data_1NGT # _entry.id 1NGT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1NGT pdb_00001ngt 10.2210/pdb1ngt/pdb NDB BD0062 ? ? RCSB RCSB017854 ? ? WWPDB D_1000017854 ? ? # 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 2003-03-04 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-11 5 'Structure model' 1 4 2018-03-07 6 'Structure model' 1 5 2024-02-14 # _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' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 6 'Structure model' 'Data collection' 6 6 'Structure model' 'Database references' 7 6 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' software 2 5 'Structure model' diffrn_source 3 6 'Structure model' chem_comp_atom 4 6 'Structure model' chem_comp_bond 5 6 'Structure model' database_2 6 6 'Structure model' pdbx_struct_conn_angle 7 6 'Structure model' struct_conn 8 6 'Structure model' struct_conn_type 9 6 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_diffrn_source.source' 2 6 'Structure model' '_database_2.pdbx_DOI' 3 6 'Structure model' '_database_2.pdbx_database_accession' 4 6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 5 6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 6 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 8 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 9 6 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 10 6 'Structure model' '_pdbx_struct_conn_angle.value' 11 6 'Structure model' '_struct_conn.conn_type_id' 12 6 'Structure model' '_struct_conn.id' 13 6 'Structure model' '_struct_conn.pdbx_dist_value' 14 6 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 15 6 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 16 6 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 17 6 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 18 6 'Structure model' '_struct_conn.ptnr1_label_asym_id' 19 6 'Structure model' '_struct_conn.ptnr1_label_atom_id' 20 6 'Structure model' '_struct_conn.ptnr1_label_comp_id' 21 6 'Structure model' '_struct_conn.ptnr1_label_seq_id' 22 6 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 23 6 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 24 6 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 25 6 'Structure model' '_struct_conn.ptnr2_label_asym_id' 26 6 'Structure model' '_struct_conn.ptnr2_label_atom_id' 27 6 'Structure model' '_struct_conn.ptnr2_label_comp_id' 28 6 'Structure model' '_struct_conn.ptnr2_label_seq_id' 29 6 'Structure model' '_struct_conn_type.id' 30 6 'Structure model' '_struct_site.pdbx_auth_asym_id' 31 6 'Structure model' '_struct_site.pdbx_auth_comp_id' 32 6 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1NGT _pdbx_database_status.recvd_initial_deposition_date 2002-12-17 _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Woods, K.K.' 1 'Lan, T.' 2 'McLaughlin, L.W.' 3 'Williams, L.D.' 4 # _citation.id primary _citation.title 'The Role of Minor Groove Functional Groups in DNA Hydration' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 31 _citation.page_first 1536 _citation.page_last 1540 _citation.year 2003 _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 12595562 _citation.pdbx_database_id_DOI 10.1093/nar/gkg240 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Woods, K.K.' 1 ? primary 'Lan, T.' 2 ? primary 'McLaughlin, L.W.' 3 ? primary 'Williams, L.D.' 4 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*CP*GP*CP*GP*AP*AP*(MTR)P*TP*CP*GP*CP*G)-3'" 3646.405 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 water nat water 18.015 82 ? ? ? ? # _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)(DA)(DA)(MTR)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTCGCG _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 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 DA n 1 6 DA n 1 7 MTR 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 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 MTR 'DNA linking' n '(5-METHYL-6-OXO-1,6-DIHYDRO-PYRIDIN-3-YL)-1,2-DIDEOXY-RIBOFURANOSE-5-MONOPHOSPHATE' ? 