 10 1_555 B C 15 1_555 -0.420 -2.153 3.838 -7.473 14.983 34.134 -5.349 -0.369 2.722 23.830 11.885 37.909 8 AA_G9G10:C15A16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A G 10 1_555 B C 15 1_555 A U 11 1_555 B A 14 1_555 -0.371 -1.519 3.302 -3.360 1.626 34.421 -2.805 0.104 3.250 2.738 5.657 34.617 9 AA_G10U11:A14C15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A U 11 1_555 B A 14 1_555 A G 12 1_555 B C 13 1_555 0.305 -1.269 3.050 7.898 8.750 28.223 -3.957 0.818 2.545 17.035 -15.376 30.540 10 AA_U11G12:C13A14_BB A 11 ? B 14 ? A 12 ? B 13 ? 1 A G 12 1_555 B C 13 1_555 A C 13 1_555 B G 12 1_555 -0.268 -1.319 3.233 -4.320 8.826 30.332 -3.917 -0.253 2.762 16.337 7.997 31.848 11 AA_G12C13:G12C13_BB A 12 ? B 13 ? A 13 ? B 12 ? 1 A C 13 1_555 B G 12 1_555 A A 14 1_555 B U 11 1_555 0.374 -1.718 2.429 -5.929 3.152 30.355 -3.634 -1.500 2.135 5.929 11.152 31.072 12 AA_C13A14:U11G12_BB A 13 ? B 12 ? A 14 ? B 11 ? 1 A A 14 1_555 B U 11 1_555 A C 15 1_555 B G 10 1_555 0.172 -1.681 3.605 4.675 5.244 34.388 -3.630 0.463 3.315 8.756 -7.806 35.077 13 AA_A14C15:G10U11_BB A 14 ? B 11 ? A 15 ? B 10 ? 1 A C 15 1_555 B G 10 1_555 A A 16 1_555 B G 9 1_555 -0.005 -1.976 3.335 9.179 12.728 34.807 -4.518 1.081 2.417 20.063 -14.470 38.081 14 AA_C15A16:G9G10_BB A 15 ? B 10 ? A 16 ? B 9 ? 1 A A 16 1_555 B G 9 1_555 A C 17 1_555 B G 7 1_555 1.298 0.020 3.349 -10.031 -0.528 40.683 0.082 -2.845 2.961 -0.745 14.169 41.854 15 AA_A16C17:G7G9_BB A 16 ? B 9 ? A 17 ? B 7 ? 1 A C 17 1_555 B G 7 1_555 A A 18 1_555 B U 6 1_555 -0.229 -1.563 2.829 -3.946 16.237 27.739 -4.962 -0.112 1.696 30.602 7.437 32.298 16 AA_C17A18:U6G7_BB A 17 ? B 7 ? A 18 ? B 6 ? 1 A A 18 1_555 B U 6 1_555 A G 19 1_555 B C 5 1_555 -0.081 -1.568 3.232 0.828 8.864 31.537 -4.196 0.276 2.701 15.916 -1.486 32.739 17 AA_A18G19:C5U6_BB A 18 ? B 6 ? A 19 ? B 5 ? 1 A G 19 1_555 B C 5 1_555 A C 20 1_555 B G 4 1_555 0.744 -1.433 3.671 0.576 3.337 34.424 -2.978 -1.153 3.532 5.622 -0.970 34.585 18 AA_G19C20:G4C5_BB A 19 ? B 5 ? A 20 ? B 4 ? 1 A C 20 1_555 B G 4 1_555 A A 21 1_555 B U 3 1_555 0.060 -1.313 2.938 1.249 8.369 31.471 -3.580 0.078 2.515 15.091 -2.252 32.561 19 AA_C20A21:U3G4_BB A 20 ? B 4 ? A 21 ? B 3 ? 1 A A 21 1_555 B U 3 1_555 A A 22 1_555 B U 2 1_555 -0.608 -1.026 2.925 0.988 9.815 32.363 -3.111 1.181 2.497 17.119 -1.723 33.794 20 AA_A21A22:U2U3_BB A 21 ? B 3 ? A 22 ? B 2 ? 1 A A 22 1_555 B U 2 1_555 A G 23 1_555 B C 1 1_555 0.419 -1.426 3.652 5.055 20.252 31.649 -4.849 0.014 2.387 33.025 -8.244 37.766 21 AA_A22G23:C1U2_BB A 22 ? B 2 ? A 23 ? B 1 ? # _atom_sites.entry_id 1Y95 _atom_sites.fract_transf_matrix[1][1] 0.016892 _atom_sites.fract_transf_matrix[1][2] 0.009753 _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] 0.019505 _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] 0.015198 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MG N O P PB # loop_