data_153D # _entry.id 153D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.385 _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 153D pdb_0000153d 10.2210/pdb153d/pdb RCSB BDLB53 ? ? WWPDB D_1000170122 ? ? # 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 1994-01-15 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-04-18 5 'Structure model' 1 4 2024-02-07 # _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 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 4 'Structure model' diffrn_detector 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 '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' '_diffrn_detector.detector' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 153D _pdbx_database_status.recvd_initial_deposition_date 1993-12-16 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ginell, S.L.' 1 'Vojtechovsky, J.' 2 'Gaffney, B.' 3 'Jones, R.' 4 'Berman, H.M.' 5 # _citation.id primary _citation.title 'Crystal structure of a mispaired dodecamer, d(CGAGAATTC(O6Me)GCG)2, containing a carcinogenic O6-methylguanine' _citation.journal_abbrev Biochemistry _citation.journal_volume 33 _citation.page_first 3487 _citation.page_last 3493 _citation.year 1994 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 8142345 _citation.pdbx_database_id_DOI 10.1021/bi00178a004 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ginell, S.L.' 1 ? primary 'Vojtechovsky, J.' 2 ? primary 'Gaffney, B.' 3 ? primary 'Jones, R.' 4 ? primary 'Berman, H.M.' 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 ;DNA (5'-D(*CP*GP*AP*GP*AP*AP*TP*TP*CP*(6OG)P*CP*G)-3') ; 3701.444 2 ? ? ? ? 2 water nat water 18.015 49 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DT)(DC)(6OG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGAGAATTCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _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 DC n 1 2 DG n 1 3 DA n 1 4 DG n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DC n 1 10 6OG n 1 11 DC n 1 12 DG 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 6OG 'DNA linking' n ;6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE ; ? 'C11 H16 N5 O7 P' 361.248 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A 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 A 1 10 6OG 10 10 10 6OG +G A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 DC 1 13 13 DC C B . n B 1 2 DG 2 14 14 DG G B . n B 1 3 DA 3 15 15 DA A B . n B 1 4 DG 4 16 16 DG G B . n B 1 5 DA 5 17 17 DA A B . n B 1 6 DA 6 18 18 DA A B . n B 1 7 DT 7 19 19 DT T B . n B 1 8 DT 8 20 20 DT T B . n B 1 9 DC 9 21 21 DC C B . n B 1 10 6OG 10 22 22 6OG +G B . n B 1 11 DC 11 23 23 DC C B . n B 1 12 DG 12 24 24 DG G 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 HOH 1 25 25 HOH HOH A . C 2 HOH 2 26 26 HOH HOH A . C 2 HOH 3 27 27 HOH HOH A . C 2 HOH 4 28 28 HOH HOH A . C 2 HOH 5 29 29 HOH HOH A . C 2 HOH 6 30 30 HOH HOH A . C 2 HOH 7 31 31 HOH HOH A . C 2 HOH 8 32 32 HOH HOH A . C 2 HOH 9 33 33 HOH HOH A . C 2 HOH 10 34 34 HOH HOH A . C 2 HOH 11 35 35 HOH HOH A . C 2 HOH 12 36 36 HOH HOH A . C 2 HOH 13 37 37 HOH HOH A . C 2 HOH 14 38 38 HOH HOH A . C 2 HOH 15 39 39 HOH HOH A . C 2 HOH 16 40 40 HOH HOH