'C11 H16 N O7 P' 305.221 # 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 DG 4 4 4 DG G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 MTR 7 7 7 MTR D A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 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 DG 4 16 16 DG G B . n B 1 5 DA 5 17 17 DA A B . n B 1 6 DA 6 18 18 DA A B . n B 1 7 MTR 7 19 19 MTR D B . n B 1 8 DT 8 20 20 DT T B . n B 1 9 DC 9 21 21 DC C B . n B 1 10 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 25 25 MG ION A . D 3 HOH 1 26 26 HOH HOH A . D 3 HOH 2 27 27 HOH HOH A . D 3 HOH 3 28 28 HOH HOH A . D 3 HOH 4 30 30 HOH HOH A . D 3 HOH 5 31 31 HOH HOH A . D 3 HOH 6 32 32 HOH HOH A . D 3 HOH 7 33 33 HOH HOH A . D 3 HOH 8 35 35 HOH HOH A . D 3 HOH 9 36 36 HOH HOH A . D 3 HOH 10 37 37 HOH HOH A . D 3 HOH 11 38 38 HOH HOH A . D 3 HOH 12 40 40 HOH HOH A . D 3 HOH 13 47 47 HOH HOH A . D 3 HOH 14 49 49 HOH HOH A . D 3 HOH 15 50 50 HOH HOH A . D 3 HOH 16 52 52 HOH HOH A . D 3 HOH 17 55 55 HOH HOH A . D 3 HOH 18 59 59 HOH HOH A . D 3 HOH 19 60 60 HOH HOH A . D 3 HOH 20 61 61 HOH HOH A . D 3 HOH 21 62 62 HOH HOH A . D 3 HOH 22 63 63 HOH HOH A . D 3 HOH 23 64 64 HOH HOH A . D 3 HOH 24 65 65 HOH HOH A . D 3 HOH 25 75 75 HOH HOH A . D 3 HOH 26 76 76 HOH HOH A . D 3 HOH 27 116 116 HOH HOH A . D 3 HOH 28 120 120 HOH HOH A . D 3 HOH 29 121 121 HOH HOH A . D 3 HOH 30 125 125 HOH HOH A . D 3 HOH 31 133 133 HOH HOH A . D 3 HOH 32 135 135 HOH HOH A . D 3 HOH 33 137 137 HOH HOH A . D 3 HOH 34 138 138 HOH HOH A . D 3 HOH 35 142 142 HOH HOH A . D 3 HOH 36 144 144 HOH HOH A . D 3 HOH 37 147 147 HOH HOH A . D 3 HOH 38 149 149 HOH HOH A . D 3 HOH 39 152 152 HOH HOH A . D 3 HOH 40 153 153 HOH HOH A . D 3 HOH 41 157 157 HOH HOH A . D 3 HOH 42 171 171 HOH HOH A . D 3 HOH 43 182 182 HOH HOH A . D 3 HOH 44 184 25 HOH ION A . D 3 HOH 45 185 25 HOH ION A . D 3 HOH 46 186 25 HOH ION A . D 3 HOH 47 187 25 HOH ION A . D 3 HOH 48 188 25 HOH ION A . E 3 HOH 1 29 29 HOH HOH B . E 3 HOH 2 34 34 HOH HOH B . E 3 HOH 3 41 41 HOH HOH B . E 3 HOH 4 42 42 HOH HOH B . E 3 HOH 5 43 43 HOH HOH B . E 3 HOH 6 46 46 HOH HOH B . E 3 HOH 7 48 48 HOH HOH B . E 3 HOH 8 53 53 HOH HOH B . E 3 HOH 9 54 54 HOH HOH B . E 3 HOH 10 56 56 HOH HOH B . E 3 HOH 11 68 68 HOH HOH B . E 3 HOH 12 79 79 HOH HOH B . E 3 HOH 13 87 87 HOH HOH B . E 3 HOH 14 88 88 HOH HOH B . E 3 HOH 15 89 89 HOH HOH B . E 3 HOH 16 98 98 HOH HOH B . E 3 HOH 17 99 99 HOH HOH B . E 3 HOH 18 106 106 HOH HOH B . E 3 HOH 19 108 108 HOH HOH B . E 3 HOH 20 109 109 HOH HOH B . E 3 HOH 21 110 110 HOH HOH B . E 3 HOH 22 122 122 HOH HOH B . E 3 HOH 23 123 123 HOH HOH B . E 3 HOH 24 126 126 HOH HOH B . E 3 HOH 25 136 136 HOH HOH B . E 3 HOH 26 141 141 HOH HOH B . E 3 HOH 27 148 148 HOH HOH B . E 3 HOH 28 150 150 HOH HOH B . E 3 HOH 29 160 160 HOH HOH B . E 3 HOH 30 161 161 HOH HOH B . E 3 HOH 31 162 162 HOH HOH B . E 3 HOH 32 169 169 HOH HOH B . E 3 HOH 33 181 181 HOH HOH B . E 3 HOH 34 183 25 HOH ION B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SAINT 'data reduction' . ? 1 CNS refinement . ? 2 SAINT 'data scaling' . ? 3 CNS phasing . ? 4 # _cell.entry_id 1NGT _cell.length_a 25.170 _cell.length_b 41.050 _cell.length_c 65.720 _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 1NGT _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # _exptl.entry_id 1NGT _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.23 _exptl_crystal.density_percent_sol 44.84 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 295 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details 'sodium cacodylate, MPD, magnesium chloride, spermine tetrahydrochloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K' _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 'sodium cacodylate' ? ? ? 