data_1UHX # _entry.id 1UHX # _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 1UHX pdb_00001uhx 10.2210/pdb1uhx/pdb NDB UD0036 ? ? RCSB RCSB005847 ? ? WWPDB D_1000005847 ? ? # 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 2004-02-03 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2014-10-22 5 'Structure model' 1 4 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' 'Derived calculations' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 '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 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' pdbx_struct_conn_angle 5 5 'Structure model' struct_conn 6 5 'Structure model' struct_conn_type 7 5 '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 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.value' 6 5 'Structure model' '_struct_conn.conn_type_id' 7 5 'Structure model' '_struct_conn.id' 8 5 'Structure model' '_struct_conn.pdbx_dist_value' 9 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 10 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 11 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 12 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 13 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 14 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 15 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 16 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 17 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 18 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 19 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 20 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 21 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 22 5 'Structure model' '_struct_conn_type.id' 23 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 24 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 25 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1UHX _pdbx_database_status.recvd_initial_deposition_date 2003-07-13 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _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 1UHY _pdbx_database_related.details 'Crystal structure of d(GCGATAGC)' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kondo, J.' 1 'Umeda, S.I.' 2 'Fujita, K.' 3 'Sunami, T.' 4 'Takenaka, A.' 5 # _citation.id primary _citation.title ;X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue. ; _citation.journal_abbrev 'J.Synchrotron Radiat.' _citation.journal_volume 11 _citation.page_first 117 _citation.page_last 120 _citation.year 2004 _citation.journal_id_ASTM JSYRES _citation.country DK _citation.journal_id_ISSN 0909-0495 _citation.journal_id_CSD 1210 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 14646150 _citation.pdbx_database_id_DOI 10.1107/S0909049503023562 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Umeda, S.I.' 2 ? primary 'Fujita, K.' 3 ? primary 'Sunami, T.' 4 ? primary 'Takenaka, A.' 5 ? # 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'-D(*GP*(CBR)P*GP*AP*GP*AP*GP*C)-3'" 2555.539 1 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 4 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 5 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 1 ? ? ? ? 