data_421D # _entry.id 421D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 421D pdb_0000421d 10.2210/pdb421d/pdb NDB DR0003 ? ? RCSB RCSB001351 ? ? WWPDB D_1000001351 ? ? # 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 1999-01-05 2 'Structure model' 1 1 2008-04-26 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-12-27 # _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' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 421D _pdbx_database_status.recvd_initial_deposition_date 1998-08-16 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Xiong, Y.' 1 'Sundaralingam, M.' 2 # _citation.id primary _citation.title 'Crystal structure and conformation of a DNA-RNA hybrid duplex with a polypurine RNA strand: d(TTCTTBr5CTTC)-r(GAAGAAGAA).' _citation.journal_abbrev Structure _citation.journal_volume 6 _citation.page_first 1493 _citation.page_last 1501 _citation.year 1998 _citation.journal_id_ASTM STRUE6 _citation.country UK _citation.journal_id_ISSN 0969-2126 _citation.journal_id_CSD 2005 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9862803 _citation.pdbx_database_id_DOI '10.1016/S0969-2126(98)00148-8' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Xiong, Y.' 1 ? primary 'Sundaralingam, M.' 2 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*TP*TP*CP*TP*TP*(CBR)P*TP*TP*C)-3') ; 2726.641 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*A)-3') ; 2965.895 1 ? ? ? ? 3 water nat water 18.015 56 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no yes '(DT)(DT)(DC)(DT)(DT)(CBR)(DT)(DT)(DC)' TTCTTCTTC A ? 2 polyribonucleotide no no GAAGAAGAA GAAGAAGAA B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DT n 1 2 DT n 1 3 DC n 1 4 DT n 1 5 DT n 1 6 CBR n 1 7 DT n 1 8 DT n 1 9 DC n 2 1 G n 2 2 A n 2 3 A n 2 4 G n 2 5 A n 2 6 A n 2 7 G n 2 8 A n 2 9 A 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 CBR 'DNA linking' n "5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 Br N3 O7 P' 386.093 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DT 1 1 1 DT T A . n A 1 2 DT 2 2 2 DT T A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 CBR 6 6 6 CBR BRO A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DC 9 9 9 DC C A . n B 2 1 G 1 10 10 G G B . n B 2 2 A 2 11 11 A A B . n B 2 3 A 3 12 12 A A B . n B 2 4 G 4 13 13 G G B . n B 2 5 A 5 14 14 A A B . n B 2 6 A 6 15 15 A A B . n B 2 7 G 7 16 16 G G B . n B 2 8 A 8 17 17 A A B . n B 2 9 A 9 18 18 A A 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 3 HOH 1 101 101 HOH HOH A . C 3 HOH 2 102 102 HOH HOH A . C 3 HOH 3 103 103 HOH HOH A . C 3 HOH 4 110 110 HOH HOH A . C 3 HOH 5 111 111 HOH HOH A . C 3 HOH 6 119 119 HOH HOH A . C 3 HOH 7 120 120 HOH HOH A . C 3 HOH 8 125 125 HOH HOH A . C 3 HOH 9 126 126 HOH HOH A . C 3 HOH 10 127 127 HOH HOH A . C 3 HOH 11 128 128 HOH HOH A . C 3 HOH 12 130 130 HOH HOH A . C 3 HOH 13 133 133 HOH HOH A . C 3 HOH 14 139 139 HOH HOH A . C 3 HOH 15 141 141 HOH HOH A . C 3 HOH 16 144 144 HOH HOH A . C 3 HOH 17 145 145 HOH HOH A . C 3 HOH 18 146 146 HOH HOH A . C 3 HOH 19 147 147 HOH HOH A . C 3 HOH 20 149 149 HOH HOH A . C 3 HOH 21 150 150 HOH HOH A . C 3 HOH 22 151 151 HOH HOH A . C 3 HOH 23 152 152 HOH HOH A . C 3 HOH 24 154 154 HOH HOH A . D 3 HOH 1 104 104 HOH HOH B . D 3 HOH 2 105 105 HOH HOH B . D 3 HOH 3 106 106 HOH HOH B . D 3 HOH 4 107 