data_1J8L # _entry.id 1J8L # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _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 1J8L pdb_00001j8l 10.2210/pdb1j8l/pdb NDB BD0053 ? ? RCSB RCSB013495 ? ? WWPDB D_1000013495 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1I3T 'Molecular and Crystal Structure of D(CGCGAATT(MO4)CGCG)' unspecified PDB 1I47 'Molecular and Crystal Structure of D(CGCGAATT(MO4)CGCG)' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1J8L _pdbx_database_status.recvd_initial_deposition_date 2001-05-22 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hossain, M.T.' 1 'Sunami, T.' 2 'Tsunoda, M.' 3 'Hikima, T.' 4 'Chatake, T.' 5 'Ueno, Y.' 6 'Matsuda, A.' 7 'Takenaka, A.' 8 # _citation.id primary _citation.title ;Crystallographic studies on damaged DNAs IV. N(4)-methoxycytosine shows a second face for Watson-Crick base-pairing, leading to purine transition mutagenesis. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 29 _citation.page_first 3949 _citation.page_last 3954 _citation.year 2001 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 11574676 _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hossain, M.T.' 1 ? primary 'Sunami, T.' 2 ? primary 'Tsunoda, M.' 3 ? primary 'Hikima, T.' 4 ? primary 'Chatake, T.' 5 ? primary 'Ueno, Y.' 6 ? primary 'Matsuda, A.' 7 ? primary 'Takenaka, A.' 8 ? # _cell.entry_id 1J8L _cell.length_a 24.8 _cell.length_b 40.3 _cell.length_c 65.5 _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 1J8L _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 # 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*CP*AP*AP*AP*TP*TP*(C45)P*GP*CP*G)-3') ; 3677.419 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 water nat water 18.015 111 ? ? ? ? # _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)(DC)(DA)(DA)(DA)(DT)(DT)(C45)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCAAATTCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # 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 DC n 1 4 DA n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 C45 n 1 10 DG n 1 11 DC n 1 12 DG n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1J8L _struct_ref.pdbx_db_accession 1J8L _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 1J8L A 1 ? 12 ? 1J8L 1 ? 12 ? 1 12 2 1 1J8L B 1 ? 12 ? 1J8L 13 ? 24 ? 13 24 # 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 C45 'DNA linking' n "N4-METHOXY-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O8 P' 337.223 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # _exptl.entry_id 1J8L _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.15 _exptl_crystal.density_percent_sol 42.77 _exptl_crystal.description ? # _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 'MPD, spermine, magnesium acetate, sodium cacodylate, sodum chloride, 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 MPD ? ? ? 1 2 1 spermine ? ? ? 1 3 1 'magnesium acetate' ? ? ? 1 4 1 'sodium cacodylate' ? ? ? 