6 water nat water 18.015 69 ? ? ? ? # _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 '(DG)(CBR)(DG)(DA)(DG)(DA)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGAGAGC _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 'MAGNESIUM ION' MG 3 'CHLORIDE ION' CL 4 'SODIUM ION' NA 5 'COBALT HEXAMMINE(III)' NCO 6 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 CBR n 1 3 DG n 1 4 DA n 1 5 DG n 1 6 DA n 1 7 DG n 1 8 DC 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 CBR 'DNA linking' n "5-BROMO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 Br N3 O7 P' 386.093 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 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 # 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 DG 1 1 1 DG G A . n A 1 2 CBR 2 2 2 CBR BRO A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DC 8 8 8 DC C 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 MG 1 79 79 MG MG A . C 3 CL 1 80 80 CL CL A . D 4 NA 1 81 81 NA NA A . E 5 NCO 1 78 78 NCO NCO A . F 6 HOH 1 9 9 HOH HOH A . F 6 HOH 2 10 10 HOH HOH A . F 6 HOH 3 11 11 HOH HOH A . F 6 HOH 4 12 12 HOH HOH A . F 6 HOH 5 13 13 HOH HOH A . F 6 HOH 6 14 14 HOH HOH A . F 6 HOH 7 15 15 HOH HOH A . F 6 HOH 8 16 16 HOH HOH A . F 6 HOH 9 17 17 HOH HOH A . F 6 HOH 10 18 18 HOH HOH A . F 6 HOH 11 19 19 HOH HOH A . F 6 HOH 12 20 20 HOH HOH A . F 6 HOH 13 21 21 HOH HOH A . F 6 HOH 14 22 22 HOH HOH A . F 6 HOH 15 23 23 HOH HOH A . F 6 HOH 16 24 24 HOH HOH A . F 6 HOH 17 25 25 HOH HOH A . F 6 HOH 18 26 26 HOH HOH A . F 6 HOH 19 27 27 HOH HOH A . F 6 HOH 20 28 28 HOH HOH A . F 6 HOH 21 29 29 HOH HOH A . F 6 HOH 22 30 30 HOH HOH A . F 6 HOH 23 31 31 HOH HOH A . F 6 HOH 24 32 32 HOH HOH A . F 6 HOH 25 33 33 HOH HOH A . F 6 HOH 26 34 34 HOH HOH A . F 6 HOH 27 35 35 HOH HOH A . F 6 HOH 28 36 36 HOH HOH A . F 6 HOH 29 37 37 HOH HOH A . F 6 HOH 30 38 38 HOH HOH A . F 6 HOH 31 39 39 HOH HOH A . F 6 HOH 32 40 40 HOH HOH A . F 6 HOH 33 41 41 HOH HOH A . F 6 HOH 34 42 42 HOH HOH A . F 6 HOH 35 43 43 HOH HOH A . F 6 HOH 36 44 44 HOH HOH A . F 6 HOH 37 45 45 HOH HOH A . F 6 HOH 38 46 46 HOH HOH A . F 6 HOH 39 47 47 HOH HOH A . F 6 HOH 40 48 48 HOH HOH A . F 6 HOH 41 49 49 HOH HOH A . F 6 HOH 42 50 50 HOH HOH A . F 6 HOH 43 51 51 HOH HOH A . F 6 HOH 44 52 52 HOH HOH A . F 6 HOH 45 53 53 HOH HOH A . F 6 HOH 46 54 54 HOH HOH A . F 6 HOH 47 55 55 HOH HOH A . F 6 HOH 48 56 56 HOH HOH A . F 6 HOH 49 57 57 HOH HOH A . F 6 HOH 50 58 58 HOH HOH A . F 6 HOH 51 59 59 HOH HOH A . F 6 HOH 52 60 60 HOH HOH A . F 6 HOH 53 61 61 HOH HOH A . F 6 HOH 54 62 62 HOH HOH A . F 6 HOH 55 63 63 HOH HOH A . F 6 HOH 56 64 64 HOH HOH A . F 6 HOH 57 65 65 HOH HOH A . F 6 HOH 58 66 66 HOH HOH A . F 6 HOH 59 67 67 HOH HOH A . F 6 HOH 60 68 68 HOH HOH A . F 6 HOH 61 69 69 HOH HOH A . F 6 HOH 62 70 70 HOH HOH A . F 6 HOH 63 71 71 HOH HOH A . F 6 HOH 64 72 72 HOH HOH A . F 6 HOH 65 73 73 HOH HOH A . F 6 HOH 66 74 74 HOH HOH A . F 6 HOH 67 75 75 HOH HOH A . F 6 HOH 68 76 76 HOH HOH A . F 6 HOH 69 77 77 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MOSFLM 'data reduction' . ? 1 SCALA 'data scaling' . ? 2 AMoRE phasing . ? 3 CNS refinement 1.0 ? 4 CCP4 'data scaling' '(SCALA)' ? 