A . C 2 HOH 17 41 41 HOH HOH A . C 2 HOH 18 42 42 HOH HOH A . C 2 HOH 19 43 43 HOH HOH A . C 2 HOH 20 44 44 HOH HOH A . C 2 HOH 21 45 45 HOH HOH A . C 2 HOH 22 46 46 HOH HOH A . C 2 HOH 23 47 47 HOH HOH A . C 2 HOH 24 48 48 HOH HOH A . C 2 HOH 25 49 49 HOH HOH A . C 2 HOH 26 50 50 HOH HOH A . C 2 HOH 27 68 68 HOH HOH A . D 2 HOH 1 51 51 HOH HOH B . D 2 HOH 2 52 52 HOH HOH B . D 2 HOH 3 53 53 HOH HOH B . D 2 HOH 4 54 54 HOH HOH B . D 2 HOH 5 55 55 HOH HOH B . D 2 HOH 6 56 56 HOH HOH B . D 2 HOH 7 57 57 HOH HOH B . D 2 HOH 8 58 58 HOH HOH B . D 2 HOH 9 59 59 HOH HOH B . D 2 HOH 10 60 60 HOH HOH B . D 2 HOH 11 61 61 HOH HOH B . D 2 HOH 12 62 62 HOH HOH B . D 2 HOH 13 63 63 HOH HOH B . D 2 HOH 14 64 64 HOH HOH B . D 2 HOH 15 65 65 HOH HOH B . D 2 HOH 16 66 66 HOH HOH B . D 2 HOH 17 67 67 HOH HOH B . D 2 HOH 18 69 69 HOH HOH B . D 2 HOH 19 70 70 HOH HOH B . D 2 HOH 20 71 71 HOH HOH B . D 2 HOH 21 72 72 HOH HOH B . D 2 HOH 22 73 73 HOH HOH B . # _software.name NUCLSQ _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 153D _cell.length_a 25.130 _cell.length_b 40.450 _cell.length_c 64.510 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 153D _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # _exptl.entry_id 153D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.21 _exptl_crystal.density_percent_sol 44.46 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 277.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'pH 7.00, VAPOR DIFFUSION, temperature 277.00K' _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 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 MGCL2 ? ? ? 1 4 1 SPERMINE_HCL ? ? ? 1 5 1 'NA CACODYLATE' ? ? ? 1 6 2 WATER ? ? ? 1 7 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 133.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type 'ENRAF-NONIUS CAD4' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'ENRAF-NONIUS FR571' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 153D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high 2.300 _reflns.number_obs 2924 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 153D _refine.ls_number_reflns_obs 1031 _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 8.000 _refine.ls_d_res_high 2.900 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.169 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _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 ? _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 ? _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.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 490 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 49 _refine_hist.number_atoms_total 541 _refine_hist.d_res_high 2.900 _refine_hist.d_res_low 8.000 # 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 n_bond_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_planar_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_hb_or_metal_coord ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_it 0.530 2.000 ? ? 'X-RAY DIFFRACTION' ? n_sugar_angle_it 0.790 2.000 ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_it 3.630 4.000 ? ? 'X-RAY DIFFRACTION' ? n_phos_angle_it 2.630 8.000 ? ? 