107 HOH HOH B . D 3 HOH 5 108 108 HOH HOH B . D 3 HOH 6 109 109 HOH HOH B . D 3 HOH 7 112 112 HOH HOH B . D 3 HOH 8 113 113 HOH HOH B . D 3 HOH 9 114 114 HOH HOH B . D 3 HOH 10 115 115 HOH HOH B . D 3 HOH 11 116 116 HOH HOH B . D 3 HOH 12 117 117 HOH HOH B . D 3 HOH 13 118 118 HOH HOH B . D 3 HOH 14 121 121 HOH HOH B . D 3 HOH 15 122 122 HOH HOH B . D 3 HOH 16 123 123 HOH HOH B . D 3 HOH 17 124 124 HOH HOH B . D 3 HOH 18 129 129 HOH HOH B . D 3 HOH 19 131 131 HOH HOH B . D 3 HOH 20 132 132 HOH HOH B . D 3 HOH 21 134 134 HOH HOH B . D 3 HOH 22 135 135 HOH HOH B . D 3 HOH 23 136 136 HOH HOH B . D 3 HOH 24 137 137 HOH HOH B . D 3 HOH 25 138 138 HOH HOH B . D 3 HOH 26 140 140 HOH HOH B . D 3 HOH 27 142 142 HOH HOH B . D 3 HOH 28 143 143 HOH HOH B . D 3 HOH 29 148 148 HOH HOH B . D 3 HOH 30 153 153 HOH HOH B . D 3 HOH 31 155 155 HOH HOH B . D 3 HOH 32 156 156 HOH HOH B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A DT 1 ? "O5'" ? A DT 1 "O5'" 2 1 Y 1 A DT 1 ? "C5'" ? A DT 1 "C5'" 3 1 Y 1 A DT 1 ? "C4'" ? A DT 1 "C4'" 4 1 Y 1 A DT 1 ? "O4'" ? A DT 1 "O4'" 5 1 Y 1 A DT 1 ? "C3'" ? A DT 1 "C3'" 6 1 Y 1 A DT 1 ? "C2'" ? A DT 1 "C2'" 7 1 Y 1 A DT 1 ? "C1'" ? A DT 1 "C1'" 8 1 Y 1 A DT 1 ? N1 ? A DT 1 N1 9 1 Y 1 A DT 1 ? C2 ? A DT 1 C2 10 1 Y 1 A DT 1 ? O2 ? A DT 1 O2 11 1 Y 1 A DT 1 ? N3 ? A DT 1 N3 12 1 Y 1 A DT 1 ? C4 ? A DT 1 C4 13 1 Y 1 A DT 1 ? O4 ? A DT 1 O4 14 1 Y 1 A DT 1 ? C5 ? A DT 1 C5 15 1 Y 1 A DT 1 ? C7 ? A DT 1 C7 16 1 Y 1 A DT 1 ? C6 ? A DT 1 C6 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR refinement 3.851 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 # _cell.entry_id 421D _cell.length_a 48.080 _cell.length_b 48.080 _cell.length_c 42.880 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _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 421D _symmetry.space_group_name_H-M 'P 61' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? # _exptl.entry_id 421D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 51.06 _exptl_crystal.density_Matthews 2.51 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'pH 7.00' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 263.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IIC' _diffrn_detector.pdbx_collection_date 1997-02-15 _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 GRAPHITE _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 421D _reflns.observed_criterion_sigma_I 1.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 24.040 _reflns.d_resolution_high 1.800 _reflns.number_obs 4948 _reflns.number_all ? _reflns.percent_possible_obs 89.3 _reflns.pdbx_Rmerge_I_obs 0.069 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.460 _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 1.80 _reflns_shell.d_res_low 1.86 _reflns_shell.percent_possible_all 77.2 _reflns_shell.Rmerge_I_obs 0.355 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _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 421D _refine.ls_number_reflns_obs 4687 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.00 _refine.ls_d_res_high 1.80 _refine.ls_percent_reflns_obs 88.9 _refine.ls_R_factor_obs 0.201 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.201 _refine.ls_R_factor_R_free 0.237 _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 245 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _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.