5 # _cell.entry_id 1UHX _cell.length_a 37.670 _cell.length_b 37.670 _cell.length_c 65.490 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 1UHX _symmetry.space_group_name_H-M 'P 63 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1UHX _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.96 _exptl_crystal.density_percent_sol 36.60 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;2-methyl-2,4-pentandiol, hexamine cobalt chloride, magnesium chloride, sodium succinate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K ; _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 2-methyl-2,4-pentandiol ? ? ? 1 2 1 'hexamine cobalt chloride' ? ? ? 1 3 1 'magnesium chloride' ? ? ? 1 4 1 'sodium succinate' ? ? ? 1 5 2 'hexamine cobalt chloride' ? ? ? 1 6 2 'magnesium chloride' ? ? ? 1 7 2 'sodium succinate' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2002-06-01 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-18B' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-18B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.entry_id 1UHX _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high 2.0 _reflns.d_resolution_low 29.2 _reflns.number_all 2142 _reflns.number_obs 2142 _reflns.percent_possible_obs 100.0 _reflns.pdbx_Rmerge_I_obs 0.075 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 4.9 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _reflns_shell.d_res_high 2.0 _reflns_shell.d_res_low 2.1 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.323 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.4 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? # _refine.entry_id 1UHX _refine.ls_d_res_high 2.0 _refine.ls_d_res_low 20.0 _refine.pdbx_ls_sigma_F 3.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 2125 _refine.ls_number_reflns_obs 2030 _refine.ls_number_reflns_R_free 179 _refine.ls_percent_reflns_obs 95.5 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.22 _refine.ls_R_factor_R_free 0.278 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean ? _refine.aniso_B[1][1] -4.633 _refine.aniso_B[1][2] -5.489 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][2] -4.633 _refine.aniso_B[2][3] 0.000 _refine.aniso_B[3][3] 9.266 _refine.details ? _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.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_phase_error ? _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_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 1UHX _refine_analyze.Luzzati_coordinate_error_obs 0.22 _refine_analyze.Luzzati_sigma_a_obs 0.19 _refine_analyze.Luzzati_d_res_low_obs 5.0 _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_non_hydrogen ? _refine_analyze.occupancy_sum_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 166 _refine_hist.pdbx_number_atoms_ligand 10 _refine_hist.number_atoms_solvent 69 _refine_hist.number_atoms_total 245 _refine_hist.d_res_high 2.0 _refine_hist.d_res_low 20.0 # 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_angle_deg 0.8 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 21.7 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.8 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.00 _refine_ls_shell.d_res_low 2.09 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.288 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.469 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 16 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 