'X-RAY DIFFRACTION' ? n_bond_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_dihedral_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_impr_tor ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_d 0.012 0.020 ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_angle_d 0.022 0.025 ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_d 0.023 0.025 ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_angle_d 0.024 0.025 ? ? 'X-RAY DIFFRACTION' ? n_plane_restr 0.012 0.020 ? ? 'X-RAY DIFFRACTION' ? n_chiral_restr 0.090 0.100 ? ? 'X-RAY DIFFRACTION' ? n_singtor_nbd 0.130 0.300 ? ? 'X-RAY DIFFRACTION' ? n_multtor_nbd 0.180 0.300 ? ? 'X-RAY DIFFRACTION' ? n_xhyhbond_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 153D _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 153D _struct.title 'CRYSTAL STRUCTURE OF A MISPAIRED DODECAMER, D(CGAGAATTC(O6ME)GCG)2, CONTAINING A CARCINOGENIC O6-METHYLGUANINE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 153D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, MODIFIED, MISMATCHED, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 153D _struct_ref.pdbx_db_accession 153D _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 153D A 1 ? 12 ? 153D 1 ? 12 ? 1 12 2 1 153D B 1 ? 12 ? 153D 13 ? 24 ? 13 24 # _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 # 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 DC 9 "O3'" ? ? ? 1_555 A 6OG 10 P ? ? A DC 9 A 6OG 10 1_555 ? ? ? ? ? ? ? 1.589 ? ? covale2 covale one ? A 6OG 10 "O3'" ? ? ? 1_555 A DC 11 P ? ? A 6OG 10 A DC 11 1_555 ? ? ? ? ? ? ? 1.551 ? ? covale3 covale both ? B DC 9 "O3'" ? ? ? 1_555 B 6OG 10 P ? ? B DC 21 B 6OG 22 1_555 ? ? ? ? ? ? ? 1.578 ? ? covale4 covale one ? B 6OG 10 "O3'" ? ? ? 1_555 B DC 11 P ? ? B 6OG 22 B DC 23 1_555 ? ? ? ? ? ? ? 1.601 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N7 ? ? ? 1_555 B 6OG 10 N2 ? ? A DA 3 B 6OG 22 1_555 ? ? ? ? ? ? 'DA-6OG MISPAIR' ? ? ? hydrog8 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A 6OG 10 N2 ? ? ? 1_555 B DA 3 N7 ? ? A 6OG 10 B DA 15 1_555 ? ? ? ? ? ? '6OG-DA MISPAIR' ? ? ? hydrog23 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DC _pdbx_validate_rmsd_bond.auth_seq_id_1 13 _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 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DG _pdbx_validate_rmsd_bond.auth_seq_id_2 14 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.521 _pdbx_validate_rmsd_bond.bond_target_value 1.607 _pdbx_validate_rmsd_bond.bond_deviation -0.086 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.012 _pdbx_validate_rmsd_bond.linker_flag Y # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O5'" A DC 1 ? ? "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? 101.49 109.40 -7.91 0.80 N 2 1 "C4'" A DC 1 ? ? "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? 97.65 102.20 -4.55 0.70 N 3 1 "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? "C1'" A DC 1 ? ? 95.55 102.40 -6.85 0.80 N 4 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 113.49 108.30 5.19 0.30 N 5 1 "C1'" A DG 2 ? ? "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? 100.97 110.10 -9.13 1.00 N 6 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.32 108.30 3.02 0.30 N 7 1 C5 A DG 2 ? ? C6 A DG 2 ? ? N1 A DG 2 ? ? 