1 2 1 MPD ? ? ? 1 3 1 'magnesium chloride' ? ? ? 1 4 1 'spermine tetrahydrochloride' ? ? ? 1 5 2 'sodium cacodylate' ? ? ? 1 6 2 MPD ? ? ? 1 7 2 'magnesium chloride' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 163 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type SIEMENS _diffrn_detector.pdbx_collection_date 2000-01-01 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 0.7107 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.7107 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type SIEMENS _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.7107 # _reflns.entry_id 1NGT _reflns.observed_criterion_sigma_F 3.00 _reflns.observed_criterion_sigma_I 0.00 _reflns.d_resolution_high 2.04 _reflns.d_resolution_low 10 _reflns.number_all 4927 _reflns.number_obs 4393 _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.04 _reflns_shell.d_res_low 2.11 _reflns_shell.percent_possible_all 74 _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.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1NGT _refine.ls_d_res_high 2.04 _refine.ls_d_res_low 10 _refine.pdbx_ls_sigma_F 3.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 4393 _refine.ls_number_reflns_obs 4393 _refine.ls_number_reflns_R_free ? _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_all 0.223 _refine.ls_R_factor_obs 0.223 _refine.ls_R_factor_R_work 0.207 _refine.ls_R_factor_R_free 0.281 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free 10 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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_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 7 _refine_hist.number_atoms_solvent 76 _refine_hist.number_atoms_total 567 _refine_hist.d_res_high 2.04 _refine_hist.d_res_low 10 # 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 0.0086 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.22460 ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1NGT _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1NGT _struct.title 'The Role of Minor Groove Functional Groups in DNA Hydration' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1NGT _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'spine of hydration, DNA conformation, modified base, 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_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1NGT _struct_ref.pdbx_db_accession 1NGT _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 1NGT A 1 ? 12 ? 1NGT 1 ? 12 ? 1 12 2 1 1NGT B 1 ? 12 ? 1NGT 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,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 # _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 DA 6 "O3'" ? ? ? 1_555 A MTR 7 P ? ? A DA 6 A MTR 7 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale2 covale both ? A MTR 7 "O3'" ? ? ? 1_555 A DT 8 P ? ? A MTR 7 A DT 8 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale3 covale both ? B DA 6 "O3'" ? ? ? 1_555 B MTR 7 P ? ? B DA 18 B MTR 19 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale4 covale both ? B MTR 7 "O3'" ? ? ? 1_555 B DT 8 P ? ? B MTR 19 B DT 20 1_555 ? ? ? ? ? ? ? 1.601 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 25 A HOH 184 1_555 ? ? ? ? ? ? ? 2.038 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 25 A HOH 185 1_555 ? ? ? ? ? ? ? 1.998 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 25 A HOH 186 1_555 ? ? ? ? ? ? ? 1.964 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 25 A HOH 187 1_555 ? ? ? ? ? ? ? 2.091 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 25 A HOH 188 1_555 ? ? ? ? ? ? ? 1.988 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 25 B HOH 183 1_555 ? ? ? ? ? ? ? 1.984 ? ? 