1UHX _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 1UHX _struct.title 'Crystal structure of d(GCGAGAGC): the base-intercalated duplex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1UHX _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'base-intercalated duplex, base-intercalated motif, sheared G:A pair, DNA, Deoxyribonucleic acid' # 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 ? F N N 6 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1UHX _struct_ref.pdbx_db_accession 1UHX _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1UHX _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 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1UHX _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _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 8 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # 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' 10_665 -y+1,-x+1,-z+1/2 0.5000000000 -0.8660254038 0.0000000000 18.8350000000 -0.8660254038 -0.5000000000 0.0000000000 32.6231769606 0.0000000000 0.0000000000 -1.0000000000 32.7450000000 3 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5000000000 -0.8660254038 0.0000000000 37.6700000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 12_555 x,x-y,-z+1/2 0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 32.7450000000 5 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5000000000 0.8660254038 0.0000000000 18.8350000000 -0.8660254038 -0.5000000000 0.0000000000 32.6231769606 0.0000000000 0.0000000000 1.0000000000 0.0000000000 6 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1.0000000000 0.0000000000 0.0000000000 37.6700000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 32.7450000000 # _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 covale1 covale both ? A DG 1 "O3'" ? ? ? 1_555 A CBR 2 P ? ? A DG 1 A CBR 2 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale2 covale both ? A CBR 2 "O3'" ? ? ? 1_555 A DG 3 P ? ? A CBR 2 A DG 3 1_555 ? ? ? ? ? ? ? 1.609 ? ? metalc1 metalc ? ? F HOH . O ? ? ? 1_555 B MG . MG ? ? A HOH 9 A MG 79 1_555 ? ? ? ? ? ? ? 2.381 ? ? metalc2 metalc ? ? F HOH . O ? ? ? 1_555 B MG . MG ? ? A HOH 27 A MG 79 1_555 ? ? ? ? ? ? ? 2.398 ? ? metalc3 metalc ? ? F HOH . O ? ? ? 1_555 B MG . MG ? ? A HOH 29 A MG 79 1_555 ? ? ? ? ? ? ? 2.394 ? ? metalc4 metalc ? ? F HOH . O ? ? ? 1_555 B MG . MG ? ? A HOH 47 A MG 79 1_555 ? ? ? ? ? ? ? 2.398 ? ? metalc5 metalc ? ? F HOH . O ? ? ? 1_555 B MG . MG ? ? A HOH 48 A MG 79 1_555 ? ? ? ? ? ? ? 2.382 ? ? metalc6 metalc ? ? F HOH . O ? ? ? 1_555 B MG . MG ? ? A HOH 67 A MG 79 1_555 ? ? ? ? ? ? ? 2.391 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 1 A DC 8 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 1 A DC 8 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 1 A DC 8 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A CBR 2 N3 ? ? ? 1_555 A DG 7 N1 ? ? A CBR 2 A DG 7 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A CBR 2 N4 ? ? ? 1_555 A DG 7 O6 ? ? A CBR 2 A DG 7 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A CBR 2 O2 ? ? ? 1_555 A DG 7 N2 ? ? A CBR 2 A DG 7 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DA 6 N7 ? ? A DG 3 A DA 6 8_665 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog8 hydrog ? ? A DG 3 N3 ? ? ? 