1 5 1 'sodum chloride' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type WEISSENBERG _diffrn_detector.pdbx_collection_date 2000-12-12 _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 1J8L _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 100 _reflns.d_resolution_high 1.6 _reflns.number_obs 7855 _reflns.number_all 62759 _reflns.percent_possible_obs 86.1 _reflns.pdbx_Rmerge_I_obs 0.058 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.0 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.6 _reflns_shell.d_res_low 1.69 _reflns_shell.percent_possible_all 38.4 _reflns_shell.Rmerge_I_obs 0.132 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 5.5 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1J8L _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 6515 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 3.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_d_res_low 10.0 _refine.ls_d_res_high 1.6 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.218 _refine.ls_R_factor_R_free 0.258 _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 685 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] 7.27 _refine.aniso_B[2][2] -0.96 _refine.aniso_B[3][3] -6.31 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _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 'PDB ENTRY 355D' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _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_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1J8L _refine_analyze.Luzzati_coordinate_error_obs 0.22 _refine_analyze.Luzzati_sigma_a_obs ? _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_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 484 _refine_hist.pdbx_number_atoms_ligand 11 _refine_hist.number_atoms_solvent 105 _refine_hist.number_atoms_total 600 _refine_hist.d_res_high 1.6 _refine_hist.d_res_low 10.0 # 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 0.9 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 20.7 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.36 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.6 _refine_ls_shell.d_res_low 1.66 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.206 _refine_ls_shell.percent_reflns_obs 5.2 _refine_ls_shell.R_factor_R_free 0.277 _refine_ls_shell.R_factor_R_free_error 0.124 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 5 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 1J8L _struct.title 'Molecular and Crystal Structure of D(CGCAAATTMO4CGCG): the Watson-Crick Type N4-Methoxycytidine/Adenosine Base Pair in B-DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1J8L _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'N4-METHOXYCYTOSINE, DNA DAMAGE, B-DNA, DOUBLE HELIX, DEOXYRIBONUCLEIC ACID, 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 3 ? E N N 3 ? # _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 DT 8 "O3'" ? ? ? 1_555 A C45 9 P ? ? A DT 8 A C45 9 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale2 covale one ? A C45 9 "O3'" ? ? ? 1_555 A DG 10 P ? ? A C45 9 A DG 10 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale3 covale both ? B DT 8 "O3'" ? ? ? 1_555 B C45 9 P ? ? B DT 20 B C45 21 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale4 covale one ? B C45 9 "O3'" ? ? ? 1_555 B DG 10 P ? ? B C45 21 B DG 22 1_555 ? ? ? ? ? ? ? 1.610 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 106 A HOH 107 1_555 ? ? ? ? ? ? ? 2.057 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 106 A HOH 108 1_555 ? ? ? ? ? ? ? 