data_4ITD # _entry.id 4ITD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.388 _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 4ITD pdb_00004itd 10.2210/pdb4itd/pdb NDB NA2222 ? ? RCSB RCSB077184 ? ? WWPDB D_1000077184 ? ? # 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 2013-05-08 2 'Structure model' 1 1 2014-03-19 3 'Structure model' 1 2 2024-03-20 # _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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 '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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_struct_conn_angle 5 3 'Structure model' struct_conn 6 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.value' 6 3 'Structure model' '_struct_conn.pdbx_dist_value' 7 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 9 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 10 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 11 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 4ITD _pdbx_database_status.status_code REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2013-01-18 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _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 4IJ0 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zhang, F.' 1 'Suzuki, K.' 2 'Tsunoda, M.' 3 'Wilkinson, O.' 4 'Millington, C.L.' 5 'Williams, D.M.' 6 'Morishita, E.C.' 7 'Takenaka, A.' 8 # _citation.id primary _citation.title ;Structures of DNA duplexes containing O6-carboxymethylguanine, a lesion associated with gastrointestinal cancer, reveal a mechanism for inducing pyrimidine transition mutations ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 41 _citation.page_first 5524 _citation.page_last 5532 _citation.year 2013 _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 23580550 _citation.pdbx_database_id_DOI 10.1093/nar/gkt198 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhang, F.' 1 ? primary 'Tsunoda, M.' 2 ? primary 'Suzuki, K.' 3 ? primary 'Kikuchi, Y.' 4 ? primary 'Wilkinson, O.' 5 ? primary 'Millington, C.L.' 6 ? primary 'Margison, G.P.' 7 ? primary 'Williams, D.M.' 8 ? primary 'Czarina Morishita, E.' 9 ? primary 'Takenaka, A.' 10 ? # 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*GP*(C6G)P*AP*TP*TP*CP*GP*CP*G)-3') ; 3737.427 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 non-polymer syn "2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" 424.498 1 ? ? ? ? 4 water nat water 18.015 80 ? ? ? ? # _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)(DG)(C6G)(DA)(DT)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGXATTCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 "2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" HT 4 water 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 DC n 1 4 DG n 1 5 C6G n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DC n 1 10 DG 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 C6G 'DNA linking' n '6-(carboxymethoxy)-9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purin-2-amine' ? 'C12 H16 N5 O9 P' 405.257 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 HT non-polymer . "2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE" 'HOECHST 33258' 'C25 H24 N6 O' 424.498 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # 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 DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 C6G 5 5 5 C6G C6G A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 DC 1 13 13 DC DC B . n B 1 2 DG 2 14 14 DG DG B . n B 1 3 DC 3 15 15 DC DC B . n B 1 4 DG 4 16 16 DG DG B . n B 1 5 C6G 5 17 17 C6G C6G B . n B 1 6 DA 6 18 18 DA DA B . n B 1 7 DT 7 19 19 DT DT B . n B 1 8 DT 8 20 20 DT DT B . n B 1 9 DC 9 21 21 DC DC B . n B 1 10 DG 10 22 22 DG DG B . n B 1 11 DC 11 23 23 DC DC B . n B 1 12 DG 12 24 24 DG DG 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 1 101 1 MG MG A . D 3 HT 1 102 59 