1_555 A DA 6 N6 ? ? A DG 3 A DA 6 8_665 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog9 hydrog ? ? A DA 6 N6 ? ? ? 1_555 A DG 3 N3 ? ? A DA 6 A DG 3 8_665 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog10 hydrog ? ? A DA 6 N7 ? ? ? 1_555 A DG 3 N2 ? ? A DA 6 A DG 3 8_665 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog11 hydrog ? ? A DG 7 N1 ? ? ? 1_555 A CBR 2 N3 ? ? A DG 7 A CBR 2 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 7 N2 ? ? ? 1_555 A CBR 2 O2 ? ? A DG 7 A CBR 2 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 7 O6 ? ? ? 1_555 A CBR 2 N4 ? ? A DG 7 A CBR 2 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 1 N1 ? ? A DC 8 A DG 1 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 8 A DG 1 8_665 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 1 N2 ? ? A DC 8 A DG 1 8_665 ? ? ? ? ? ? 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 O ? F HOH . ? A HOH 9 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 27 ? 1_555 89.6 ? 2 O ? F HOH . ? A HOH 9 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 29 ? 1_555 93.3 ? 3 O ? F HOH . ? A HOH 27 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 29 ? 1_555 88.8 ? 4 O ? F HOH . ? A HOH 9 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 47 ? 1_555 86.9 ? 5 O ? F HOH . ? A HOH 27 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 47 ? 1_555 90.9 ? 6 O ? F HOH . ? A HOH 29 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 47 ? 1_555 179.7 ? 7 O ? F HOH . ? A HOH 9 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 48 ? 1_555 90.3 ? 8 O ? F HOH . ? A HOH 27 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 48 ? 1_555 173.7 ? 9 O ? F HOH . ? A HOH 29 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 48 ? 1_555 84.9 ? 10 O ? F HOH . ? A HOH 47 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 48 ? 1_555 95.3 ? 11 O ? F HOH . ? A HOH 9 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 67 ? 1_555 179.0 ? 12 O ? F HOH . ? A HOH 27 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 67 ? 1_555 89.8 ? 13 O ? F HOH . ? A HOH 29 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 67 ? 1_555 87.5 ? 14 O ? F HOH . ? A HOH 47 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 67 ? 1_555 92.3 ? 15 O ? F HOH . ? A HOH 48 ? 1_555 MG ? B MG . ? A MG 79 ? 1_555 O ? F HOH . ? A HOH 67 ? 1_555 90.4 ? # 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 MG 79 ? 6 'BINDING SITE FOR RESIDUE MG A 79' AC2 Software A CL 80 ? 6 'BINDING SITE FOR RESIDUE CL A 80' AC3 Software A NA 81 ? 3 'BINDING SITE FOR RESIDUE NA A 81' AC4 Software A NCO 78 ? 12 'BINDING SITE FOR RESIDUE NCO A 78' # 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 6 HOH F . ? HOH A 9 . ? 1_555 ? 2 AC1 6 HOH F . ? HOH A 27 . ? 1_555 ? 3 AC1 6 HOH F . ? HOH A 29 . ? 1_555 ? 4 AC1 6 HOH F . ? HOH A 47 . ? 1_555 ? 5 AC1 6 HOH F . ? HOH A 48 . ? 1_555 ? 6 AC1 6 HOH F . ? HOH A 67 . ? 1_555 ? 7 AC2 6 DA A 4 ? DA A 4 . ? 10_665 ? 8 AC2 6 DA A 4 ? DA A 4 . ? 12_555 ? 9 AC2 6 DA A 4 ? DA A 4 . ? 11_655 ? 10 AC2 6 NCO E . ? NCO A 78 . ? 11_655 ? 11 AC2 6 NCO E . ? NCO A 78 . ? 12_555 ? 12 AC2 6 NCO E . ? NCO A 78 . ? 10_665 ? 13 AC3 3 DG A 5 ? DG A 5 . ? 2_655 ? 14 AC3 3 DG A 5 ? DG A 5 . ? 