2.066 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 106 A HOH 109 1_555 ? ? ? ? ? ? ? 2.063 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 106 A HOH 110 1_555 ? ? ? ? ? ? ? 2.063 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 106 B HOH 107 1_555 ? ? ? ? ? ? ? 2.066 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 106 B HOH 108 1_555 ? ? ? ? ? ? ? 2.069 ? ? 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 DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 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 ? ? metalc ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id MG _struct_site.pdbx_auth_seq_id 106 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE MG A 106' # 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 D . ? HOH A 107 . ? 1_555 ? 2 AC1 6 HOH D . ? HOH A 108 . ? 1_555 ? 3 AC1 6 HOH D . ? HOH A 109 . ? 1_555 ? 4 AC1 6 HOH D . ? HOH A 110 . ? 1_555 ? 5 AC1 6 HOH E . ? HOH B 107 . ? 1_555 ? 6 AC1 6 HOH E . ? HOH B 108 . ? 1_555 ? # _database_PDB_matrix.entry_id 1J8L _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 # _atom_sites.entry_id 1J8L _atom_sites.fract_transf_matrix[1][1] 0.040323 _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] 0.024814 _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] 0.015267 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MG N O P # 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 DC 3 3 3 DC C A . n A 1 4 DA 4 4 4 DA A 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 C45 9 9 9 C45 +C A . n A 1 10 DG 10 10 10 DG 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 DC 3 15 15 DC C B . n B 1 4 DA 4 16 16 DA A 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 C45 9 21 21 C45 +C B . n B 1 10 DG 10 22 22 DG 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 MG 1 106 106 MG MO6 A . D 3 HOH 1 107 106 HOH MO6 A . D 3 HOH 2 108 106 HOH MO6 A . D 3 HOH 3 109 106 HOH MO6 A . D 3 HOH 4 110 106 HOH MO6 A . D 3 HOH 5 111 1 HOH HOH A . D 3 HOH 6 112 4 HOH HOH A . D 3 HOH 7 113 5 HOH HOH A . D 3 HOH 8 114 7 HOH HOH A . D 3 HOH 9 115 10 HOH HOH A . D 3 HOH 10 116 13 HOH HOH A . D 3 HOH 11 117 15 HOH HOH A . D 3 HOH 12 118 16 HOH HOH A . D 3 HOH 13 119 17 HOH HOH A . D 3 HOH 14 120 18 HOH HOH A . D 3 HOH 15 121 19 HOH HOH A . D 3 HOH 16 122 23 HOH HOH A . D 3 HOH 17 123 30 HOH HOH A . D 3 HOH 18 124 40 HOH HOH A . D 3 HOH 19 125 42 HOH HOH A . D 3 HOH 20 126 44 HOH HOH A . D 3 HOH 21 127 47 HOH HOH A . D 3 HOH 22 128 50 HOH HOH A . D 3 HOH 23 129 52 HOH HOH A . D 3 HOH 24 130 54 HOH HOH A . D 3 HOH 25 131 55 HOH HOH A . D 3 HOH 26 132 57 HOH HOH A . D 3 HOH 27 133 63 HOH HOH A . D 3 HOH 28 134 64 HOH HOH A . D 3 HOH 29 135 68 HOH HOH A . D 3 HOH 30 136 70 HOH HOH A . D 3 HOH 31 137 72 HOH HOH A . D 3 HOH 32 138 73 HOH HOH A . D 3 HOH 33 139 74 HOH HOH A . D 3 HOH 34 140 75 HOH HOH A . D 3 HOH 35 141 79 HOH HOH A . D 3 HOH 36 142 80 HOH HOH A . D 3 HOH 37 143 81 HOH HOH A . D 3 HOH 38 144 82 HOH HOH A . D 3 HOH 39 145 84 HOH HOH A . D 3 HOH 40 146 86 HOH HOH A . D 3 HOH 41 147 88 HOH HOH A . D 3 HOH 42 148 89 HOH HOH A . D 3 HOH 43 149 91 HOH HOH A . D 3 HOH 44 150 92 HOH HOH A . D 3 HOH 45 151 94 HOH HOH A . D 3 HOH 46 152 95 HOH HOH A . D 3 HOH 47 153 97 HOH HOH A . D 3 HOH 