HT HT A . E 4 HOH 1 201 8 HOH HOH A . E 4 HOH 2 202 14 HOH HOH A . E 4 HOH 3 203 18 HOH HOH A . E 4 HOH 4 204 25 HOH HOH A . E 4 HOH 5 205 26 HOH HOH A . E 4 HOH 6 206 27 HOH HOH A . E 4 HOH 7 207 28 HOH HOH A . E 4 HOH 8 208 36 HOH HOH A . E 4 HOH 9 209 40 HOH HOH A . E 4 HOH 10 210 54 HOH HOH A . E 4 HOH 11 211 57 HOH HOH A . E 4 HOH 12 212 62 HOH HOH A . E 4 HOH 13 213 63 HOH HOH A . E 4 HOH 14 214 67 HOH HOH A . E 4 HOH 15 215 68 HOH HOH A . E 4 HOH 16 216 72 HOH HOH A . E 4 HOH 17 217 73 HOH HOH A . E 4 HOH 18 218 75 HOH HOH A . E 4 HOH 19 219 83 HOH HOH A . E 4 HOH 20 220 84 HOH HOH A . E 4 HOH 21 221 89 HOH HOH A . E 4 HOH 22 222 90 HOH HOH A . E 4 HOH 23 223 95 HOH HOH A . E 4 HOH 24 224 101 HOH HOH A . E 4 HOH 25 225 102 HOH HOH A . E 4 HOH 26 226 104 HOH HOH A . E 4 HOH 27 227 111 HOH HOH A . E 4 HOH 28 228 112 HOH HOH A . E 4 HOH 29 229 115 HOH HOH A . E 4 HOH 30 230 4 HOH HOH A . E 4 HOH 31 231 8 HOH HOH A . E 4 HOH 32 232 9 HOH HOH A . E 4 HOH 33 233 10 HOH HOH A . E 4 HOH 34 234 11 HOH HOH A . E 4 HOH 35 235 2 HOH HOH A . E 4 HOH 36 236 15 HOH HOH A . E 4 HOH 37 237 33 HOH HOH A . E 4 HOH 38 238 46 HOH HOH A . E 4 HOH 39 239 52 HOH HOH A . E 4 HOH 40 240 93 HOH HOH A . F 4 HOH 1 201 3 HOH HOH B . F 4 HOH 2 202 4 HOH HOH B . F 4 HOH 3 203 5 HOH HOH B . F 4 HOH 4 204 7 HOH HOH B . F 4 HOH 5 205 12 HOH HOH B . F 4 HOH 6 206 13 HOH HOH B . F 4 HOH 7 207 16 HOH HOH B . F 4 HOH 8 208 20 HOH HOH B . F 4 HOH 9 209 21 HOH HOH B . F 4 HOH 10 210 30 HOH HOH B . F 4 HOH 11 211 34 HOH HOH B . F 4 HOH 12 212 38 HOH HOH B . F 4 HOH 13 213 42 HOH HOH B . F 4 HOH 14 214 44 HOH HOH B . F 4 HOH 15 215 45 HOH HOH B . F 4 HOH 16 216 47 HOH HOH B . F 4 HOH 17 217 49 HOH HOH B . F 4 HOH 18 218 53 HOH HOH B . F 4 HOH 19 219 61 HOH HOH B . F 4 HOH 20 220 64 HOH HOH B . F 4 HOH 21 221 65 HOH HOH B . F 4 HOH 22 222 69 HOH HOH B . F 4 HOH 23 223 70 HOH HOH B . F 4 HOH 24 224 71 HOH HOH B . F 4 HOH 25 225 74 HOH HOH B . F 4 HOH 26 226 78 HOH HOH B . F 4 HOH 27 227 79 HOH HOH B . F 4 HOH 28 228 80 HOH HOH B . F 4 HOH 29 229 82 HOH HOH B . F 4 HOH 30 230 87 HOH HOH B . F 4 HOH 31 231 96 HOH HOH B . F 4 HOH 32 232 98 HOH HOH B . F 4 HOH 33 233 99 HOH HOH B . F 4 HOH 34 234 100 HOH HOH B . F 4 HOH 35 235 108 HOH HOH B . F 4 HOH 36 236 1 HOH HOH B . F 4 HOH 37 237 5 HOH HOH B . F 4 HOH 38 238 6 HOH HOH B . F 4 HOH 39 239 12 HOH HOH B . F 4 HOH 40 240 13 HOH HOH B . # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SCALEPACK . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 2 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 3 PDB_EXTRACT 3.11 'April 22, 2011' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? # _cell.entry_id 4ITD _cell.length_a 25.051 _cell.length_b 40.404 _cell.length_c 65.667 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 4ITD _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 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4ITD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.22 _exptl_crystal.density_percent_sol 44.67 _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_pH_range ? _exptl_crystal_grow.pdbx_details ;10%(v/v)MPD, 12mM spermine 4HCL, 80mM NaCL, 12mM KCL, 20mM MgCL2, 40mM Na cacodylate(pH7.0), 1mM Hoechst 33258, 1mM DNA, vapor diffusion, hanging drop, temperature 277K ; # _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 315r' _diffrn_detector.pdbx_collection_date 2011-03-06 _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 1.00 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-5A' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-5A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.00 # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 4ITD _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50.000 _reflns.d_resolution_high 1.940 _reflns.number_obs 4877 _reflns.number_all ? _reflns.percent_possible_obs 91.000 _reflns.pdbx_Rmerge_I_obs 0.057 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 12.000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.700 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # loop_ _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_unique_obs _reflns_shell.pdbx_chi_squared 1 1 1.940 1.970 33.700 ? ? ? 