3_665 ? 15 AC3 3 DG A 5 ? DG A 5 . ? 1_555 ? 16 AC4 12 CBR A 2 ? CBR A 2 . ? 1_555 ? 17 AC4 12 CBR A 2 ? CBR A 2 . ? 2_655 ? 18 AC4 12 CBR A 2 ? CBR A 2 . ? 3_665 ? 19 AC4 12 DG A 3 ? DG A 3 . ? 3_665 ? 20 AC4 12 DG A 3 ? DG A 3 . ? 1_555 ? 21 AC4 12 DG A 3 ? DG A 3 . ? 2_655 ? 22 AC4 12 HOH F . ? HOH A 12 . ? 1_555 ? 23 AC4 12 HOH F . ? HOH A 12 . ? 3_665 ? 24 AC4 12 HOH F . ? HOH A 12 . ? 2_655 ? 25 AC4 12 CL C . ? CL A 80 . ? 12_555 ? 26 AC4 12 CL C . ? CL A 80 . ? 11_655 ? 27 AC4 12 CL C . ? CL A 80 . ? 10_665 ? # _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 2 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id CBR _pdbx_struct_mod_residue.auth_seq_id 2 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DC _pdbx_struct_mod_residue.details ? # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A CL 80 ? C CL . 2 1 A NA 81 ? D NA . 3 1 A NCO 78 ? E NCO . 4 1 A HOH 24 ? F HOH . 5 1 A HOH 37 ? F HOH . 6 1 A HOH 45 ? F HOH . 7 1 A HOH 46 ? F HOH . 8 1 A HOH 59 ? F HOH . 9 1 A HOH 61 ? F HOH . 10 1 A HOH 75 ? F HOH . # 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 CBR BR BR N N 1 CBR P P N N 2 CBR OP1 O N N 3 CBR OP2 O N N 4 CBR "O5'" O N N 5 CBR N1 N N N 6 CBR C6 C N N 7 CBR C2 C N N 8 CBR O2 O N N 9 CBR N3 N N N 10 CBR C4 C N N 11 CBR N4 N N N 12 CBR C5 C N N 13 CBR "C2'" C N N 14 CBR "C5'" C N N 15 CBR "C4'" C N R 16 CBR "O4'" O N N 17 CBR "C1'" C N R 18 CBR "C3'" C N S 19 CBR "O3'" O N N 20 CBR OP3 O N N 21 CBR HOP2 H N N 22 CBR H6 H N N 23 CBR H41 H N N 24 CBR H42 H N N 25 CBR "H2'" H N N 26 CBR "H2''" H N N 27 CBR "H5'" H N N 28 CBR "H5''" H N N 29 CBR "H4'" H N N 30 CBR "H1'" H N N 31 CBR "H3'" H N N 32 CBR "HO3'" H N N 33 CBR HOP3 H N N 34 CL CL CL N N 35 DA OP3 O N N 36 DA P P N N 37 DA OP1 O N N 38 DA OP2 O N N 39 DA "O5'" O N N 40 DA "C5'" C N N 41 DA "C4'" C N R 42 DA "O4'" O N N 43 DA "C3'" C N S 44 DA "O3'" O N N 45 DA "C2'" C N N 46 DA "C1'" C N R 47 DA N9 N Y N 48 DA C8 C Y N 49 DA N7 N Y N 50 DA C5 C Y N 51 DA C6 C Y N 52 DA N6 N N N 53 DA N1 N Y N 54 DA C2 C Y N 55 DA N3 N Y N 56 DA C4 C Y N 57 DA HOP3 H N N 58 DA HOP2 H N N 59 DA "H5'" H N N 60 DA "H5''" H N N 61 DA "H4'" H N N 62 DA "H3'" H N N 63 DA "HO3'" H N N 64 DA "H2'" H N N 65 DA "H2''" H N N 66 DA "H1'" H N N 67 DA H8 H N N 68 DA H61 H N N 69 DA H62 H N N 70 DA H2 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 DG OP3 O N N 106 DG P P N N 107 DG OP1 O N N 108 DG OP2 O N N 109 DG "O5'" O N N 110 DG "C5'" C N N 111 DG "C4'" C N R 112 DG "O4'" O N N 113 DG "C3'" C N S 114 DG "O3'" O N N 115 DG "C2'" C N N 116 DG "C1'" C N R 117 DG N9 N Y N 118 DG C8 C Y N 119 DG N7 N Y N 120 DG C5 C Y N 121 DG C6 C N N 122 DG O6 O N N 123 DG N1 N N N 124 DG C2 C N N 125 DG N2 N N N 126 DG N3 N N N 127 DG C4 C Y N 128 DG HOP3 H N N 129 DG HOP2 H N N 130 DG "H5'" H N N 131 DG "H5''" H N N 132 DG "H4'" H N N 133 DG "H3'" H N N 134 DG "HO3'" H N N 135 DG "H2'" H N N 136 DG "H2''" H N N 137 DG "H1'" H N N 138 DG H8 H N N 139 DG H1 H N N 140 DG H21 H N N 141 DG H22 H N N 142 HOH O O N N 143 HOH H1 H N N 144 HOH H2 H N N 145 MG MG MG N N 146 NA NA NA N N 147 NCO CO CO N N 148 NCO N1 N N N 149 NCO N2 N N N 150 NCO N3 N N N 151 NCO N4 N N N 152 NCO N5 N N N 153 NCO N6 N N N 154 NCO HN11 H N N 155 NCO HN12 H N N 156 NCO