48 154 99 HOH HOH A . D 3 HOH 49 155 100 HOH HOH A . D 3 HOH 50 156 102 HOH HOH A . D 3 HOH 51 157 103 HOH HOH A . D 3 HOH 52 158 104 HOH HOH A . E 3 HOH 1 107 106 HOH MO6 B . E 3 HOH 2 108 106 HOH MO6 B . E 3 HOH 3 109 2 HOH HOH B . E 3 HOH 4 110 3 HOH HOH B . E 3 HOH 5 111 6 HOH HOH B . E 3 HOH 6 112 8 HOH HOH B . E 3 HOH 7 113 9 HOH HOH B . E 3 HOH 8 114 11 HOH HOH B . E 3 HOH 9 115 12 HOH HOH B . E 3 HOH 10 116 14 HOH HOH B . E 3 HOH 11 117 20 HOH HOH B . E 3 HOH 12 118 21 HOH HOH B . E 3 HOH 13 119 22 HOH HOH B . E 3 HOH 14 120 24 HOH HOH B . E 3 HOH 15 121 25 HOH HOH B . E 3 HOH 16 122 26 HOH HOH B . E 3 HOH 17 123 27 HOH HOH B . E 3 HOH 18 124 28 HOH HOH B . E 3 HOH 19 125 29 HOH HOH B . E 3 HOH 20 126 31 HOH HOH B . E 3 HOH 21 127 32 HOH HOH B . E 3 HOH 22 128 33 HOH HOH B . E 3 HOH 23 129 34 HOH HOH B . E 3 HOH 24 130 35 HOH HOH B . E 3 HOH 25 131 36 HOH HOH B . E 3 HOH 26 132 37 HOH HOH B . E 3 HOH 27 133 38 HOH HOH B . E 3 HOH 28 134 39 HOH HOH B . E 3 HOH 29 135 41 HOH HOH B . E 3 HOH 30 136 43 HOH HOH B . E 3 HOH 31 137 45 HOH HOH B . E 3 HOH 32 138 46 HOH HOH B . E 3 HOH 33 139 48 HOH HOH B . E 3 HOH 34 140 49 HOH HOH B . E 3 HOH 35 141 51 HOH HOH B . E 3 HOH 36 142 53 HOH HOH B . E 3 HOH 37 143 56 HOH HOH B . E 3 HOH 38 144 58 HOH HOH B . E 3 HOH 39 145 59 HOH HOH B . E 3 HOH 40 146 60 HOH HOH B . E 3 HOH 41 147 61 HOH HOH B . E 3 HOH 42 148 62 HOH HOH B . E 3 HOH 43 149 65 HOH HOH B . E 3 HOH 44 150 66 HOH HOH B . E 3 HOH 45 151 67 HOH HOH B . E 3 HOH 46 152 69 HOH HOH B . E 3 HOH 47 153 71 HOH HOH B . E 3 HOH 48 154 76 HOH HOH B . E 3 HOH 49 155 77 HOH HOH B . E 3 HOH 50 156 78 HOH HOH B . E 3 HOH 51 157 83 HOH HOH B . E 3 HOH 52 158 85 HOH HOH B . E 3 HOH 53 159 87 HOH HOH B . E 3 HOH 54 160 90 HOH HOH B . E 3 HOH 55 161 93 HOH HOH B . E 3 HOH 56 162 96 HOH HOH B . E 3 HOH 57 163 98 HOH HOH B . E 3 HOH 58 164 101 HOH HOH B . E 3 HOH 59 165 105 HOH HOH B . # 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 C45 9 A C45 9 ? DC ? 2 B C45 9 B C45 21 ? DC ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _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 # 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 ? D HOH . ? A HOH 107 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? D HOH . ? A HOH 108 ? 1_555 90.4 ? 2 O ? D HOH . ? A HOH 107 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? D HOH . ? A HOH 109 ? 1_555 89.8 ? 3 O ? D HOH . ? A HOH 108 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? D HOH . ? A HOH 109 ? 1_555 89.6 ? 4 O ? D HOH . ? A HOH 107 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? D HOH . ? A HOH 110 ? 1_555 89.9 ? 5 O ? D HOH . ? A HOH 108 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? D HOH . ? A HOH 110 ? 1_555 90.1 ? 6 O ? D HOH . ? A HOH 109 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? D HOH . ? A HOH 110 ? 1_555 179.6 ? 7 O ? D HOH . ? A HOH 107 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? E HOH . ? B HOH 107 ? 1_555 179.6 ? 8 O ? D HOH . ? A HOH 108 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? E HOH . ? B HOH 107 ? 1_555 90.0 ? 9 O ? D HOH . ? A HOH 109 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? E HOH . ? B HOH 107 ? 1_555 90.3 ? 