1.400 ? ? ? ? ? ? 1 2 1.970 2.010 52.600 ? ? ? 1.800 ? ? ? ? ? ? 1 3 2.010 2.050 69.300 ? ? ? 2.400 ? ? ? ? ? ? 1 4 2.050 2.090 77.800 ? ? ? 3.000 ? ? ? ? ? ? 1 5 2.090 2.140 91.600 ? ? ? 3.700 ? ? ? ? ? ? 1 6 2.140 2.180 96.000 ? ? ? 4.600 ? ? ? ? ? ? 1 7 2.180 2.240 98.800 ? ? ? 5.500 ? ? ? ? ? ? 1 8 2.240 2.300 100.000 ? ? ? 6.100 ? ? ? ? ? ? 1 9 2.300 2.370 99.600 ? ? ? 6.600 ? ? ? ? ? ? 1 10 2.370 2.440 100.000 0.951 ? ? 6.600 ? ? ? ? ? ? 1 11 2.440 2.530 100.000 0.641 ? ? 6.700 ? ? ? ? ? ? 1 12 2.530 2.630 100.000 0.417 ? ? 6.800 ? ? ? ? ? ? 1 13 2.630 2.750 100.000 0.260 ? ? 6.700 ? ? ? ? ? ? 1 14 2.750 2.900 100.000 0.205 ? ? 6.900 ? ? ? ? ? ? 1 15 2.900 3.080 100.000 0.146 ? ? 6.800 ? ? ? ? ? ? 1 16 3.080 3.320 99.200 0.053 ? ? 6.600 ? ? ? ? ? ? 1 17 3.320 3.650 99.700 0.047 ? ? 6.600 ? ? ? ? ? ? 1 18 3.650 4.180 100.000 0.042 ? ? 6.400 ? ? ? ? ? ? 1 19 4.180 5.260 100.000 0.039 ? ? 6.300 ? ? ? ? ? ? 1 20 5.260 50.000 95.000 0.036 ? ? 5.600 ? ? ? ? ? ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 4ITD _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 3654 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 34.41 _refine.ls_d_res_high 1.94 _refine.ls_percent_reflns_obs 72.45 _refine.ls_R_factor_obs 0.22763 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.22611 _refine.ls_R_factor_R_free 0.25351 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.9 _refine.ls_number_reflns_R_free 188 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min 1.000 _refine.occupancy_max 1.000 _refine.correlation_coeff_Fo_to_Fc 0.966 _refine.correlation_coeff_Fo_to_Fc_free 0.952 _refine.B_iso_mean 38.682 _refine.aniso_B[1][1] 2.33 _refine.aniso_B[2][2] -0.98 _refine.aniso_B[3][3] -1.35 _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 MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.344 _refine.pdbx_overall_ESU_R_Free 0.226 _refine.overall_SU_ML 0.200 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 9.113 _refine.overall_SU_R_Cruickshank_DPI 0.3415 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? # _refine_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 496 _refine_hist.pdbx_number_atoms_ligand 33 _refine_hist.number_atoms_solvent 80 _refine_hist.number_atoms_total 609 _refine_hist.d_res_high 1.94 _refine_hist.d_res_low 34.41 # 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 r_bond_refined_d 0.023 0.011 ? 583 'X-RAY DIFFRACTION' ? r_bond_other_d 0.035 0.020 ? 292 'X-RAY DIFFRACTION' ? r_angle_refined_deg 2.168 1.270 ? 894 'X-RAY DIFFRACTION' ? r_angle_other_deg 4.873 3.000 ? 685 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.109 0.200 ? 74 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.019 0.020 ? 318 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.031 0.020 ? 134 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 4.181 3.000 ? 589 'X-RAY DIFFRACTION' ? r_scangle_it 5.740 4.500 ? 894 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.940 _refine_ls_shell.d_res_low 1.991 _refine_ls_shell.number_reflns_R_work 79 _refine_ls_shell.R_factor_R_work 0.514 _refine_ls_shell.percent_reflns_obs 21.37 _refine_ls_shell.R_factor_R_free 0.557 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 2 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? # _struct.entry_id 4ITD _struct.title ;Structures of DNA duplexes containing O6-carboxymethylguanine, a lesion associated with gastrointestinal cancer, reveal a mechanism for inducing transition mutation ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4ITD _struct_keywords.text 'damaged DNA, O6-carboxymethylguanine, mutagenesis, DNA' _struct_keywords.pdbx_keywords 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 4 ? F N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4ITD _struct_ref.pdbx_db_accession 4ITD _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 4ITD A 1 ? 