data_1NZG # _entry.id 1NZG # _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 1NZG pdb_00001nzg 10.2210/pdb1nzg/pdb NDB AD0029 ? ? RCSB RCSB018385 ? ? WWPDB D_1000018385 ? ? # 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 2003-08-26 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-11-02 5 'Structure model' 1 4 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' 'Non-polymer description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_struct_conn.pdbx_dist_value' 4 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 6 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 7 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 8 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 9 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 10 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 11 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 12 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 13 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 14 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 15 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 16 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1NZG _pdbx_database_status.recvd_initial_deposition_date 2003-02-17 _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.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Prhavc, M.' 1 'Prakash, T.P.' 2 'Minasov, G.' 3 'Egli, M.' 4 'Manoharan, M.' 5 # _citation.id primary _citation.title ;2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] modified oligonucleotides: symbiosis of charge interaction factors and stereoelectronic effects ; _citation.journal_abbrev Org.Lett. _citation.journal_volume 5 _citation.page_first 2017 _citation.page_last 2020 _citation.year 2003 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1523-7060 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12790517 _citation.pdbx_database_id_DOI 10.1021/ol0340991 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Prhavc, M.' 1 ? primary 'Prakash, T.P.' 2 ? primary 'Minasov, G.' 3 ? primary 'Cook, P.D.' 4 ? primary 'Egli, M.' 5 ? primary 'Manoharan, M.' 6 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*GP*CP*GP*TP*AP*(3ME)P*AP*CP*GP*C)-3'" 3176.178 2 ? ? ? ? 2 water nat water 18.015 101 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DC)(DG)(DT)(DA)(3ME)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTAUACGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 3ME n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 3ME 'RNA linking' n ;2'-O-{2-[2-(dimethylamino)ethoxy]ethyl}-5-methyluridine 5'-(dihydrogen phosphate) ; ? 'C16 H28 N3 O10 P' 453.381 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 3ME 6 6 6 3ME 3ME A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DC 10 10 10 DC C A . n B 1 1 DG 1 11 11 DG G B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DG 3 13 13 DG G B . n B 1 4 DT 4 14 14 DT T B . n B 1 5 DA 5 15 15 DA A B . n B 1 6 3ME 6 16 16 3ME 3ME B . n B 1 7 DA 7 17 17 DA A B . n B 1 8 DC 8 18 18 DC C B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DC 10 20 20 DC C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 101 101 HOH HOH A . C 2 HOH 2 102 102 HOH HOH A . C 2 HOH 3 104 104 HOH HOH A . C 2 HOH 4 106 106 HOH HOH A . C 2 HOH 5 108 108 HOH HOH A . C 2 HOH 6 109 109 HOH HOH A . C 2 HOH 7 111 111 HOH HOH A . C 2 HOH 8 112 112 HOH HOH A . C 2 HOH 9 113 113 HOH HOH A . C 2 HOH 10 114 114 HOH HOH A . C 2 HOH 11 115 115 HOH HOH A . C 2 HOH 12 116 116 HOH HOH A . C 2 HOH 13 118 118 HOH HOH A . C 2 HOH 14 119 119 HOH HOH A . C 2 HOH 15 120 120 HOH HOH A . C 2 HOH 16 121 121 HOH HOH A . C 2 HOH 17 123 123 HOH HOH A . C 2 HOH 18 126 126 HOH HOH A . C 2 HOH 19 127 127 HOH HOH A . C 2 HOH 20 128 128 HOH HOH A . C 2 HOH 21 131 131 HOH HOH A . C 2 HOH 22 133 133 HOH HOH A . C 2 HOH 23 