10 O ? D HOH . ? A HOH 110 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? E HOH . ? B HOH 107 ? 1_555 90.0 ? 11 O ? D HOH . ? A HOH 107 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? E HOH . ? B HOH 108 ? 1_555 89.8 ? 12 O ? D HOH . ? A HOH 108 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? E HOH . ? B HOH 108 ? 1_555 179.7 ? 13 O ? D HOH . ? A HOH 109 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? E HOH . ? B HOH 108 ? 1_555 90.1 ? 14 O ? D HOH . ? A HOH 110 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? E HOH . ? B HOH 108 ? 1_555 90.1 ? 15 O ? E HOH . ? B HOH 107 ? 1_555 MG ? C MG . ? A MG 106 ? 1_555 O ? E HOH . ? B HOH 108 ? 1_555 89.8 ? # 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 2001-09-28 2 'Structure model' 1 1 2007-10-16 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-16 # _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' 6 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_initial_refinement_model 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_conn_type 8 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.value' 6 4 'Structure model' '_struct_conn.conn_type_id' 7 4 'Structure model' '_struct_conn.id' 8 4 'Structure model' '_struct_conn.pdbx_dist_value' 9 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 10 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 11 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 12 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 13 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 14 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 15 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 16 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 17 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 18 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 19 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 20 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 21 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 22 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 23 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 24 4 'Structure model' '_struct_conn_type.id' 25 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 26 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 27 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal AMoRE phasing . ? 1 CNS refinement 1.0 ? 2 MOSFLM 'data reduction' . ? 3 CCP4 'data scaling' '(SCALA)' ? 4 # 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 C45 N1 N N N 1 C45 C2 C N N 2 C45 N3 N N N 3 C45 C4 C N N 4 C45 C5 C N N 5 C45 C6 C N N 6 C45 O2 O N N 7 C45 N4 N N N 8 C45 "C1'" C N R 9 C45 "C2'" C N N 10 C45 CM2 C N N 11 C45 "C3'" C N S 12 C45 "C4'" C N R 13 C45 "O4'" O N N 14 C45 "O3'" O N N 15 C45 "C5'" C N N 16 C45 "O5'" O N N 17 C45 P P N N 18 C45 O1P O N N 19 C45 O2P O N N 20 C45 O O N N 21 C45 O3P O N N 22 C45 H5 H N N 23 C45 H6 H N N 24 C45 H4 H N N 25 C45 "H1'" H N N 26 C45 "H2'1" H N N 27 C45 "H2'2" H N N 28 C45 HM21 H N N 29 C45 HM22 H N N 30 C45 HM23 H N N 31 C45 "H3'" H N N 32 C45 "H4'" H N N 33 C45 HA H N N 34 C45 "H5'1" H N N 35 C45 "H5'2" H N N 36 C45 H1P H N N 37 C45 H2P H N N 38 DA OP3 O N N 39 DA P P N N 40 DA OP1 O N N 41 DA OP2 O N N 42 DA "O5'" O N N 43 DA "C5'" C N N 44 DA "C4'" C N R 45 DA "O4'" O