12 ? 4ITD 1 ? 12 ? 1 12 2 1 4ITD B 1 ? 12 ? 4ITD 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1330 ? 1 MORE -11 ? 1 'SSA (A^2)' 5200 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DG 4 "O3'" ? ? ? 1_555 A C6G 5 P ? ? A DG 4 A C6G 5 1_555 ? ? ? ? ? ? ? 1.526 ? ? covale2 covale one ? A C6G 5 "O3'" ? ? ? 1_555 A DA 6 P ? ? A C6G 5 A DA 6 1_555 ? ? ? ? ? ? ? 1.521 ? ? covale3 covale both ? B DG 4 "O3'" ? ? ? 1_555 B C6G 5 P ? ? B DG 16 B C6G 17 1_555 ? ? ? ? ? ? ? 1.485 ? ? covale4 covale one ? B C6G 5 "O3'" ? ? ? 1_555 B DA 6 P ? ? B C6G 17 B DA 18 1_555 ? ? ? ? ? ? ? 1.596 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 203 1_555 ? ? ? ? ? ? ? 1.988 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 231 1_555 ? ? ? ? ? ? ? 2.037 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 232 1_555 ? ? ? ? ? ? ? 2.111 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 233 1_555 ? ? ? ? ? ? ? 2.120 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 A HOH 234 1_555 ? ? ? ? ? ? ? 2.038 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? A MG 101 B HOH 238 1_555 ? ? ? ? ? ? ? 2.151 ? ? 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 DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 21 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 DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? 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 ? ? 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 ? E HOH . ? A HOH 203 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 231 ? 1_555 81.6 ? 2 O ? E HOH . ? A HOH 203 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 232 ? 1_555 91.9 ? 3 O ? E HOH . ? A HOH 231 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 232 ? 1_555 173.0 ? 4 O ? E HOH . ? A HOH 203 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 233 ? 1_555 97.0 ? 5 O ? E HOH . ? A HOH 231 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 233 ? 1_555 97.3 ? 6 O ? E HOH . ? A HOH 232 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 233 ? 1_555 80.7 ? 7 O ? E HOH . ? A HOH 203 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 234 ? 1_555 174.6 ? 8 O ? E HOH . ? A HOH 231 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 234 ? 1_555 103.5 ? 9 O ? E HOH . ? A HOH 232 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 234 ? 1_555 83.0 ? 10 O ? E HOH . ? A HOH 233 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? A HOH 234 ? 1_555 83.9 ? 11 O ? E HOH . ? A HOH 203 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? F HOH . ? B HOH 238 ? 1_555 93.3 ? 12 O ? E HOH . ? A HOH 231 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? F HOH . ? B HOH 238 ? 1_555 84.1 ? 13 O ? E HOH . ? A HOH 232 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? F HOH . ? B HOH 238 ? 1_555 99.1 ? 14 O ? E HOH . ? A HOH 233 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? F HOH . ? B HOH 238 ? 1_555 169.7 ? 15 O ? E HOH . ? A HOH 234 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? F HOH . ? B HOH 238 ? 1_555 85.9 ? # 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 101 ? 6 'BINDING SITE FOR RESIDUE MG A 101' AC2 Software A HT 102 ? 12 'BINDING SITE FOR RESIDUE HT A 102' 1 ? ? ? ? ? ? ? # 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 E . ? HOH A 203 . ? 1_555 ? 2 AC1 6 HOH E . ? HOH A 231 . ? 1_555 ? 3 AC1 6 HOH E . ? HOH A 232 . ? 1_555 ? 4 AC1 6 HOH E . ? HOH A 233 . ? 1_555 ? 5 AC1 6 HOH E . ? HOH A 234 . ? 1_555 ? 6 AC1 6 HOH F . ? HOH B 238 . ? 1_555 ? 7 AC2 12 C6G A 5 ? C6G A 5 . ? 1_555 ? 8 AC2 12 DA A 6 ? DA A 6 . ? 1_555 ? 9 AC2 12 DT A 7 ? DT A 7 . ? 1_555 ? 