134 134 HOH HOH A . C 2 HOH 24 135 135 HOH HOH A . C 2 HOH 25 136 136 HOH HOH A . C 2 HOH 26 138 138 HOH HOH A . C 2 HOH 27 142 142 HOH HOH A . C 2 HOH 28 143 143 HOH HOH A . C 2 HOH 29 144 144 HOH HOH A . C 2 HOH 30 145 145 HOH HOH A . C 2 HOH 31 148 148 HOH HOH A . C 2 HOH 32 149 149 HOH HOH A . C 2 HOH 33 150 150 HOH HOH A . C 2 HOH 34 151 151 HOH HOH A . C 2 HOH 35 152 152 HOH HOH A . C 2 HOH 36 153 153 HOH HOH A . C 2 HOH 37 154 154 HOH HOH A . C 2 HOH 38 159 159 HOH HOH A . C 2 HOH 39 160 160 HOH HOH A . C 2 HOH 40 161 161 HOH HOH A . C 2 HOH 41 163 163 HOH HOH A . C 2 HOH 42 164 164 HOH HOH A . C 2 HOH 43 165 165 HOH HOH A . C 2 HOH 44 166 166 HOH HOH A . C 2 HOH 45 167 167 HOH HOH A . C 2 HOH 46 168 168 HOH HOH A . C 2 HOH 47 169 169 HOH HOH A . C 2 HOH 48 173 173 HOH HOH A . C 2 HOH 49 175 175 HOH HOH A . C 2 HOH 50 177 177 HOH HOH A . C 2 HOH 51 178 178 HOH HOH A . C 2 HOH 52 180 180 HOH HOH A . C 2 HOH 53 184 184 HOH HOH A . C 2 HOH 54 186 186 HOH HOH A . C 2 HOH 55 187 187 HOH HOH A . C 2 HOH 56 191 191 HOH HOH A . C 2 HOH 57 195 195 HOH HOH A . C 2 HOH 58 196 196 HOH HOH A . C 2 HOH 59 197 197 HOH HOH A . C 2 HOH 60 199 199 HOH HOH A . C 2 HOH 61 201 201 HOH HOH A . C 2 HOH 62 204 204 HOH HOH A . D 2 HOH 1 103 103 HOH HOH B . D 2 HOH 2 105 105 HOH HOH B . D 2 HOH 3 107 107 HOH HOH B . D 2 HOH 4 110 110 HOH HOH B . D 2 HOH 5 117 117 HOH HOH B . D 2 HOH 6 122 122 HOH HOH B . D 2 HOH 7 125 125 HOH HOH B . D 2 HOH 8 129 129 HOH HOH B . D 2 HOH 9 130 130 HOH HOH B . D 2 HOH 10 132 132 HOH HOH B . D 2 HOH 11 137 137 HOH HOH B . D 2 HOH 12 139 139 HOH HOH B . D 2 HOH 13 140 140 HOH HOH B . D 2 HOH 14 141 141 HOH HOH B . D 2 HOH 15 146 146 HOH HOH B . D 2 HOH 16 147 147 HOH HOH B . D 2 HOH 17 155 155 HOH HOH B . D 2 HOH 18 156 156 HOH HOH B . D 2 HOH 19 157 157 HOH HOH B . D 2 HOH 20 158 158 HOH HOH B . D 2 HOH 21 162 162 HOH HOH B . D 2 HOH 22 170 170 HOH HOH B . D 2 HOH 23 171 171 HOH HOH B . D 2 HOH 24 172 172 HOH HOH B . D 2 HOH 25 174 174 HOH HOH B . D 2 HOH 26 176 176 HOH HOH B . D 2 HOH 27 181 181 HOH HOH B . D 2 HOH 28 182 182 HOH HOH B . D 2 HOH 29 185 185 HOH HOH B . D 2 HOH 30 188 188 HOH HOH B . D 2 HOH 31 189 189 HOH HOH B . D 2 HOH 32 190 190 HOH HOH B . D 2 HOH 33 192 192 HOH HOH B . D 2 HOH 34 193 193 HOH HOH B . D 2 HOH 35 194 194 HOH HOH B . D 2 HOH 36 198 198 HOH HOH B . D 2 HOH 37 203 203 HOH HOH B . D 2 HOH 38 206 206 HOH HOH B . D 2 HOH 39 208 208 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 AMoRE phasing . ? 3 CNS refinement . ? 4 # _cell.entry_id 1NZG _cell.length_a 25.260 _cell.length_b 44.110 _cell.length_c 45.530 _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 1NZG _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 1NZG _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.71 _exptl_crystal.density_percent_sol 27.47 _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 295.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details 'MPD, Sodium Cacodylate, Spermine, Sodium Chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 'Sodium Cacodylate' ? ? ? 1 3 1 Spermine ? ? ? 1 4 1 'Sodium Chloride' ? ? ? 1 5 2 MPD ? ? ? 1 6 2 'Sodium Chloride' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 1999-06-08 _diffrn_detector.details Mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator Graphite _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 5ID-B' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 5ID-B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.00000 # _reflns.entry_id 1NZG _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I -3.0 _reflns.d_resolution_high 1.60 _reflns.d_resolution_low 20.0 _reflns.number_all 7031 _reflns.number_obs 7031 _reflns.percent_possible_obs 97.6 _reflns.pdbx_Rmerge_I_obs 0.063 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 22.9 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 8.2 _reflns.R_free_details ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _reflns_shell.d_res_high 1.60 _reflns_shell.d_res_low 1.66 _reflns_shell.percent_possible_all 82.9 _reflns_shell.Rmerge_I_obs 0.182 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 6.5 _reflns_shell.pdbx_redundancy 4.9 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 575 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? # _refine.entry_id 1NZG _refine.ls_d_res_high 1.60 _refine.ls_d_res_low 20.