N N 46 DA "C3'" C N S 47 DA "O3'" O N N 48 DA "C2'" C N N 49 DA "C1'" C N R 50 DA N9 N Y N 51 DA C8 C Y N 52 DA N7 N Y N 53 DA C5 C Y N 54 DA C6 C Y N 55 DA N6 N N N 56 DA N1 N Y N 57 DA C2 C Y N 58 DA N3 N Y N 59 DA C4 C Y N 60 DA HOP3 H N N 61 DA HOP2 H N N 62 DA "H5'" H N N 63 DA "H5''" H N N 64 DA "H4'" H N N 65 DA "H3'" H N N 66 DA "HO3'" H N N 67 DA "H2'" H N N 68 DA "H2''" H N N 69 DA "H1'" H N N 70 DA H8 H N N 71 DA H61 H N N 72 DA H62 H N N 73 DA H2 H N N 74 DC OP3 O N N 75 DC P P N N 76 DC OP1 O N N 77 DC OP2 O N N 78 DC "O5'" O N N 79 DC "C5'" C N N 80 DC "C4'" C N R 81 DC "O4'" O N N 82 DC "C3'" C N S 83 DC "O3'" O N N 84 DC "C2'" C N N 85 DC "C1'" C N R 86 DC N1 N N N 87 DC C2 C N N 88 DC O2 O N N 89 DC N3 N N N 90 DC C4 C N N 91 DC N4 N N N 92 DC C5 C N N 93 DC C6 C N N 94 DC HOP3 H N N 95 DC HOP2 H N N 96 DC "H5'" H N N 97 DC "H5''" H N N 98 DC "H4'" H N N 99 DC "H3'" H N N 100 DC "HO3'" H N N 101 DC "H2'" H N N 102 DC "H2''" H N N 103 DC "H1'" H N N 104 DC H41 H N N 105 DC H42 H N N 106 DC H5 H N N 107 DC H6 H N N 108 DG OP3 O N N 109 DG P P N N 110 DG OP1 O N N 111 DG OP2 O N N 112 DG "O5'" O N N 113 DG "C5'" C N N 114 DG "C4'" C N R 115 DG "O4'" O N N 116 DG "C3'" C N S 117 DG "O3'" O N N 118 DG "C2'" C N N 119 DG "C1'" C N R 120 DG N9 N Y N 121 DG C8 C Y N 122 DG N7 N Y N 123 DG C5 C Y N 124 DG C6 C N N 125 DG O6 O N N 126 DG N1 N N N 127 DG C2 C N N 128 DG N2 N N N 129 DG N3 N N N 130 DG C4 C Y N 131 DG HOP3 H N N 132 DG HOP2 H N N 133 DG "H5'" H N N 134 DG "H5''" H N N 135 DG "H4'" H N N 136 DG "H3'" H N N 137 DG "HO3'" H N N 138 DG "H2'" H N N 139 DG "H2''" H N N 140 DG "H1'" H N N 141 DG H8 H N N 142 DG H1 H N N 143 DG H21 H N N 144 DG H22 H N N 145 DT OP3 O N N 146 DT P P N N 147 DT OP1 O N N 148 DT OP2 O N N 149 DT "O5'" O N N 150 DT "C5'" C N N 151 DT "C4'" C N R 152 DT "O4'" O N N 153 DT "C3'" C N S 154 DT "O3'" O N N 155 DT "C2'" C N N 156 DT "C1'" C N R 157 DT N1 N N N 158 DT C2 C N N 159 DT O2 O N N 160 DT N3 N N N 161 DT C4 C N N 162 DT O4 O N N 163 DT C5 C N N 164 DT C7 C N N 165 DT C6 C N N 166 DT HOP3 H N N 167 DT HOP2 H N N 168 DT "H5'" H N N 169 DT "H5''" H N N 170 DT "H4'" H N N 171 DT "H3'" H N N 172 DT "HO3'" H N N 173 DT "H2'" H N N 174 DT "H2''" H N N 175 DT "H1'" H N N 176 DT H3 H N N 177 DT H71 H N N 178 DT H72 H N N 179 DT H73 H N N 180 DT H6 H N N 181 HOH O O N N 182 HOH H1 H N N 183 HOH H2 H N N 184 MG MG MG N N 185 # 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 C45 N1 C2 sing N N 1 C45 N1 C6 sing N N 2 C45 N1 "C1'" sing N N 3 C45 C2 N3 sing N N 4 C45 C2 O2 doub N N 5 C45 N3 C4 doub N N 6 C45 C4 C5 sing N N 7 C45 C4 N4 sing N N 8 C45 C5 C6 doub N N 9 C45 C5 H5 sing N N 10 C45 C6 H6 sing N N 11 C45 N4 O sing N N 12 C45 N4 H4 sing N N 13 C45 "C1'" "C2'" sing N N 14 C45 "C1'" "O4'" sing N N 15 C45 "C1'" "H1'" sing N N 16 C45 "C2'" "C3'" sing N N 17 C45 "C2'" "H2'1" sing N N 18 C45 "C2'" "H2'2" sing N N 19 C45 CM2 O sing N N 20 C45 CM2 HM21 sing N N 21 C45 CM2 HM22 sing N N 22 C45 CM2 HM23 sing N N 23 C45 "C3'" "C4'" sing N N 24 C45 "C3'" "O3'" sing N N 25 C45 "C3'" "H3'" sing N N 26 C45 "C4'" "O4'" sing N N 27 C45 "C4'" "C5'" sing N N 28 C45 "C4'" "H4'" sing N N 29 C45 "O3'" HA sing N N 30 C45 "C5'" "O5'" sing N N 31 C45 "C5'" "H5'1" sing