10 AC2 12 DT A 8 ? DT A 8 . ? 1_555 ? 11 AC2 12 DC A 9 ? DC A 9 . ? 1_555 ? 12 AC2 12 DG A 12 ? DG A 12 . ? 2_455 ? 13 AC2 12 DA B 6 ? DA B 18 . ? 1_555 ? 14 AC2 12 DT B 7 ? DT B 19 . ? 1_555 ? 15 AC2 12 DT B 8 ? DT B 20 . ? 1_555 ? 16 AC2 12 DC B 9 ? DC B 21 . ? 1_555 ? 17 AC2 12 DG B 10 ? DG B 22 . ? 1_555 ? 18 AC2 12 DC B 11 ? DC B 23 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A HOH 211 ? ? O A HOH 228 ? ? 1.67 2 1 O A HOH 236 ? ? O A HOH 239 ? ? 1.76 3 1 O B C6G 17 ? ? O B HOH 225 ? ? 2.12 4 1 O A HOH 205 ? ? O A HOH 206 ? ? 2.12 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 217 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 230 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 2_455 _pdbx_validate_symm_contact.dist 2.19 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A DG 2 ? ? P A DC 3 ? ? 1.501 1.607 -0.106 0.012 Y 2 1 "O3'" A DC 3 ? ? P A DG 4 ? ? 1.525 1.607 -0.082 0.012 Y 3 1 "O3'" A DG 4 ? ? P A C6G 5 ? ? 1.526 1.607 -0.081 0.012 Y 4 1 "O3'" A C6G 5 ? ? P A DA 6 ? ? 1.521 1.607 -0.086 0.012 Y 5 1 "O3'" A DA 6 ? ? P A DT 7 ? ? 1.499 1.607 -0.108 0.012 Y 6 1 "O3'" A DT 7 ? ? P A DT 8 ? ? 1.481 1.607 -0.126 0.012 Y 7 1 "O3'" A DT 8 ? ? P A DC 9 ? ? 1.514 1.607 -0.093 0.012 Y 8 1 "O3'" A DG 10 ? ? P A DC 11 ? ? 1.523 1.607 -0.084 0.012 Y 9 1 "O3'" B DG 16 ? ? P B C6G 17 ? ? 1.485 1.607 -0.122 0.012 Y 10 1 "O3'" B DT 19 ? ? P B DT 20 ? ? 1.530 1.607 -0.077 0.012 Y 11 1 "O3'" B DT 20 ? ? P B DC 21 ? ? 1.517 1.607 -0.090 0.012 Y 12 1 "O3'" B DC 21 ? ? P B DG 22 ? ? 1.505 1.607 -0.102 0.012 Y 13 1 "O3'" B DG 22 ? ? P B DC 23 ? ? 1.527 1.607 -0.080 0.012 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 DA 6 ? ? P A DA 6 ? ? OP1 A DA 6 ? ? 100.28 105.70 -5.42 0.90 N 2 1 "O5'" A DT 8 ? ? P A DT 8 ? ? OP2 A DT 8 ? ? 96.49 105.70 -9.21 0.90 N 3 1 "O5'" B DT 19 ? ? P B DT 19 ? ? OP1 B DT 19 ? ? 97.47 105.70 -8.23 0.90 N 4 1 "C3'" B DG 22 ? ? "C2'" B DG 22 ? ? "C1'" B DG 22 ? ? 97.57 102.40 -4.83 0.80 N 5 1 "O5'" B DC 23 ? ? P B DC 23 ? ? OP1 B DC 23 ? ? 98.98 105.70 -6.72 0.90 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 C6G 5 A C6G 5 ? DG ? 2 B C6G 5 B C6G 17 ? DG ? # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MAJOR GROOVE BINDER' # 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 C6G P P N N 1 C6G OP1 O N N 2 C6G OP2 O N N 3 C6G "O5'" O N N 4 C6G "C5'" C N N 5 C6G "C4'" C N R 6 C6G "O4'" O N N 7 C6G "C1'" C N R 8 C6G N9 N Y N 9 C6G C8 C Y N 10 C6G N7 N Y N 11 C6G C5 C Y N 12 C6G C4 C Y N 13 C6G N3 N Y N 14 C6G C2 C Y N 15 C6G N2 N N N 16 C6G N1 N Y N 17 C6G C6 C Y N 18 C6G O6 O N N 19 C6G "C2'" C N N 20 C6G "C3'" C N S 21 C6G "O3'" O N N 22 C6G C C N N 23 C6G O O N N 24 C6G O7 O N N 25 C6G CH3 C N N 26 C6G HOP2 H N N 27 C6G "H5'" H N N 28 C6G "H5''" H N N 29 C6G "H4'" H N N 30 C6G "H1'" H N N 31 C6G H8 H N N 32 C6G H21 H N N 33 C6G H22 H N N 34 C6G "H2'" H N N 35 C6G "H2''" H N N 36 C6G "H3'" H N N 37 C6G "HO3'" H N N 38 C6G HO7 H N N 39 C6G H31 H N N 40 C6G H32 H N N 41 C6G OP3 O N N 42 C6G HOP3 H N N 43 DA OP3 O N N 44 DA P P N N 45 DA OP1 O N N 46 DA OP2 O N N 47 DA "O5'" O N N 48 DA "C5'" C N N 49 DA "C4'" C N R 50 DA "O4'" O N N 51 DA "C3'" C N S 52 DA "O3'" O N N 53 DA "C2'" C N N 54 DA "C1'" C N R 55 DA N9 N Y N 56 DA C8 C Y N 57 DA N7 N Y N 58 DA C5 C Y N 59 DA C6 C Y N 60 DA N6 N N N 61 DA N1 N Y N 62 DA C2 C Y N 63 DA N3 N Y N 64 DA C4 C Y N 65 DA HOP3 H N N 66 DA HOP2 H N N 67 DA "H5'" H N N 68 DA "H5''" H N N 69 DA "H4'" H N N 70 DA "H3'" H N N 71 DA "HO3'" H N N 72 DA "H2'" H N N 73 DA "H2''" H N N 74 DA "H1'" H N N 75 DA H8 H N N 76 DA H61 H N N 77 DA H62 H N N 78 DA H2 H N N 79 DC OP3 O N N 80 DC P P N N 81 DC OP1 O N N 82 DC OP2 O N N 83 DC "O5'" O N N 84 DC "C5'" C N N 85 DC "C4'" C N R 86 DC "O4'" O N N 87 DC "C3'" C N S 88 DC "O3'" O N N 89 DC "C2'" C N N 90 DC "C1'" C N R 91 DC N1 N N N 92 DC C2 C N N 93 DC O2 O N N 94 DC N3 N N N 95 DC C4 C N