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 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B MTR 7 N3 ? ? A DA 6 B MTR 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B MTR 7 O4 ? ? A DA 6 B MTR 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A MTR 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A MTR 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A MTR 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A MTR 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 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 ? D HOH . ? A HOH 184 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? D HOH . ? A HOH 185 ? 1_555 92.6 ? 2 O ? D HOH . ? A HOH 184 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? D HOH . ? A HOH 186 ? 1_555 175.4 ? 3 O ? D HOH . ? A HOH 185 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? D HOH . ? A HOH 186 ? 1_555 83.8 ? 4 O ? D HOH . ? A HOH 184 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? D HOH . ? A HOH 187 ? 1_555 86.3 ? 5 O ? D HOH . ? A HOH 185 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? D HOH . ? A HOH 187 ? 1_555 77.1 ? 6 O ? D HOH . ? A HOH 186 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? D HOH . ? A HOH 187 ? 1_555 90.1 ? 7 O ? D HOH . ? A HOH 184 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? D HOH . ? A HOH 188 ? 1_555 96.0 ? 8 O ? D HOH . ? A HOH 185 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? D HOH . ? A HOH 188 ? 1_555 95.4 ? 9 O ? D HOH . ? A HOH 186 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? D HOH . ? A HOH 188 ? 1_555 87.1 ? 10 O ? D HOH . ? A HOH 187 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? D HOH . ? A HOH 188 ? 1_555 172.3 ? 11 O ? D HOH . ? A HOH 184 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? B HOH 183 ? 1_555 94.4 ? 12 O ? D HOH . ? A HOH 185 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? B HOH 183 ? 1_555 168.2 ? 13 O ? D HOH . ? A HOH 186 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? B HOH 183 ? 1_555 88.7 ? 14 O ? D HOH . ? A HOH 187 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? B HOH 183 ? 1_555 93.8 ? 15 O ? D HOH . ? A HOH 188 ? 1_555 MG ? C MG . ? A MG 25 ? 1_555 O ? E HOH . ? B HOH 183 ? 1_555 93.3 ? # _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 25 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE MG A 25' # 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 184 . ? 1_555 ? 2 AC1 6 HOH D . ? HOH A 185 . ? 1_555 ? 3 AC1 6 HOH D . ? HOH A 186 . ? 1_555 ? 4 AC1 6 HOH D . ? HOH A 187 . ? 1_555 ? 5 AC1 6 HOH D . ? HOH A 188 . ? 1_555 ? 6 AC1 6 HOH E . ? HOH B 183 . ? 1_555 ? # 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 MTR 7 A MTR 7 ? DT ? 2 B MTR 7 B MTR 19 ? DT ? # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 MG MG MG N N 147 MTR P P N N 148 MTR OP1 O N N 149 MTR OP2 O N N 150 MTR "O5'" O N N 151 MTR C1 C N N 152 MTR C6 C N N 153 MTR C2 C N N 154 MTR N3 N N N 155 MTR C4 C N N 156 MTR O4 O N N 157 MTR C5 C N N 158 MTR C5M C N N 159 MTR "C2'" C N N 160 MTR "C5'" C N N 161 MTR "C4'" C N R 162 MTR "O4'" O N N 163 MTR "C1'" C N R 164 MTR "C3'" C N S 165 MTR "O3'" O N N 166 MTR OP3 O N N 167 MTR HOP2 H N N 168 MTR H6 H N N 169 MTR H2 H N N 170 MTR H3 H N N 171 MTR H71 H N N 172 MTR H72 H N N 173 MTR H73 H N N 174 MTR "H2'" H N N 175 MTR "H2''" H N N 176 MTR "H5'" H N N 177 MTR "H5''" H N N 178 MTR "H4'" H N N 179 MTR "H1'" H N N 180 MTR "H3'" H N N 181 MTR "HO3'" H N N 182 MTR HOP3 H N N 183 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 MTR P OP1 doub N N 152 MTR P OP2 sing N N 153 MTR P "O5'" sing N N 154 MTR P OP3 sing N N 155 MTR OP2 HOP2 sing N N 156 MTR "O5'" "C5'" sing N N 157 MTR C1 C6 sing N N 158 MTR C1 C2 doub N N 159 MTR C1 "C1'" sing N N 160 MTR C6 C5 doub N N 161 MTR C6 H6 sing N N 162 MTR C2 N3 sing N N 163 MTR C2 H2 sing N N 164 MTR N3 C4 sing N N 165 MTR N3 H3 sing N N 166 MTR C4 O4 doub N N 167 MTR C4 C5 sing N N 168 MTR