HN13 H N N 157 NCO HN21 H N N 158 NCO HN22 H N N 159 NCO HN23 H N N 160 NCO HN31 H N N 161 NCO HN32 H N N 162 NCO HN33 H N N 163 NCO HN41 H N N 164 NCO HN42 H N N 165 NCO HN43 H N N 166 NCO HN51 H N N 167 NCO HN52 H N N 168 NCO HN53 H N N 169 NCO HN61 H N N 170 NCO HN62 H N N 171 NCO HN63 H N N 172 # 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 CBR BR C5 sing N N 1 CBR P OP1 doub N N 2 CBR P OP2 sing N N 3 CBR P "O5'" sing N N 4 CBR P OP3 sing N N 5 CBR OP2 HOP2 sing N N 6 CBR "O5'" "C5'" sing N N 7 CBR N1 C6 sing N N 8 CBR N1 C2 sing N N 9 CBR N1 "C1'" sing N N 10 CBR C6 C5 doub N N 11 CBR C6 H6 sing N N 12 CBR C2 O2 doub N N 13 CBR C2 N3 sing N N 14 CBR N3 C4 doub N N 15 CBR C4 N4 sing N N 16 CBR C4 C5 sing N N 17 CBR N4 H41 sing N N 18 CBR N4 H42 sing N N 19 CBR "C2'" "C1'" sing N N 20 CBR "C2'" "C3'" sing N N 21 CBR "C2'" "H2'" sing N N 22 CBR "C2'" "H2''" sing N N 23 CBR "C5'" "C4'" sing N N 24 CBR "C5'" "H5'" sing N N 25 CBR "C5'" "H5''" sing N N 26 CBR "C4'" "O4'" sing N N 27 CBR "C4'" "C3'" sing N N 28 CBR "C4'" "H4'" sing N N 29 CBR "O4'" "C1'" sing N N 30 CBR "C1'" "H1'" sing N N 31 CBR "C3'" "O3'" sing N N 32 CBR "C3'" "H3'" sing N N 33 CBR "O3'" "HO3'" sing N N 34 CBR OP3 HOP3 sing N N 35 DA OP3 P sing N N 36 DA OP3 HOP3 sing N N 37 DA P OP1 doub N N 38 DA P OP2 sing N N 39 DA P "O5'" sing N N 40 DA OP2 HOP2 sing N N 41 DA "O5'" "C5'" sing N N 42 DA "C5'" "C4'" sing N N 43 DA "C5'" "H5'" sing N N 44 DA "C5'" "H5''" sing N N 45 DA "C4'" "O4'" sing N N 46 DA "C4'" "C3'" sing N N 47 DA "C4'" "H4'" sing N N 48 DA "O4'" "C1'" sing N N 49 DA "C3'" "O3'" sing N N 50 DA "C3'" "C2'" sing N N 51 DA "C3'" "H3'" sing N N 52 DA "O3'" "HO3'" sing N N 53 DA "C2'" "C1'" sing N N 54 DA "C2'" "H2'" sing N N 55 DA "C2'" "H2''" sing N N 56 DA "C1'" N9 sing N N 57 DA "C1'" "H1'" sing N N 58 DA N9 C8 sing Y N 59 DA N9 C4 sing Y N 60 DA C8 N7 doub Y N 61 DA C8 H8 sing N N 62 DA N7 C5 sing Y N 63 DA C5 C6 sing Y N 64 DA C5 C4 doub Y N 65 DA C6 N6 sing N N 66 DA C6 N1 doub Y N 67 DA N6 H61 sing N N 68 DA N6 H62 sing N N 69 DA N1 C2 sing Y N 70 DA C2 N3 doub Y N 71 DA C2 H2 sing N N 72 DA N3 C4 sing Y N 73 DC OP3 P sing N N 74 DC OP3 HOP3 sing N N 75 DC P OP1 doub N N 76 DC P OP2 sing N N 77 DC P "O5'" sing N N 78 DC OP2 HOP2 sing N N 79 DC "O5'" "C5'" sing N N 80 DC "C5'" "C4'" sing N N 81 DC "C5'" "H5'" sing N N 82 DC "C5'" "H5''" sing N N 83 DC "C4'" "O4'" sing N N 84 DC "C4'" "C3'" sing N N 85 DC "C4'" "H4'" sing N N 86 DC "O4'" "C1'" sing N N 87 DC "C3'" "O3'" sing N N 88 DC "C3'" "C2'" sing N N 89 DC "C3'" "H3'" sing N N 90 DC "O3'" "HO3'" sing N N 91 DC "C2'" "C1'" sing N N 92 DC "C2'" "H2'" sing N N 93 DC "C2'" "H2''" sing N N 94 DC "C1'" N1 sing N N 95 DC "C1'" "H1'" sing N N 96 DC N1 C2 sing N N 97 DC N1 C6 sing N N 98 DC C2 O2 doub N N 99 DC C2 N3 sing N N 100 DC N3 C4 doub N N 101 DC C4 N4 sing N N 102 DC C4 C5 sing N N 103 DC N4 H41 sing N N 104 DC N4 H42 sing N N 105 DC C5 C6 doub N N 106 DC C5 H5 sing N N 107 DC C6 H6 sing N N 108 DG OP3 P sing N N 109 DG OP3 HOP3 sing N N 110 DG P OP1 doub N N 111 DG P OP2 sing N N 112 DG P "O5'" sing N N 113 DG OP2 HOP2 sing N N 114 DG "O5'" "C5'" sing N N 115 DG "C5'" "C4'" sing N N 116 DG "C5'" "H5'" sing N N 117 DG "C5'" "H5''" sing N N 118 DG "C4'" "O4'" sing