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 421D _refine_analyze.Luzzati_coordinate_error_obs 0.27 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _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 401 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 168 _refine_hist.number_atoms_total 569 _refine_hist.d_res_high 1.80 _refine_hist.d_res_low 10.00 # 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 x_bond_d 0.008 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 1.34 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d 7.70 ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d 1.70 ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_xplor_file.serial_no 1 _pdbx_xplor_file.param_file DNA-RNA.PARAM _pdbx_xplor_file.topol_file DNA-RNA.TOP _pdbx_xplor_file.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 421D _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 421D _struct.title ;5'-D(*TP*TP*CP*TP*TP*(BRO)CP*TP*TP*C)-3', 5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*A)-3' ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 421D _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' _struct_keywords.text 'DNA:RNA HYBRID DUPLEX, DNA-RNA COMPLEX, DNA-RNA HYBRID' # 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 3 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 1 PDB 421D 421D ? ? ? 2 2 PDB 421D 421D ? ? ? # 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 421D A 1 ? 9 ? 421D 1 ? 9 ? 1 9 2 2 421D B 1 ? 9 ? 421D 10 ? 18 ? 10 18 # _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 # _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.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 both ? A DT 5 "O3'" ? ? ? 1_555 A CBR 6 P ? ? A DT 5 A CBR 6 1_555 ? ? ? ? ? ? ? 1.587 ? ? covale2 covale both ? A CBR 6 "O3'" ? ? ? 1_555 A DT 7 P ? ? A CBR 6 A DT 7 1_555 ? ? ? ? ? ? ? 1.592 ? ? hydrog1 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B A 8 N1 ? ? A DT 2 B A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B A 8 N6 ? ? A DT 2 B A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B G 7 N1 ? ? A DC 3 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B G 7 O6 ? ? A DC 3 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B G 7 N2 ? ? A DC 3 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B A 6 N1 ? ? A DT 4 B A 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B A 6 N6 ? ? A DT 4 B A 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B A 5 N1 ? ? A DT 5 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B A 5 N6 ? ? A DT 5 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A CBR 6 N3 ? ? ? 1_555 B G 4 N1 ? ? A CBR 6 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A CBR 6 N4 ? ? ? 1_555 B G 4 O6 ? ? A CBR 6 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A CBR 6 O2 ? ? ? 