114.75 111.50 3.25 0.50 N 8 1 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? "C2'" A DA 3 ? ? 100.48 105.90 -5.42 0.80 N 9 1 C6 A DA 3 ? ? N1 A DA 3 ? ? C2 A DA 3 ? ? 122.24 118.60 3.64 0.60 N 10 1 N1 A DA 3 ? ? C2 A DA 3 ? ? N3 A DA 3 ? ? 126.14 129.30 -3.16 0.50 N 11 1 "O5'" A DG 4 ? ? P A DG 4 ? ? OP1 A DG 4 ? ? 117.94 110.70 7.24 1.20 N 12 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 110.48 108.30 2.18 0.30 N 13 1 C5 A DG 4 ? ? C6 A DG 4 ? ? N1 A DG 4 ? ? 114.55 111.50 3.05 0.50 N 14 1 N1 A DA 5 ? ? C2 A DA 5 ? ? N3 A DA 5 ? ? 126.20 129.30 -3.10 0.50 N 15 1 "O5'" A DA 6 ? ? "C5'" A DA 6 ? ? "C4'" A DA 6 ? ? 104.39 109.40 -5.01 0.80 N 16 1 "C3'" A DA 6 ? ? "O3'" A DA 6 ? ? P A DT 7 ? ? 130.18 119.70 10.48 1.20 Y 17 1 "O5'" A DT 7 ? ? "C5'" A DT 7 ? ? "C4'" A DT 7 ? ? 104.37 109.40 -5.03 0.80 N 18 1 C2 A DT 7 ? ? N3 A DT 7 ? ? C4 A DT 7 ? ? 122.10 127.20 -5.10 0.60 N 19 1 N3 A DT 7 ? ? C4 A DT 7 ? ? C5 A DT 7 ? ? 119.52 115.20 4.32 0.60 N 20 1 "C3'" A DT 7 ? ? "O3'" A DT 7 ? ? P A DT 8 ? ? 127.91 119.70 8.21 1.20 Y 21 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? N1 A DT 8 ? ? 110.41 108.30 2.11 0.30 N 22 1 C2 A DT 8 ? ? N3 A DT 8 ? ? C4 A DT 8 ? ? 122.86 127.20 -4.34 0.60 N 23 1 "C3'" A DT 8 ? ? "O3'" A DT 8 ? ? P A DC 9 ? ? 128.26 119.70 8.56 1.20 Y 24 1 N3 A DC 9 ? ? C4 A DC 9 ? ? C5 A DC 9 ? ? 119.16 121.90 -2.74 0.40 N 25 1 "C3'" A 6OG 10 ? ? "O3'" A 6OG 10 ? ? P A DC 11 ? ? 141.30 119.70 21.60 1.20 Y 26 1 P A DC 11 ? ? "O5'" A DC 11 ? ? "C5'" A DC 11 ? ? 107.30 120.90 -13.60 1.60 N 27 1 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 111.65 108.30 3.35 0.30 N 28 1 "C4'" B DC 13 ? ? "C3'" B DC 13 ? ? "C2'" B DC 13 ? ? 97.98 102.20 -4.22 0.70 N 29 1 "O4'" B DC 13 ? ? "C1'" B DC 13 ? ? N1 B DC 13 ? ? 111.66 108.30 3.36 0.30 N 30 1 "C3'" B DC 13 ? ? "O3'" B DC 13 ? ? P B DG 14 ? ? 145.70 119.70 26.00 1.20 Y 31 1 OP1 B DG 14 ? ? P B DG 14 ? ? OP2 B DG 14 ? ? 110.04 119.60 -9.56 1.50 N 32 1 P B DG 14 ? ? "O5'" B DG 14 ? ? "C5'" B DG 14 ? ? 111.25 120.90 -9.65 1.60 N 33 1 "O5'" B DA 15 ? ? "C5'" B DA 15 ? ? "C4'" B DA 15 ? ? 100.56 109.40 -8.84 0.80 N 34 1 "O4'" B DA 15 ? ? "C1'" B DA 15 ? ? N9 B DA 15 ? ? 112.46 108.30 4.16 0.30 N 35 1 C5 B DA 15 ? ? C6 B DA 15 ? ? N1 B DA 15 ? ? 114.46 117.70 -3.24 0.50 N 36 1 "C3'" B DA 15 ? ? "O3'" B DA 15 ? ? P B DG 16 ? ? 127.70 119.70 8.00 1.20 Y 37 1 "C1'" B DG 16 ? ? "O4'" B DG 16 ? ? "C4'" B DG 16 ? ? 103.81 110.10 -6.29 1.00 N 38 1 "O4'" B DG 16 ? ? "C1'" B DG 16 ? ? N9 B DG 16 ? ? 112.37 108.30 4.07 0.30 N 39 1 C5 B DG 16 ? ? C6 B DG 16 ? ? N1 B DG 16 ? ? 114.61 111.50 3.11 0.50 N 40 1 "O5'" B DA 17 ? ? "C5'" B DA 17 ? ? "C4'" B DA 17 ? ? 104.30 109.40 -5.10 0.80 N 41 1 N1 B DA 17 ? ? C2 B DA 17 ? ? N3 B DA 17 ? ? 125.76 129.30 -3.54 0.50 N 42 1 OP1 B DA 18 ? ? P B DA 18 ? ? OP2 B DA 18 ? ? 110.09 119.60 -9.51 1.50 N 43 1 "O5'" B DA 18 ? ? P B DA 18 ? ? OP2 B DA 18 ? ? 118.55 110.70 7.85 1.20 N 44 1 C5 B DA 18 ? ? C6 B DA 18 ? ? N1 B DA 18 ? ? 114.60 117.70 -3.10 0.50 N 45 1 "O5'" B DT 19 ? ? "C5'" B DT 19 ? ? "C4'" B DT 19 ? ? 103.59 109.40 -5.81 0.80 N 46 1 C2 B DT 19 ? ? N3 B DT 19 ? ? C4 B DT 19 ? ? 