N 96 DC N4 N N N 97 DC C5 C N N 98 DC C6 C N N 99 DC HOP3 H N N 100 DC HOP2 H N N 101 DC "H5'" H N N 102 DC "H5''" H N N 103 DC "H4'" H N N 104 DC "H3'" H N N 105 DC "HO3'" H N N 106 DC "H2'" H N N 107 DC "H2''" H N N 108 DC "H1'" H N N 109 DC H41 H N N 110 DC H42 H N N 111 DC H5 H N N 112 DC H6 H N N 113 DG OP3 O N N 114 DG P P N N 115 DG OP1 O N N 116 DG OP2 O N N 117 DG "O5'" O N N 118 DG "C5'" C N N 119 DG "C4'" C N R 120 DG "O4'" O N N 121 DG "C3'" C N S 122 DG "O3'" O N N 123 DG "C2'" C N N 124 DG "C1'" C N R 125 DG N9 N Y N 126 DG C8 C Y N 127 DG N7 N Y N 128 DG C5 C Y N 129 DG C6 C N N 130 DG O6 O N N 131 DG N1 N N N 132 DG C2 C N N 133 DG N2 N N N 134 DG N3 N N N 135 DG C4 C Y N 136 DG HOP3 H N N 137 DG HOP2 H N N 138 DG "H5'" H N N 139 DG "H5''" H N N 140 DG "H4'" H N N 141 DG "H3'" H N N 142 DG "HO3'" H N N 143 DG "H2'" H N N 144 DG "H2''" H N N 145 DG "H1'" H N N 146 DG H8 H N N 147 DG H1 H N N 148 DG H21 H N N 149 DG H22 H N N 150 DT OP3 O N N 151 DT P P N N 152 DT OP1 O N N 153 DT OP2 O N N 154 DT "O5'" O N N 155 DT "C5'" C N N 156 DT "C4'" C N R 157 DT "O4'" O N N 158 DT "C3'" C N S 159 DT "O3'" O N N 160 DT "C2'" C N N 161 DT "C1'" C N R 162 DT N1 N N N 163 DT C2 C N N 164 DT O2 O N N 165 DT N3 N N N 166 DT C4 C N N 167 DT O4 O N N 168 DT C5 C N N 169 DT C7 C N N 170 DT C6 C N N 171 DT HOP3 H N N 172 DT HOP2 H N N 173 DT "H5'" H N N 174 DT "H5''" H N N 175 DT "H4'" H N N 176 DT "H3'" H N N 177 DT "HO3'" H N N 178 DT "H2'" H N N 179 DT "H2''" H N N 180 DT "H1'" H N N 181 DT H3 H N N 182 DT H71 H N N 183 DT H72 H N N 184 DT H73 H N N 185 DT H6 H N N 186 HOH O O N N 187 HOH H1 H N N 188 HOH H2 H N N 189 HT O1 O N N 190 HT C1 C Y N 191 HT C4 C Y N 192 HT C2 C Y N 193 HT C3 C Y N 194 HT C6 C Y N 195 HT C5 C Y N 196 HT C7 C Y N 197 HT N1 N Y N 198 HT C8 C Y N 199 HT C9 C Y N 200 HT N2 N Y N 201 HT C10 C Y N 202 HT C11 C Y N 203 HT C12 C Y N 204 HT C13 C Y N 205 HT C14 C Y N 206 HT N3 N Y N 207 HT C15 C Y N 208 HT C16 C Y N 209 HT N4 N Y N 210 HT C17 C Y N 211 HT C18 C Y N 212 HT C19 C Y N 213 HT C20 C Y N 214 HT N5 N N N 215 HT C21 C N N 216 HT C22 C N N 217 HT N6 N N N 218 HT C23 C N N 219 HT C24 C N N 220 HT C25 C N N 221 HT HO1 H N N 222 HT H2 H N N 223 HT H3 H N N 224 HT H5 H N N 225 HT H6 H N N 226 HT HN1 H N N 227 HT H10 H N N 228 HT H11 H N N 229 HT H13 H N N 230 HT HN3 H N N 231 HT H17 H N N 232 HT H18 H N N 233 HT H20 H N N 234 HT H211 H N N 235 HT H212 H N N 236 HT H221 H N N 237 HT H222 H N N 238 HT H231 H N N 239 HT H232 H N N 240 HT H241 H N N 241 HT H242 H N N 242 HT H253 H N N 243 HT H252 H N N 244 HT H251 H N N 245 MG MG MG N N 246 # 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 C6G OP1 P doub N N 1 C6G P OP2 sing N N 2 C6G P "O5'" sing N N 3 C6G O C doub N N 4 C6G C O7 sing N N 5 C6G C CH3 sing N N 6 C6G "O5'" "C5'" sing N N 7 C6G "C5'" "C4'" sing N N 8 C6G N7 C8 doub Y N 9 C6G N7 C5 sing Y N 10 C6G C8 N9 sing Y N 11 C6G O6 CH3 sing N N 12 C6G O6 C6 sing N N 13 C6G "C2'" "C3'" sing N N 14 C6G "C2'" "C1'" sing N N 15 C6G C5 C6 doub Y N 16 C6G C5 C4 sing Y N 17 C6G C6 N1 sing Y N 18 C6G N9 C4 sing Y N 19 C6G N9 "C1'" sing N N 20 C6G "C3'" "C4'" sing N N 21 C6G "C3'" "O3'" sing N N 22 C6G C4 N3 doub Y N 23 C6G "C4'" "O4'" sing N N 24 C6G N1 C2 doub Y N 25 C6G "C1'" "O4'" sing N N 26 C6G N3 C2 sing Y N 27 C6G C2 N2 sing N N 28 C6G OP2 HOP2 sing N N 29 C6G "C5'" "H5'" sing N N 30 C6G "C5'" "H5''" sing N N 31 C6G "C4'" "H4'" sing N N 32 C6G "C1'" "H1'" sing N N 33 C6G C8 H8 sing N N 34 C6G N2 H21 sing N N 35 C6G N2 H22 sing N N 36 C6G "C2'" "H2'" sing N N 37 C6G "C2'" "H2''" sing N N 38 C6G "C3'" "H3'" sing N N 39 C6G "O3'" "HO3'" sing N N 40 C6G O7 HO7 sing N N 41 C6G CH3 H31 sing N N 42 C6G CH3 H32 sing N N 43 C6G P OP3 sing N N 44 C6G OP3 HOP3 sing N N 45 DA OP3 P sing N N 46 DA OP3 HOP3 sing N N 47 DA P OP1 doub N N 48 DA P OP2 sing N N 49 DA P "O5'" sing N N 50 DA OP2 HOP2 sing N N 51 