N N 119 DG "C4'" "C3'" sing N N 120 DG "C4'" "H4'" sing N N 121 DG "O4'" "C1'" sing N N 122 DG "C3'" "O3'" sing N N 123 DG "C3'" "C2'" sing N N 124 DG "C3'" "H3'" sing N N 125 DG "O3'" "HO3'" sing N N 126 DG "C2'" "C1'" sing N N 127 DG "C2'" "H2'" sing N N 128 DG "C2'" "H2''" sing N N 129 DG "C1'" N9 sing N N 130 DG "C1'" "H1'" sing N N 131 DG N9 C8 sing Y N 132 DG N9 C4 sing Y N 133 DG C8 N7 doub Y N 134 DG C8 H8 sing N N 135 DG N7 C5 sing Y N 136 DG C5 C6 sing N N 137 DG C5 C4 doub Y N 138 DG C6 O6 doub N N 139 DG C6 N1 sing N N 140 DG N1 C2 sing N N 141 DG N1 H1 sing N N 142 DG C2 N2 sing N N 143 DG C2 N3 doub N N 144 DG N2 H21 sing N N 145 DG N2 H22 sing N N 146 DG N3 C4 sing N N 147 HOH O H1 sing N N 148 HOH O H2 sing N N 149 NCO CO N1 sing N N 150 NCO CO N2 sing N N 151 NCO CO N3 sing N N 152 NCO CO N4 sing N N 153 NCO CO N5 sing N N 154 NCO CO N6 sing N N 155 NCO N1 HN11 sing N N 156 NCO N1 HN12 sing N N 157 NCO N1 HN13 sing N N 158 NCO N2 HN21 sing N N 159 NCO N2 HN22 sing N N 160 NCO N2 HN23 sing N N 161 NCO N3 HN31 sing N N 162 NCO N3 HN32 sing N N 163 NCO N3 HN33 sing N N 164 NCO N4 HN41 sing N N 165 NCO N4 HN42 sing N N 166 NCO N4 HN43 sing N N 167 NCO N5 HN51 sing N N 168 NCO N5 HN52 sing N N 169 NCO N5 HN53 sing N N 170 NCO N6 HN61 sing N N 171 NCO N6 HN62 sing N N 172 NCO N6 HN63 sing N N 173 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1UHX 'b-form double helix' 1UHX 'mismatched base pair' 1UHX 'internal loop' # 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 DG 1 1_555 A DC 8 8_665 -0.414 -0.131 -0.301 -5.444 4.606 -1.535 1 A_DG1:DC8_A A 1 ? A 8 ? 19 1 1 A CBR 2 1_555 A DG 7 8_665 0.263 -0.139 -0.224 16.673 5.856 2.048 2 A_CBR2:DG7_A A 2 ? A 7 ? 19 1 1 A DG 3 1_555 A DA 6 8_665 6.492 -4.244 1.298 30.871 -13.071 10.409 3 A_DG3:DA6_A A 3 ? A 6 ? 11 9 1 A DG 1 1_555 A DC 8 1_555 -0.414 -0.131 -0.301 -5.444 4.606 -1.535 4 A_DG1:DC8_A A 1 ? A 8 ? 19 1 1 A CBR 2 1_555 A DG 7 1_555 0.263 -0.139 -0.224 16.673 5.856 2.048 5 A_CBR2:DG7_A A 2 ? A 7 ? 19 1 1 A DG 3 1_555 A DA 6 1_555 6.492 -4.244 1.298 30.871 -13.071 10.409 6 A_DG3:DA6_A A 3 ? A 6 ? 11 9 # 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 DG 1 1_555 A DC 8 8_665 A CBR 2 1_555 A DG 7 8_665 0.435 0.028 2.855 -1.570 0.447 26.863 -0.039 -1.285 2.826 0.961 3.375 26.912 1 AA_DG1CBR2:DG7DC8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A CBR 2 1_555 A DG 7 8_665 A DG 3 1_555 A DA 6 8_665 0.522 1.479 3.232 0.007 7.032 52.631 1.198 -0.584 3.389 7.890 -0.008 53.066 2 AA_CBR2DG3:DA6DG7_AA A 2 ? A 7 ? A 3 ? A 6 ? 1 A DG 1 1_555 A DC 8 1_555 A CBR 2 1_555 A DG 7 1_555 0.435 0.028 2.855 -1.570 0.447 26.863 -0.039 -1.285 2.826 0.961 3.375 26.912 3 AA_DG1CBR2:DG7DC8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A CBR 2 1_555 A DG 7 1_555 A DG 3 1_555 A DA 6 1_555 0.522 1.479 3.232 0.007 7.032 52.631 1.198 -0.584 3.389 7.890 -0.008 53.066 4 AA_CBR2DG3:DA6DG7_AA A 2 ? A 7 ? A 3 ? A 6 ? # _atom_sites.entry_id 1UHX _atom_sites.fract_transf_matrix[1][1] 0.026546 _atom_sites.fract_transf_matrix[1][2] 0.015327 _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] 0.030653 _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] 0.015270 _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 CL CO MG N NA O P # loop_