122.11 127.20 -5.09 0.60 N 47 1 N3 B DT 19 ? ? C4 B DT 19 ? ? C5 B DT 19 ? ? 119.28 115.20 4.08 0.60 N 48 1 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 111.65 108.30 3.35 0.30 N 49 1 C2 B DT 20 ? ? N3 B DT 20 ? ? C4 B DT 20 ? ? 122.49 127.20 -4.71 0.60 N 50 1 N3 B DT 20 ? ? C4 B DT 20 ? ? C5 B DT 20 ? ? 119.68 115.20 4.48 0.60 N 51 1 "O5'" B DC 21 ? ? "C5'" B DC 21 ? ? "C4'" B DC 21 ? ? 101.31 109.40 -8.09 0.80 N 52 1 "O4'" B DC 23 ? ? "C1'" B DC 23 ? ? N1 B DC 23 ? ? 112.87 108.30 4.57 0.30 N 53 1 "O5'" B DG 24 ? ? "C5'" B DG 24 ? ? "C4'" B DG 24 ? ? 104.29 109.40 -5.11 0.80 N 54 1 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 115.73 108.30 7.43 0.30 N 55 1 C5 B DG 24 ? ? C6 B DG 24 ? ? N1 B DG 24 ? ? 114.66 111.50 3.16 0.50 N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 6OG 10 A 6OG 10 ? DG ;6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE ; 2 B 6OG 10 B 6OG 22 ? DG ;6-O-METHYL GUANOSINE-5'-MONOPHOSPHATE ; # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TR isotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TR isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix 'X-RAY DIFFRACTION' # 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 6OG P P N N 1 6OG OP1 O N N 2 6OG OP2 O N N 3 6OG "O5'" O N N 4 6OG N9 N Y N 5 6OG C4 C Y N 6 6OG N3 N Y N 7 6OG C2 C Y N 8 6OG N2 N N N 9 6OG N1 N Y N 10 6OG C6 C Y N 11 6OG O6 O N N 12 6OG C5 C Y N 13 6OG N7 N Y N 14 6OG C8 C Y N 15 6OG "C2'" C N N 16 6OG "C5'" C N N 17 6OG "C4'" C N R 18 6OG "O4'" O N N 19 6OG "C1'" C N R 20 6OG "C3'" C N S 21 6OG "O3'" O N N 22 6OG C C N N 23 6OG HOP2 H N N 24 6OG HN21 H N N 25 6OG HN22 H N N 26 6OG H8 H N N 27 6OG "H2'" H N N 28 6OG "H2''" H N N 29 6OG "H5'" H N N 30 6OG "H5''" H N N 31 6OG "H4'" H N N 32 6OG "H1'" H N N 33 6OG "H3'" H N N 34 6OG "HO3'" H N N 35 6OG H1 H N N 36 6OG H2 H N N 37 6OG H3 H N N 38 6OG OP3 O N N 39 6OG HOP3 H N N 40 DA OP3 O N N 41 DA P P N N 42 DA OP1 O N N 43 DA OP2 O N N 44 DA "O5'" O N N 45 DA "C5'" C N N 46 DA "C4'" C N R 47 DA "O4'" O N N 48 DA "C3'" C N S 49 DA "O3'" O N N 50 DA "C2'" C N N 51 DA "C1'" C N R 52 DA N9 N Y N 53 DA C8 C Y N 54 DA N7 N Y N 55 DA C5 C Y N 56 DA C6 C Y N 57 DA N6 N N N 58 DA N1 N Y N 59 DA C2 C Y N 60 DA N3 N Y N 61 DA C4 C Y N 62 DA HOP3 H N N 63 DA HOP2 H N N 64 DA "H5'" H N N 65 DA "H5''" H N N 66 DA "H4'" H N N 67 DA "H3'" H N N 68 DA "HO3'" H N N 69 DA "H2'" H N N 70 DA "H2''" H N N 71 DA "H1'" H N N 72 DA H8 H N N 73 DA H61 H N N 74 DA H62 H N N 75 DA H2 H N N 76 DC OP3 O N N 77 DC P P N N 78 DC OP1 O N N 79 DC OP2 O N N 80 DC "O5'" O N N 81 DC "C5'" C N N 82 DC "C4'" C N R 83 DC "O4'" O N N 84 DC "C3'" C N S 85 DC "O3'" O N N 86 DC "C2'" C N N 87 DC "C1'" C N R 88 DC N1 N N N 89 DC C2 C N N 90 DC O2 O N N 91 DC N3 N N N 92 DC C4 C N N 93 DC N4 N N N 94 DC C5 C N N 95 DC C6 C N N 96 DC HOP3 H N N 97 DC HOP2 H N N 98 DC "H5'" H N N 99 DC "H5''" H N N 100 DC "H4'" H N N 101 DC "H3'" H N N 102 DC "HO3'" H N N 103 DC "H2'" H N N 104 DC "H2''" H N N 105 DC "H1'" H N N 106 DC H41 H N N 107 DC H42 H N N 108 DC H5 H N N 109 DC H6 H N N 110 DG OP3 O N N 111 DG P P N N 112 DG OP1 O N N 113 DG OP2 O N N 114 DG "O5'" O N N 115 DG "C5'" C N N 116 DG "C4'" C N R 117 DG "O4'" O N N 118 DG "C3'" C N S 119 DG "O3'" O N N 120 DG "C2'" C N N 121 DG "C1'" C N R 122 DG N9 N Y N 123 DG C8 C Y N 124 DG N7 N Y N 125 DG C5 C Y N 126 DG C6 C N N 127 DG O6 O N N 128 DG N1 N N N 129 DG C2 C N N 130 DG N2 N N N 131 DG N3 N N N 132 DG C4 C Y N 133 DG HOP3 H N N 134 DG HOP2 H N N 135 DG "H5'" H N N 136 DG "H5''" H N N 137 DG "H4'" H N N 138 DG "H3'" H N N 139 DG "HO3'" H N N 140 DG "H2'" H N N 141 DG "H2''" H N N 142 DG "H1'" H N N 143 DG H8 H N N 144 DG H1 H N N 145 DG H21 H N N 146 DG H22 H N N 147 DT OP3 O N N 148 DT P P N N 149 DT OP1 O N N 150 DT OP2 O N N 151 DT "O5'" O N N 152 DT "C5'" C N N 153 DT "C4'" C N R 154 DT "O4'" O N N 155 DT "C3'" C N S 156 DT "O3'" O N N 157 DT "C2'" C N N 158 DT "C1'" C N R 159 DT N1 N N N 160 DT C2 C N N 161 DT O2 O N N 162 DT N3 N N N 163 DT C4 C N N 164 DT O4 O N N 165 DT C5 C N N 166 DT C7 C N N 167 DT C6 C N N 168 DT HOP3 H N N 169 DT HOP2 H N N 170 DT "H5'" H N N 171 DT "H5''" H N N 172 DT "H4'" H N N 173 DT "H3'" H N N 174 DT "HO3'" H N N 175 DT "H2'" H N N 176 DT "H2''" H N N 177 DT "H1'" H N N 178 DT H3 H N N 179 DT H71 H N N 180 DT H72 H N N 181 DT H73 H N N 182 DT H6 H N N 183 HOH O O N N 184 HOH H1 H N N 185 HOH H2 H N N 186 # 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 6OG P OP1 doub N N 1 6OG P OP2 sing N N 2 6OG P "O5'" sing N N 3 6OG OP2 HOP2 sing N N 4 6OG "O5'" "C5'" sing N N 5 6OG N9 C4 sing Y N 6 6OG N9 C8 sing Y N 7 6OG N9 "C1'" sing N N 8 6OG C4 N3 sing Y N 9 6OG C4 C5 doub Y N 10 6OG N3 C2 doub Y N 11 6OG C2 N2 sing N N 12 6OG C2 N1 sing Y N 13 6OG N2 HN21 sing N N 14 6OG N2 HN22 sing N N 15 6OG N1 C6 doub Y N 16 6OG C6 O6 sing N N 17 6OG C6 C5 sing Y N 18 6OG O6 C sing N N 19 6OG C5 N7 sing Y N 20 6OG N7 C8 doub Y N 21 6OG C8 H8 sing N N 22 6OG "C2'" "C1'" sing N N 23 6OG "C2'" "C3'" sing N N 24 6OG "C2'" "H2'" sing N N 25 6OG "C2'" "H2''" sing N N 26 6OG "C5'" "C4'" sing N N 27 6OG "C5'" "H5'" sing N N 28 6OG "C5'" "H5''" sing N N 29 6OG "C4'" "O4'" sing N N 30 6OG "C4'" "C3'" sing N N 31 6OG "C4'" "H4'" sing N N 32 6OG "O4'" "C1'" sing N N 33 6OG "C1'" "H1'" sing N N 34 6OG "C3'" "O3'" sing N N 35 6OG "C3'" "H3'" sing N N 36 6OG "O3'" "HO3'" sing N N 37 6OG C H1 sing N N 38 6OG C H2 sing N N 39 6OG C H3 sing N N 40 6OG P OP3 sing N N 41 6OG OP3 HOP3 sing N N 42 DA OP3 P sing N N 43 DA OP3 HOP3 sing N N 44 DA P OP1 doub N N 45 DA P OP2 sing N N 46 DA P "O5'" sing N N 47 DA OP2 HOP2 sing N N 48 DA "O5'" "C5'" sing N N 49 DA "C5'" "C4'" sing N N 50 DA "C5'" "H5'" sing N N 51 DA "C5'" "H5''" sing N N 52 DA "C4'" "O4'" sing N N 53 DA "C4'" "C3'" sing N N 54 DA "C4'" "H4'" sing N N 55 DA "O4'" "C1'" sing N N 56 DA "C3'" "O3'" sing N N 57 DA "C3'" "C2'" sing N N 58 DA "C3'" "H3'" sing N N 59 DA "O3'" "HO3'" sing N N 60 DA "C2'" "C1'" sing N N 61 DA "C2'" "H2'" sing N N 62 DA "C2'" "H2''" sing N N 63 DA "C1'" N9 sing N N 64 DA "C1'" "H1'" sing N N 65 DA N9 C8 sing Y N 66 DA N9 C4 sing Y N 67 DA C8 N7 doub Y N 68 DA C8 H8 sing N N 69 DA N7 C5 sing Y N 70 DA C5 C6 sing Y N 71 DA C5 C4 doub Y N 72 DA C6 N6 sing N N 73 DA C6 N1 doub Y N 74 DA N6 H61 sing N N 75 DA N6 H62 sing N N 76 DA N1 C2 sing Y N 77 DA C2 N3 doub Y N 78 DA C2 H2 sing