DA "O5'" "C5'" sing N N 52 DA "C5'" "C4'" sing N N 53 DA "C5'" "H5'" sing N N 54 DA "C5'" "H5''" sing N N 55 DA "C4'" "O4'" sing N N 56 DA "C4'" "C3'" sing N N 57 DA "C4'" "H4'" sing N N 58 DA "O4'" "C1'" sing N N 59 DA "C3'" "O3'" sing N N 60 DA "C3'" "C2'" sing N N 61 DA "C3'" "H3'" sing N N 62 DA "O3'" "HO3'" sing N N 63 DA "C2'" "C1'" sing N N 64 DA "C2'" "H2'" sing N N 65 DA "C2'" "H2''" sing N N 66 DA "C1'" N9 sing N N 67 DA "C1'" "H1'" sing N N 68 DA N9 C8 sing Y N 69 DA N9 C4 sing Y N 70 DA C8 N7 doub Y N 71 DA C8 H8 sing N N 72 DA N7 C5 sing Y N 73 DA C5 C6 sing Y N 74 DA C5 C4 doub Y N 75 DA C6 N6 sing N N 76 DA C6 N1 doub Y N 77 DA N6 H61 sing N N 78 DA N6 H62 sing N N 79 DA N1 C2 sing Y N 80 DA C2 N3 doub Y N 81 DA C2 H2 sing N N 82 DA N3 C4 sing Y N 83 DC OP3 P sing N N 84 DC OP3 HOP3 sing N N 85 DC P OP1 doub N N 86 DC P OP2 sing N N 87 DC P "O5'" sing N N 88 DC OP2 HOP2 sing N N 89 DC "O5'" "C5'" sing N N 90 DC "C5'" "C4'" sing N N 91 DC "C5'" "H5'" sing N N 92 DC "C5'" "H5''" sing N N 93 DC "C4'" "O4'" sing N N 94 DC "C4'" "C3'" sing N N 95 DC "C4'" "H4'" sing N N 96 DC "O4'" "C1'" sing N N 97 DC "C3'" "O3'" sing N N 98 DC "C3'" "C2'" sing N N 99 DC "C3'" "H3'" sing N N 100 DC "O3'" "HO3'" sing N N 101 DC "C2'" "C1'" sing N N 102 DC "C2'" "H2'" sing N N 103 DC "C2'" "H2''" sing N N 104 DC "C1'" N1 sing N N 105 DC "C1'" "H1'" sing N N 106 DC N1 C2 sing N N 107 DC N1 C6 sing N N 108 DC C2 O2 doub N N 109 DC C2 N3 sing N N 110 DC N3 C4 doub N N 111 DC C4 N4 sing N N 112 DC C4 C5 sing N N 113 DC N4 H41 sing N N 114 DC N4 H42 sing N N 115 DC C5 C6 doub N N 116 DC C5 H5 sing N N 117 DC C6 H6 sing N N 118 DG OP3 P sing N N 119 DG OP3 HOP3 sing N N 120 DG P OP1 doub N N 121 DG P OP2 sing N N 122 DG P "O5'" sing N N 123 DG OP2 HOP2 sing N N 124 DG "O5'" "C5'" sing N N 125 DG "C5'" "C4'" sing N N 126 DG "C5'" "H5'" sing N N 127 DG "C5'" "H5''" sing N N 128 DG "C4'" "O4'" sing N N 129 DG "C4'" "C3'" sing N N 130 DG "C4'" "H4'" sing N N 131 DG "O4'" "C1'" sing N N 132 DG "C3'" "O3'" sing N N 133 DG "C3'" "C2'" sing N N 134 DG "C3'" "H3'" sing N N 135 DG "O3'" "HO3'" sing N N 136 DG "C2'" "C1'" sing N N 137 DG "C2'" "H2'" sing N N 138 DG "C2'" "H2''" sing N N 139 DG "C1'" N9 sing N N 140 DG "C1'" "H1'" sing N N 141 DG N9 C8 sing Y N 142 DG N9 C4 sing Y N 143 DG C8 N7 doub Y N 144 DG C8 H8 sing N N 145 DG N7 C5 sing Y N 146 DG C5 C6 sing N N 147 DG C5 C4 doub Y N 148 DG C6 O6 doub N N 149 DG C6 N1 sing N N 150 DG N1 C2 sing N N 151 DG N1 H1 sing N N 152 DG C2 N2 sing N N 153 DG C2 N3 doub N N 154 DG N2 H21 sing N N 155 DG N2 H22 sing N N 156 DG N3 C4 sing N N 157 DT OP3 P sing N N 158 DT OP3 HOP3 sing N N 159 DT P OP1 doub N N 160 DT P OP2 sing N N 161 DT P "O5'" sing N N 162 DT OP2 HOP2 sing N N 163 DT "O5'" "C5'" sing N N 164 DT "C5'" "C4'" sing N N 165 DT "C5'" "H5'" sing N N 166 DT "C5'" "H5''" sing N N 167 DT "C4'" "O4'" sing N N 168 DT "C4'" "C3'" sing N N 169 DT "C4'" "H4'" sing N N 170 DT "O4'" "C1'" sing N N 171 DT "C3'" "O3'" sing N N 172 DT "C3'" "C2'" sing N N 173 DT "C3'" "H3'" sing N N 174 DT "O3'" "HO3'" sing N N 175 DT "C2'" "C1'" sing N N 176 DT "C2'" "H2'" sing N N 177 DT "C2'" "H2''" sing N N 178 DT "C1'" N1 sing N N 179 DT "C1'" "H1'" sing N N 180 DT N1 C2 sing N N 181 DT N1 C6 sing N N 182 DT C2 O2 doub N N 183 DT C2 N3 sing N N 184 DT N3 C4 sing N N 185 DT N3 H3 sing N N 186 DT C4 O4 doub N N 187 DT C4 C5 sing N N 188 DT C5 C7 sing N N 189 DT C5 C6 doub N N 190 DT C7 H71 sing N N 191 DT C7 H72 sing N N 192 DT C7 H73 sing N N 193 DT C6 H6 sing N N 194 HOH O H1 sing N N 195 HOH O H2 sing N N 196 HT O1 C1 sing N N 197 HT O1 HO1 sing N N 198 HT C1 C2 doub Y N 199 HT C1 C6 sing Y N 200 HT C2 C3 sing Y N 201 HT C2 H2 sing N N 202 HT C3 C4 doub Y N 203 HT C3 H3 sing N N 204 HT C4 C5 sing Y N 205 HT C4 C7 sing Y N 206 HT C5 C6 doub Y N 207 HT C5 H5 sing N N 208 HT C6 H6 sing N N 209 HT C7 N1 sing Y N 