1_555 B G 4 N2 ? ? A CBR 6 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B A 3 N1 ? ? A DT 7 B A 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B A 3 N6 ? ? A DT 7 B A 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B A 2 N1 ? ? A DT 8 B A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B A 2 N6 ? ? A DT 8 B A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B G 1 N1 ? ? A DC 9 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B G 1 O6 ? ? A DC 9 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B G 1 N2 ? ? A DC 9 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 H2 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 102 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 115 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 4_654 _pdbx_validate_symm_contact.dist 1.59 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 DT _pdbx_validate_rmsd_bond.auth_seq_id_1 1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 P _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 DT _pdbx_validate_rmsd_bond.auth_seq_id_2 2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.526 _pdbx_validate_rmsd_bond.bond_target_value 1.607 _pdbx_validate_rmsd_bond.bond_deviation -0.081 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.012 _pdbx_validate_rmsd_bond.linker_flag Y # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id CBR _pdbx_struct_mod_residue.label_seq_id 6 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id CBR _pdbx_struct_mod_residue.auth_seq_id 6 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DC _pdbx_struct_mod_residue.details ? # 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 CBR BR BR N N 38 CBR P P N N 39 CBR OP1 O N N 40 CBR OP2 O N N 41 CBR "O5'" O N N 42 CBR N1 N N N 43 CBR C6 C N N 44 CBR C2 C N N 45 CBR O2 O N N 46 CBR N3 N N N 47 CBR C4 C N N 48 CBR N4 N N N 49 CBR C5 C N N 50 CBR "C2'" C N N 51 CBR "C5'" C N N 52 CBR "C4'" C N R 53 CBR "O4'" O N N 54 CBR "C1'" C N R 55 CBR "C3'" C N S 56 CBR "O3'" O N N 57 CBR OP3 O N N 58 CBR HOP2 H N N 59 CBR H6 H N N 60 CBR H41 H N N 61 CBR H42 H N N 62 CBR "H2'" H N N 63 CBR "H2''" H N N 64 CBR "H5'" H N N 65 CBR "H5''" H N N 66 CBR "H4'" H N N 67 CBR "H1'" H N N 68 CBR "H3'" H N N 69 CBR "HO3'" H N N 70 CBR HOP3 H N N 71 DC OP3 O N N 72 DC P P N N 73 DC OP1 O N N 74 DC OP2 O N N 75 DC "O5'" O N N 76 DC "C5'" C N N 77 DC "C4'" C N R 78 DC "O4'" O N N 79 DC "C3'" C N S 80 DC "O3'" O N N 81 DC "C2'" C N N 82 DC "C1'" C N R 83 DC N1 N N N 84 DC C2 C N N 85 DC O2 O N N 86 DC N3 N N N 87 DC C4 C N N 88 DC N4 N N N 89 DC C5 C N N 90 DC C6 C N N 91 DC HOP3 H N N 92 DC HOP2 H N N 93 DC "H5'" H N N 94 DC "H5''" H N N 95 DC "H4'" H N N 96 DC "H3'" H N N 97 DC "HO3'" H N N 98 DC "H2'" H N N 99 DC "H2''" H N N 100 DC "H1'" H N N 101 DC H41 H N N 102 DC H42 H N N 103 DC H5 H N N 104 DC H6 H N N 105 DT OP3 O N N 106 DT P P N N 107 DT OP1 O N N 108 DT OP2 O N N 109 DT "O5'" O N N 110 DT "C5'" C N N 111 DT "C4'" C N R 112 DT "O4'" O N N 113 DT "C3'" C N S 114 DT "O3'" O N N 115 DT "C2'" C N N 116 DT "C1'" C N R 117 DT N1 N N N 118 DT C2 C N N 119 DT O2 O N N 120 DT N3 N N N 121 DT C4 C N N 122 DT O4 O N N 123 DT C5 C N N 124 DT C7 C N N 125 DT C6 C N N 126 DT HOP3 H N N 127 DT HOP2 H N N 128 DT "H5'" H N N 129 DT "H5''" H N N 130 DT "H4'" H N N 131 DT "H3'" H N N 132 DT "HO3'" H N N 133 DT "H2'" H N N 134 DT "H2''" H N N 135 DT "H1'" H N N 136 DT H3 H N N 137 DT H71 H N N 138 DT H72 H N N 139 DT H73 H N N 140 DT H6 H N N 141 G OP3 O N N 142 G P P N N 143 G OP1 O N N 144 G OP2 O N N 145 G "O5'" O N N 146 G "C5'" C N N 147 G "C4'" C N R 148 G "O4'" O N N 149 G "C3'" C N S 150 G "O3'" O N N 151 G "C2'" C N R 152 G "O2'" O N N 153 G "C1'" C N R 154 G N9 N Y N 155 G C8 C Y N 156 G N7 N Y N 157 G