N N 32 C45 "C5'" "H5'2" sing N N 33 C45 "O5'" P sing N N 34 C45 P O1P sing N N 35 C45 P O2P sing N N 36 C45 P O3P doub N N 37 C45 O1P H1P sing N N 38 C45 O2P H2P sing N N 39 DA OP3 P sing N N 40 DA OP3 HOP3 sing N N 41 DA P OP1 doub N N 42 DA P OP2 sing N N 43 DA P "O5'" sing N N 44 DA OP2 HOP2 sing N N 45 DA "O5'" "C5'" sing N N 46 DA "C5'" "C4'" sing N N 47 DA "C5'" "H5'" sing N N 48 DA "C5'" "H5''" sing N N 49 DA "C4'" "O4'" sing N N 50 DA "C4'" "C3'" sing N N 51 DA "C4'" "H4'" sing N N 52 DA "O4'" "C1'" sing N N 53 DA "C3'" "O3'" sing N N 54 DA "C3'" "C2'" sing N N 55 DA "C3'" "H3'" sing N N 56 DA "O3'" "HO3'" sing N N 57 DA "C2'" "C1'" sing N N 58 DA "C2'" "H2'" sing N N 59 DA "C2'" "H2''" sing N N 60 DA "C1'" N9 sing N N 61 DA "C1'" "H1'" sing N N 62 DA N9 C8 sing Y N 63 DA N9 C4 sing Y N 64 DA C8 N7 doub Y N 65 DA C8 H8 sing N N 66 DA N7 C5 sing Y N 67 DA C5 C6 sing Y N 68 DA C5 C4 doub Y N 69 DA C6 N6 sing N N 70 DA C6 N1 doub Y N 71 DA N6 H61 sing N N 72 DA N6 H62 sing N N 73 DA N1 C2 sing Y N 74 DA C2 N3 doub Y N 75 DA C2 H2 sing N N 76 DA N3 C4 sing Y N 77 DC OP3 P sing N N 78 DC OP3 HOP3 sing N N 79 DC P OP1 doub N N 80 DC P OP2 sing N N 81 DC P "O5'" sing N N 82 DC OP2 HOP2 sing N N 83 DC "O5'" "C5'" sing N N 84 DC "C5'" "C4'" sing N N 85 DC "C5'" "H5'" sing N N 86 DC "C5'" "H5''" sing N N 87 DC "C4'" "O4'" sing N N 88 DC "C4'" "C3'" sing N N 89 DC "C4'" "H4'" sing N N 90 DC "O4'" "C1'" sing N N 91 DC "C3'" "O3'" sing N N 92 DC "C3'" "C2'" sing N N 93 DC "C3'" "H3'" sing N N 94 DC "O3'" "HO3'" sing N N 95 DC "C2'" "C1'" sing N N 96 DC "C2'" "H2'" sing N N 97 DC "C2'" "H2''" sing N N 98 DC "C1'" N1 sing N N 99 DC "C1'" "H1'" sing N N 100 DC N1 C2 sing N N 101 DC N1 C6 sing N N 102 DC C2 O2 doub N N 103 DC C2 N3 sing N N 104 DC N3 C4 doub N N 105 DC C4 N4 sing N N 106 DC C4 C5 sing N N 107 DC N4 H41 sing N N 108 DC N4 H42 sing N N 109 DC C5 C6 doub N N 110 DC C5 H5 sing N N 111 DC C6 H6 sing N N 112 DG OP3 P sing N N 113 DG OP3 HOP3 sing N N 114 DG P OP1 doub N N 115 DG P OP2 sing N N 116 DG P "O5'" sing N N 117 DG OP2 HOP2 sing N N 118 DG "O5'" "C5'" sing N N 119 DG "C5'" "C4'" sing N N 120 DG "C5'" "H5'" sing N N 121 DG "C5'" "H5''" sing N N 122 DG "C4'" "O4'" sing N N 123 DG "C4'" "C3'" sing N N 124 DG "C4'" "H4'" sing N N 125 DG "O4'" "C1'" sing N N 126 DG "C3'" "O3'" sing N N 127 DG "C3'" "C2'" sing N N 128 DG "C3'" "H3'" sing N N 129 DG "O3'" "HO3'" sing N N 130 DG "C2'" "C1'" sing N N 131 DG "C2'" "H2'" sing N N 132 DG "C2'" "H2''" sing N N 133 DG "C1'" N9 sing N N 134 DG "C1'" "H1'" sing N N 135 DG N9 C8 sing Y N 136 DG N9 C4 sing Y N 137 DG C8 N7 doub Y N 138 DG C8 H8 sing N N 139 DG N7 C5 sing Y N 140 DG C5 C6 sing N N 141 DG C5 C4 doub Y N 142 DG C6 O6 doub N N 143 DG C6 N1 sing N N 144 DG N1 C2 sing N N 145 DG N1 H1 sing N N 146 DG C2 N2 sing N N 147 DG C2 N3 doub N N 148 DG N2 H21 sing N N 149 DG N2 H22 sing N N 150 DG N3 C4 sing N N 151 DT OP3 P sing N N 152 DT OP3 HOP3 sing N N 153 DT P OP1 doub N N 154 DT P OP2 sing N N 155 DT P "O5'" sing N N 156 DT OP2 HOP2 sing N N 157 DT "O5'" "C5'" sing N N 158 DT "C5'" "C4'" sing N N 159 DT "C5'" "H5'" sing N N 160 DT "C5'" "H5''" sing N N 161 DT "C4'" "O4'" sing N N 162 DT "C4'" "C3'" sing N N 163 DT "C4'" "H4'" sing