210 HT C7 N2 doub Y N 211 HT N1 C8 sing Y N 212 HT N1 HN1 sing N N 213 HT C8 C9 doub Y N 214 HT C8 C13 sing Y N 215 HT C9 N2 sing Y N 216 HT C9 C10 sing Y N 217 HT C10 C11 doub Y N 218 HT C10 H10 sing N N 219 HT C11 C12 sing Y N 220 HT C11 H11 sing N N 221 HT C12 C13 doub Y N 222 HT C12 C14 sing Y N 223 HT C13 H13 sing N N 224 HT C14 N3 sing Y N 225 HT C14 N4 doub Y N 226 HT N3 C15 sing Y N 227 HT N3 HN3 sing N N 228 HT C15 C16 doub Y N 229 HT C15 C20 sing Y N 230 HT C16 N4 sing Y N 231 HT C16 C17 sing Y N 232 HT C17 C18 doub Y N 233 HT C17 H17 sing N N 234 HT C18 C19 sing Y N 235 HT C18 H18 sing N N 236 HT C19 C20 doub Y N 237 HT C19 N5 sing N N 238 HT C20 H20 sing N N 239 HT N5 C21 sing N N 240 HT N5 C24 sing N N 241 HT C21 C22 sing N N 242 HT C21 H211 sing N N 243 HT C21 H212 sing N N 244 HT C22 N6 sing N N 245 HT C22 H221 sing N N 246 HT C22 H222 sing N N 247 HT N6 C23 sing N N 248 HT N6 C25 sing N N 249 HT C23 C24 sing N N 250 HT C23 H231 sing N N 251 HT C23 H232 sing N N 252 HT C24 H241 sing N N 253 HT C24 H242 sing N N 254 HT C25 H253 sing N N 255 HT C25 H252 sing N N 256 HT C25 H251 sing N N 257 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4ITD 'double helix' 4ITD 'b-form double helix' 4ITD '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 -0.228 -0.170 -0.158 1.721 -11.640 0.688 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.172 0.053 0.344 2.142 -17.014 7.510 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.166 -0.059 0.107 -6.016 -4.479 -4.230 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 0.162 0.005 0.314 15.545 -9.213 0.429 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 6 1_555 B DT 7 1_555 -0.149 0.244 0.282 -0.777 -22.353 2.882 5 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.539 0.080 0.082 -2.033 -27.311 8.754 6 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 -0.195 0.113 0.440 -23.750 -1.637 -0.504 7 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 0.318 0.031 0.091 6.405 2.224 2.149 8 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.439 -0.068 -0.155 11.341 -24.140 0.068 9 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.166 0.081 0.074 5.046 5.069 -1.963 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 -0.119 0.482 3.379 -5.507 6.960 35.263 -0.249 -0.617 3.390 11.270 8.918 36.328 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 0.468 0.796 3.625 3.470 -6.102 42.397 1.751 -0.261 3.509 -8.368 -4.758 42.948 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 DG 4 1_555 B DC 9 1_555 0.054 0.792 2.960 -0.602 6.583 24.845 0.046 -0.280 3.062 14.966 1.369 25.696 3 AA_DC3DG4:DC21DG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 6 1_555 B DT 7 1_555 -0.170 0.061 6.921 -1.389 0.445 78.892 0.022 0.054 6.923 0.350 1.093 78.904 4 AA_DG4DA6:DT19DC21_BB A 4 ? B 21 ? 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 0.253 -0.519 3.215 2.065 -0.922 27.879 -0.858 -0.040 3.240 -1.909 -4.278 27.968 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 DC 9 1_555 B DG 4 1_555 -0.035 -0.219 7.209 0.125 1.525 79.549 -0.261 0.035 7.205 1.192 -0.098 79.561 6 AA_DT7DC9:DG16DA18_BB A 7 ? B 18 ? A 9 ? B 16 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 0.070 0.916 2.775 -1.176 2.963 26.845 1.309 -0.408 2.852 6.354 2.523 27.030 7 AA_DC9DG10:DC15DG16_BB A 9 ? B 16 ? 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 -1.080 0.871 3.195 1.193 -7.462 40.303 2.018 1.667 2.963 -10.716 -1.713 40.977 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 0.887 0.616 3.656 -0.943 -5.517 36.146 1.819 -1.557 3.504 -8.826 1.509 36.562 9 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _atom_sites.entry_id 4ITD _atom_sites.fract_transf_matrix[1][1] 0.039919 _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] 0.024750 _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] 0.015228 _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_