N N 79 DA N3 C4 sing Y N 80 DC OP3 P sing N N 81 DC OP3 HOP3 sing N N 82 DC P OP1 doub N N 83 DC P OP2 sing N N 84 DC P "O5'" sing N N 85 DC OP2 HOP2 sing N N 86 DC "O5'" "C5'" sing N N 87 DC "C5'" "C4'" sing N N 88 DC "C5'" "H5'" sing N N 89 DC "C5'" "H5''" sing N N 90 DC "C4'" "O4'" sing N N 91 DC "C4'" "C3'" sing N N 92 DC "C4'" "H4'" sing N N 93 DC "O4'" "C1'" sing N N 94 DC "C3'" "O3'" sing N N 95 DC "C3'" "C2'" sing N N 96 DC "C3'" "H3'" sing N N 97 DC "O3'" "HO3'" sing N N 98 DC "C2'" "C1'" sing N N 99 DC "C2'" "H2'" sing N N 100 DC "C2'" "H2''" sing N N 101 DC "C1'" N1 sing N N 102 DC "C1'" "H1'" sing N N 103 DC N1 C2 sing N N 104 DC N1 C6 sing N N 105 DC C2 O2 doub N N 106 DC C2 N3 sing N N 107 DC N3 C4 doub N N 108 DC C4 N4 sing N N 109 DC C4 C5 sing N N 110 DC N4 H41 sing N N 111 DC N4 H42 sing N N 112 DC C5 C6 doub N N 113 DC C5 H5 sing N N 114 DC C6 H6 sing N N 115 DG OP3 P sing N N 116 DG OP3 HOP3 sing N N 117 DG P OP1 doub N N 118 DG P OP2 sing N N 119 DG P "O5'" sing N N 120 DG OP2 HOP2 sing N N 121 DG "O5'" "C5'" sing N N 122 DG "C5'" "C4'" sing N N 123 DG "C5'" "H5'" sing N N 124 DG "C5'" "H5''" sing N N 125 DG "C4'" "O4'" sing N N 126 DG "C4'" "C3'" sing N N 127 DG "C4'" "H4'" sing N N 128 DG "O4'" "C1'" sing N N 129 DG "C3'" "O3'" sing N N 130 DG "C3'" "C2'" sing N N 131 DG "C3'" "H3'" sing N N 132 DG "O3'" "HO3'" sing N N 133 DG "C2'" "C1'" sing N N 134 DG "C2'" "H2'" sing N N 135 DG "C2'" "H2''" sing N N 136 DG "C1'" N9 sing N N 137 DG "C1'" "H1'" sing N N 138 DG N9 C8 sing Y N 139 DG N9 C4 sing Y N 140 DG C8 N7 doub Y N 141 DG C8 H8 sing N N 142 DG N7 C5 sing Y N 143 DG C5 C6 sing N N 144 DG C5 C4 doub Y N 145 DG C6 O6 doub N N 146 DG C6 N1 sing N N 147 DG N1 C2 sing N N 148 DG N1 H1 sing N N 149 DG C2 N2 sing N N 150 DG C2 N3 doub N N 151 DG N2 H21 sing N N 152 DG N2 H22 sing N N 153 DG N3 C4 sing N N 154 DT OP3 P sing N N 155 DT OP3 HOP3 sing N N 156 DT P OP1 doub N N 157 DT P OP2 sing N N 158 DT P "O5'" sing N N 159 DT OP2 HOP2 sing N N 160 DT "O5'" "C5'" sing N N 161 DT "C5'" "C4'" sing N N 162 DT "C5'" "H5'" sing N N 163 DT "C5'" "H5''" sing N N 164 DT "C4'" "O4'" sing N N 165 DT "C4'" "C3'" sing N N 166 DT "C4'" "H4'" sing N N 167 DT "O4'" "C1'" sing N N 168 DT "C3'" "O3'" sing N N 169 DT "C3'" "C2'" sing N N 170 DT "C3'" "H3'" sing N N 171 DT "O3'" "HO3'" sing N N 172 DT "C2'" "C1'" sing N N 173 DT "C2'" "H2'" sing N N 174 DT "C2'" "H2''" sing N N 175 DT "C1'" N1 sing N N 176 DT "C1'" "H1'" sing N N 177 DT N1 C2 sing N N 178 DT N1 C6 sing N N 179 DT C2 O2 doub N N 180 DT C2 N3 sing N N 181 DT N3 C4 sing N N 182 DT N3 H3 sing N N 183 DT C4 O4 doub N N 184 DT C4 C5 sing N N 185 DT C5 C7 sing N N 186 DT C5 C6 doub N N 187 DT C7 H71 sing N N 188 DT C7 H72 sing N N 189 DT C7 H73 sing N N 190 DT C6 H6 sing N N 191 HOH O H1 sing N N 192 HOH O H2 sing N N 193 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 153D 'double helix' 153D 'b-form double helix' 153D '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 DC 1 1_555 B DG 12 1_555 -0.436 -0.121 -0.041 10.044 -3.031 -0.435 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.601 -0.542 0.211 -0.233 -8.791 -2.324 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DA 3 1_555 B 6OG 10 1_555 -2.639 -2.973 -0.523 8.504 0.936 78.360 3 A_DA3:6OG22_B A 3 ? B 22 ? ? ? 