N N 164 DT "O4'" "C1'" sing N N 165 DT "C3'" "O3'" sing N N 166 DT "C3'" "C2'" sing N N 167 DT "C3'" "H3'" sing N N 168 DT "O3'" "HO3'" sing N N 169 DT "C2'" "C1'" sing N N 170 DT "C2'" "H2'" sing N N 171 DT "C2'" "H2''" sing N N 172 DT "C1'" N1 sing N N 173 DT "C1'" "H1'" sing N N 174 DT N1 C2 sing N N 175 DT N1 C6 sing N N 176 DT C2 O2 doub N N 177 DT C2 N3 sing N N 178 DT N3 C4 sing N N 179 DT N3 H3 sing N N 180 DT C4 O4 doub N N 181 DT C4 C5 sing N N 182 DT C5 C7 sing N N 183 DT C5 C6 doub N N 184 DT C7 H71 sing N N 185 DT C7 H72 sing N N 186 DT C7 H73 sing N N 187 DT C6 H6 sing N N 188 HOH O H1 sing N N 189 HOH O H2 sing N N 190 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1J8L 'double helix' 1J8L 'b-form double helix' 1J8L '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 0.406 -0.233 0.190 2.188 -15.862 0.910 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.317 -0.249 0.409 2.709 -9.982 -2.357 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 -0.061 -0.156 0.044 1.814 -2.184 -0.103 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.077 -0.137 0.311 10.212 -16.948 4.339 4 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.004 -0.105 0.264 3.773 -17.869 5.175 5 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.010 -0.099 0.200 -2.425 -17.854 4.494 6 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.082 -0.144 0.190 -9.314 -14.363 4.325 7 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DG 10 1_555 B DC 3 1_555 -0.041 -0.129 0.140 5.260 -5.873 3.937 8 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.064 -0.159 0.318 1.248 -16.442 -4.345 9 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.133 -0.230 0.250 3.782 -5.284 -2.558 10 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 -0.285 0.141 3.286 -3.419 3.248 35.561 -0.241 -0.032 3.298 5.289 5.567 35.862 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 DC 3 1_555 B DG 10 1_555 0.691 0.454 3.420 3.186 -5.005 39.577 1.264 -0.628 3.383 -7.341 -4.674 40.002 2 AA_DG2DC3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DC 3 1_555 B DG 10 1_555 A DA 5 1_555 B DT 8 1_555 0.111 0.287 6.472 1.354 3.449 65.555 -0.015 0.007 6.479 3.183 -1.249 65.648 3 AA_DC3DA5:DT20DG22_BB A 3 ? B 22 ? 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 0.147 -0.415 3.367 -0.025 -0.132 36.658 -0.642 -0.238 3.369 -0.210 0.039 36.659 4 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 -0.066 -0.710 3.330 0.246 -0.289 31.928 -1.238 0.164 3.336 -0.526 -0.446 31.931 5 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 -0.227 -0.431 3.384 0.237 -1.717 35.254 -0.447 0.411 3.399 -2.833 -0.392 35.295 6 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DG 10 1_555 B DC 3 1_555 -0.220 0.983 6.313 -2.501 -4.647 69.335 1.185 0.019 6.248 -4.079 2.195 69.511 7 AA_DT8DG10:DC15DA17_BB A 8 ? B 17 ? A 10 ? B 15 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -1.267 0.448 3.455 -4.206 -9.890 41.600 1.656 1.288 3.374 -13.653 5.806 42.907 8 AA_DG10DC11:DG14DC15_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 0.674 0.471 3.309 3.640 0.112 36.869 0.726 -0.561 3.359 0.177 -5.739 37.043 9 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 355D _pdbx_initial_refinement_model.details 'PDB ENTRY 355D' #