C5 C5M sing N N 169 MTR C5M H71 sing N N 170 MTR C5M H72 sing N N 171 MTR C5M H73 sing N N 172 MTR "C2'" "C1'" sing N N 173 MTR "C2'" "C3'" sing N N 174 MTR "C2'" "H2'" sing N N 175 MTR "C2'" "H2''" sing N N 176 MTR "C5'" "C4'" sing N N 177 MTR "C5'" "H5'" sing N N 178 MTR "C5'" "H5''" sing N N 179 MTR "C4'" "O4'" sing N N 180 MTR "C4'" "C3'" sing N N 181 MTR "C4'" "H4'" sing N N 182 MTR "O4'" "C1'" sing N N 183 MTR "C1'" "H1'" sing N N 184 MTR "C3'" "O3'" sing N N 185 MTR "C3'" "H3'" sing N N 186 MTR "O3'" "HO3'" sing N N 187 MTR OP3 HOP3 sing N N 188 # _ndb_struct_conf_na.entry_id 1NGT _ndb_struct_conf_na.feature 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 12 1_555 0.052 0.043 0.006 3.669 -13.308 -0.841 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.047 -0.062 0.163 -0.799 -8.433 -5.369 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 0.239 0.058 -0.018 -5.067 -2.365 -1.732 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.702 -0.310 -0.214 5.229 -1.812 -3.468 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 -0.087 -0.094 0.213 14.901 -9.807 9.169 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B MTR 7 1_555 0.130 0.218 0.166 3.900 -19.679 2.258 6 A_DA6:MTR19_B A 6 ? B 19 ? 20 1 1 A MTR 7 1_555 B DA 6 1_555 -0.246 0.088 0.075 -0.714 -15.184 -0.106 7 A_MTR7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 0.201 -0.283 0.158 -4.183 -14.678 3.245 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.275 0.030 0.241 -18.581 -8.401 -1.600 9 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.053 -0.167 0.057 -2.969 -1.431 0.374 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.111 -0.001 0.388 -2.454 -18.464 -2.015 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.047 -0.295 0.364 8.055 0.413 -6.147 12 A_DG12:DC13_B A 12 ? B 13 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 12 1_555 A DG 2 1_555 B DC 11 1_555 -0.127 0.294 3.360 -0.527 8.170 37.144 -0.629 0.126 3.349 12.638 0.815 38.004 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 0.711 0.494 3.375 1.989 -1.437 38.538 0.930 -0.822 3.387 -2.175 -3.010 38.613 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 -0.186 0.988 3.136 4.034 4.577 29.407 0.987 1.171 3.196 8.896 -7.841 30.019 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 5 1_555 B DT 8 1_555 0.555 0.279 3.045 -3.534 9.915 29.585 -1.232 -1.651 2.901 18.687 6.661 31.362 4 AA_DG4DA5:DT20DC21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B MTR 7 1_555 -0.906 0.325 3.501 -1.675 -3.990 43.040 0.859 1.054 3.490 -5.422 2.276 43.247 5 AA_DA5DA6:MTR19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B MTR 7 1_555 A MTR 7 1_555 B DA 6 1_555 0.314 -0.719 3.316 0.866 0.078 29.151 -1.444 -0.431 3.322 0.156 -1.721 29.163 6 AA_DA6MTR7:DA18MTR19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A MTR 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.054 -0.498 3.290 0.536 1.345 36.143 -0.993 0.162 3.269 2.166 -0.864 36.171 7 AA_MTR7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DC 9 1_555 B DG 4 1_555 -0.367 -0.254 3.547 0.450 -3.702 41.369 0.070 0.569 3.551 -5.227 -0.635 41.530 8 AA_DT8DC9:DG16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 0.767 0.759 3.033 -0.500 2.306 29.298 1.033 -1.611 3.069 4.551 0.987 29.391 9 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 -1.206 0.509 3.380 -3.493 -8.314 39.693 1.687 1.334 3.302 -12.056 5.065 40.664 10 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 -0.031 0.267 3.013 -0.475 4.732 36.383 -0.176 -0.010 3.023 7.539 0.757 36.682 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _atom_sites.entry_id 1NGT _atom_sites.fract_transf_matrix[1][1] 0.039730 _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] 0.024361 _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] 0.015216 _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_