C5 C Y N 158 G C6 C N N 159 G O6 O N N 160 G N1 N N N 161 G C2 C N N 162 G N2 N N N 163 G N3 N N N 164 G C4 C Y N 165 G HOP3 H N N 166 G HOP2 H N N 167 G "H5'" H N N 168 G "H5''" H N N 169 G "H4'" H N N 170 G "H3'" H N N 171 G "HO3'" H N N 172 G "H2'" H N N 173 G "HO2'" H N N 174 G "H1'" H N N 175 G H8 H N N 176 G H1 H N N 177 G H21 H N N 178 G H22 H N N 179 HOH O O N N 180 HOH H1 H N N 181 HOH H2 H N N 182 # 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 CBR BR C5 sing N N 40 CBR P OP1 doub N N 41 CBR P OP2 sing N N 42 CBR P "O5'" sing N N 43 CBR P OP3 sing N N 44 CBR OP2 HOP2 sing N N 45 CBR "O5'" "C5'" sing N N 46 CBR N1 C6 sing N N 47 CBR N1 C2 sing N N 48 CBR N1 "C1'" sing N N 49 CBR C6 C5 doub N N 50 CBR C6 H6 sing N N 51 CBR C2 O2 doub N N 52 CBR C2 N3 sing N N 53 CBR N3 C4 doub N N 54 CBR C4 N4 sing N N 55 CBR C4 C5 sing N N 56 CBR N4 H41 sing N N 57 CBR N4 H42 sing N N 58 CBR "C2'" "C1'" sing N N 59 CBR "C2'" "C3'" sing N N 60 CBR "C2'" "H2'" sing N N 61 CBR "C2'" "H2''" sing N N 62 CBR "C5'" "C4'" sing N N 63 CBR "C5'" "H5'" sing N N 64 CBR "C5'" "H5''" sing N N 65 CBR "C4'" "O4'" sing N N 66 CBR "C4'" "C3'" sing N N 67 CBR "C4'" "H4'" sing N N 68 CBR "O4'" "C1'" sing N N 69 CBR "C1'" "H1'" sing N N 70 CBR "C3'" "O3'" sing N N 71 CBR "C3'" "H3'" sing N N 72 CBR "O3'" "HO3'" sing N N 73 CBR OP3 HOP3 sing N N 74 DC OP3 P sing N N 75 DC OP3 HOP3 sing N N 76 DC P OP1 doub N N 77 DC P OP2 sing N N 78 DC P "O5'" sing N N 79 DC OP2 HOP2 sing N N 80 DC "O5'" "C5'" sing N N 81 DC "C5'" "C4'" sing N N 82 DC "C5'" "H5'" sing N N 83 DC "C5'" "H5''" sing N N 84 DC "C4'" "O4'" sing N N 85 DC "C4'" "C3'" sing N N 86 DC "C4'" "H4'" sing N N 87 DC "O4'" "C1'" sing N N 88 DC "C3'" "O3'" sing N N 89 DC "C3'" "C2'" sing N N 90 DC "C3'" "H3'" sing N N 91 DC "O3'" "HO3'" sing N N 92 DC "C2'" "C1'" sing N N 93 DC "C2'" "H2'" sing N N 94 DC "C2'" "H2''" sing N N 95 DC "C1'" N1 sing N N 96 DC "C1'" "H1'" sing N N 97 DC N1 C2 sing N N 98 DC N1 C6 sing N N 99 DC C2 O2 doub N N 100 DC C2 N3 sing N N 101 DC N3 C4 doub N N 102 DC C4 N4 sing N N 103 DC C4 C5 sing N N 104 DC N4 H41 sing N N 105 DC N4 H42 sing N N 106 DC C5 C6 doub N N 107 DC C5 H5 sing N N 108 DC C6 H6 sing N N 109 DT OP3 P sing N N 110 DT OP3 HOP3 sing N N 111 DT P OP1 doub N N 112 DT P OP2 sing N N 113 DT P "O5'" sing N N 114 DT OP2 HOP2 sing N N 115 DT "O5'" "C5'" sing N N 116 DT "C5'" "C4'" sing N N 117 DT "C5'" "H5'" sing N N 118 DT "C5'" "H5''" sing N N 119 DT "C4'" "O4'" sing N N 120 DT "C4'" "C3'" sing N N 121 DT "C4'" "H4'" sing N N 122 DT "O4'" "C1'" sing N N 123 DT "C3'" "O3'" sing N N 124 DT "C3'" "C2'" sing N N 125 DT "C3'" "H3'" sing N N 126 DT "O3'" "HO3'" sing N N 127 DT "C2'" "C1'" sing N N 128 DT "C2'" "H2'" sing N N 129 DT "C2'" "H2''" sing N N 130 DT "C1'" N1 sing N N 131 DT "C1'" "H1'" sing N N 132 DT N1 C2 sing N N 133 DT N1 C6 sing N N 134 DT C2 O2 doub N N 135 DT C2 N3 sing N N 136 DT N3 C4 sing N N 137 DT N3 H3 sing N N 138 DT C4 O4 doub N N 139 DT C4 C5 sing N N 140 DT C5 C7 sing N N 141 DT C5 C6 doub N N 142 DT C7 H71 sing N N 143 DT C7 H72 sing N N 144 DT C7 H73 sing N N 145 DT C6 H6 sing N N 146 G OP3 P sing N N 147 G OP3 HOP3 sing N N 148 G P OP1 doub N N 149 G P OP2 sing N N 150 G P "O5'" sing N N 151 G OP2 HOP2 sing N N 152 G "O5'" "C5'" sing N N 153 G "C5'" "C4'" sing N N 154 G "C5'" "H5'" sing N N 155 G "C5'" "H5''" sing N N 156 G "C4'" "O4'" sing N N 157 G "C4'" "C3'" sing N N 158 G "C4'" "H4'" sing N N 159 G "O4'" "C1'" sing N N 160 G "C3'" "O3'" sing N N 161 G "C3'" "C2'" sing N N 162 G "C3'" "H3'" sing N N 163 G "O3'" "HO3'" sing N N 164 G "C2'" "O2'" sing N N 165 G "C2'" "C1'" sing N N 166 G "C2'" "H2'" sing N N 167 G "O2'" "HO2'" sing N N 168 G "C1'" N9 sing N N 169 G "C1'" "H1'" sing N N 170 G N9 C8 sing Y N 171 G N9 C4 sing Y N 172 G C8 N7 doub Y N 173 G C8 H8 sing N N 174 G N7 C5 sing Y N 175 G C5 C6 sing N N 176 G C5 C4 doub Y N 177 G C6 O6 doub N N 178 G C6 N1 sing N N 179 G N1 C2 sing N N 180 G N1 H1 sing N N 181 G C2 N2 sing N N 182 G C2 N3 doub N N 183 G N2 H21 sing N N 184 G N2 H22 sing N N 185 G N3 C4 sing N N 186 HOH O H1 sing N N 187 HOH O H2 sing N N 188 # _ndb_struct_conf_na.entry_id 421D _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DT 2 1_555 B A 8 1_555 -0.025 -0.299 0.439 -7.859 -8.303 6.347 1 A_DT2:A17_B A 2 ? B 17 ? 20 1 1 A DC 3 1_555 B G 7 1_555 0.433 -0.172 -0.050 1.330 -14.648 3.738 2 A_DC3:G16_B A 3 ? B 16 ? 19 1 1 A DT 4 1_555 B A 6 1_555 0.050 -0.377 -0.352 8.854 -14.565 -0.008 3 A_DT4:A15_B A 4 ? B 15 ? 20 1 1 A DT 5 1_555 B A 5 1_555 0.194 -0.323 0.061 8.120 -16.599 1.024 4 A_DT5:A14_B A 5 ? B 14 ? 20 1 1 A CBR 6 1_555 B G 4 1_555 0.165 -0.284 -0.150 7.168 -16.587 0.555 5 A_CBR6:G13_B A 6 ? B 13 ? 19 1 1 A DT 7 1_555 B A 3 1_555 -0.078 -0.187 0.138 -0.542 -21.284 5.645 6 A_DT7:A12_B A 7 ? B 12 ? 20 1 1 A DT 8 1_555 B A 2 1_555 0.104 -0.225 -0.057 0.547 -13.890 2.230 7 A_DT8:A11_B A 8 ? B 11 ? 20 1 1 A DC 9 1_555 B G 1 1_555 0.650 -0.166 -0.092 6.784 -3.587 1.867 8 A_DC9:G10_B A 9 ? B 10 ? 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 DT 2 1_555 B A 8 1_555 A DC 3 1_555 B G 7 1_555 -0.825 -1.525 3.079 2.200 -3.781 30.675 -2.155 1.953 3.174 -7.102 -4.132 30.978 1 AA_DT2DC3:G16A17_BB A 2 ? B 17 ? A 3 ? B 16 ? 1 A DC 3 1_555 B G 7 1_555 A DT 4 1_555 B A 6 1_555 -0.917 -1.470 3.129 -1.608 6.540 24.507 -5.055 1.664 2.705 15.048 3.699 25.402 2 AA_DC3DT4:A15G16_BB A 3 ? B 16 ? A 4 ? B 15 ? 1 A DT 4 1_555 B A 6 1_555 A DT 5 1_555 B A 5 1_555 0.172 -0.955 3.360 -3.384 4.319 34.748 -2.230 -0.794 3.191 7.177 5.623 35.165 3 AA_DT4DT5:A14A15_BB A 4 ? B 15 ? A 5 ? B 14 ? 1 A DT 5 1_555 B A 5 1_555 A CBR 6 1_555 B G 4 1_555 -0.199 -1.411 3.314 0.138 6.263 32.513 -3.505 0.371 2.997 11.057 -0.244 33.095 4 AA_DT5CBR6:G13A14_BB A 5 ? B 14 ? A 6 ? B 13 ? 1 A CBR 6 1_555 B G 4 1_555 A DT 7 1_555 B A 3 1_555 0.261 -1.210 3.423 1.176 10.153 31.884 -3.769 -0.261 2.919 17.915 -2.076 33.442 5 AA_CBR6DT7:A12G13_BB A 6 ? B 13 ? A 7 ? B 12 ? 1 A DT 7 1_555 B A 3 1_555 A DT 8 1_555 B A 2 1_555 -0.564 -0.972 3.265 -1.567 8.271 33.656 -2.862 0.714 2.973 14.015 2.654 34.663 6 AA_DT7DT8:A11A12_BB A 7 ? B 12 ? A 8 ? B 11 ? 1 A DT 8 1_555 B A 2 1_555 A DC 9 1_555 B G 1 1_555 0.286 -0.679 3.218 0.464 6.634 32.798 -2.237 -0.423 3.030 11.600 -0.811 33.448 7 AA_DT8DC9:G10A11_BB A 8 ? B 11 ? A 9 ? B 10 ? # _atom_sites.entry_id 421D _atom_sites.fract_transf_matrix[1][1] 0.020799 _atom_sites.fract_transf_matrix[1][2] 0.012008 _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] 0.024016 _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] 0.023321 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol BR C H N O P # loop_