1 A DG 4 1_555 B DC 9 1_555 -0.058 -0.295 0.372 12.398 -12.455 1.342 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.365 -0.135 0.313 4.498 -11.522 1.100 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.114 -0.239 0.422 4.844 -17.320 -4.365 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.005 -0.147 0.640 -2.121 -14.344 5.933 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 0.167 -0.495 -0.062 -1.167 -17.321 -4.548 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.435 -0.123 0.039 -11.785 -15.596 1.670 9 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A 6OG 10 1_555 B DA 3 1_555 2.635 3.475 0.357 -11.221 -3.410 -74.116 10 A_6OG10:DA15_B A 10 ? B 15 ? ? ? 1 A DC 11 1_555 B DG 2 1_555 0.171 0.022 0.404 -3.766 -10.087 1.839 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.391 -0.333 -0.075 -9.137 -1.825 -0.924 12 A_DG12:DC13_B A 12 ? B 13 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 12 1_555 A DG 2 1_555 B DC 11 1_555 1.062 -0.182 3.323 5.699 3.064 32.158 -0.871 -0.861 3.424 5.463 -10.159 32.786 1 AA_DC1DG2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DA 3 1_555 B 6OG 10 1_555 -2.313 3.678 -0.463 176.513 -18.515 -152.597 -1.841 -1.173 0.186 9.261 88.292 -179.404 2 AA_DG2DA3:6OG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DA 3 1_555 B 6OG 10 1_555 A DG 4 1_555 B DC 9 1_555 -2.395 -1.703 -2.108 128.718 -118.230 79.244 -1.476 0.519 -1.816 -59.754 -65.056 175.977 3 AA_DA3DG4:DC216OG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 5 1_555 B DT 8 1_555 -0.319 -0.025 3.444 -4.458 1.457 39.742 -0.213 -0.074 3.455 2.134 6.530 40.007 4 AA_DG4DA5:DT20DC21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 -0.465 -0.561 3.126 -2.300 -6.205 34.404 -0.021 0.435 3.199 -10.372 3.845 35.016 5 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.767 -0.865 3.469 0.614 -4.970 30.676 -0.582 -1.304 3.576 -9.317 -1.152 31.072 6 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.512 -0.280 2.965 6.302 -0.864 38.357 -0.326 1.456 2.854 -1.305 -9.511 38.861 7 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DC 9 1_555 B DG 4 1_555 0.099 0.019 3.571 -0.661 -4.129 45.273 0.422 -0.192 3.554 -5.350 0.857 45.456 8 AA_DT8DC9:DG16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DC 9 1_555 B DG 4 1_555 A 6OG 10 1_555 B DA 3 1_555 1.924 -1.707 2.940 4.917 0.044 76.863 -1.372 -1.415 3.038 0.036 -3.951 76.995 9 AA_DC96OG10:DA15DG16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A 6OG 10 1_555 B DA 3 1_555 A DC 11 1_555 B DG 2 1_555 -0.255 3.458 3.626 -9.639 -2.938 -7.000 -11.676 -15.984 2.700 16.126 -52.897 -12.265 10 AA_6OG10DC11:DG14DA15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 -0.396 -0.163 3.509 5.585 6.021 28.162 -1.696 2.057 3.267 12.053 -11.181 29.312 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _atom_sites.entry_id 153D _atom_sites.fract_transf_matrix[1][1] 0.039793 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.024722 _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] 0.015501 _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 N O P # loop_