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_ls_sigma_I 0.0 _refine.ls_number_reflns_all 7114 _refine.ls_number_reflns_obs 6676 _refine.ls_number_reflns_R_free 687 _refine.ls_percent_reflns_obs 93.8 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.192 _refine.ls_R_factor_R_free 0.224 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details Random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'PARKINSON ET AL.' _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 Isotropic _refine.B_iso_mean ? _refine.aniso_B[1][1] 2.756 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][2] -10.058 _refine.aniso_B[2][3] 0.000 _refine.aniso_B[3][3] 7.302 _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_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_phase_error ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_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 422 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 101 _refine_hist.number_atoms_total 523 _refine_hist.d_res_high 1.60 _refine_hist.d_res_low 20.0 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.30 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.60 _refine_ls_shell.d_res_low 1.64 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.312 _refine_ls_shell.percent_reflns_obs 80.1 _refine_ls_shell.R_factor_R_free 0.353 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 35 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 1NZG _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 1NZG _struct.title 'Crystal structure of A-DNA decamer GCGTA(3ME)ACGC, with a modified 5-methyluridine' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1NZG _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;A-DNA, 2'-modified oligonucleotides, DNA ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1NZG _struct_ref.pdbx_db_accession 1NZG _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 1NZG A 1 ? 10 ? 1NZG 1 ? 10 ? 1 10 2 1 1NZG B 1 ? 10 ? 1NZG 11 ? 20 ? 11 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _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 5 "O3'" ? ? ? 1_555 A 3ME 6 P ? ? A DA 5 A 3ME 6 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale2 covale both ? A 3ME 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A 3ME 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.597 ? ? covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B 3ME 6 P ? ? B DA 15 B 3ME 16 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale4 covale both ? B 3ME 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B 3ME 16 B DA 17 1_555 ? ? ? ? ? ? ? 1.607 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B 3ME 6 N3 ? ? A DA 5 B 3ME 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B 3ME 6 O4 ? ? A DA 5 B 3ME 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A 3ME 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A 3ME 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A 3ME 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A 3ME 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 3ME 6 A 3ME 6 ? U ? 2 B 3ME 6 B 3ME 16 ? U ? # 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 3ME P P N N 1 3ME OP1 O N N 2 3ME OP2 O N N 3 3ME "O5'" O N N 4 3ME "C5'" C N N 5 3ME "C4'" C N R 6 3ME "O4'" O N N 7 3ME "C1'" C N R 8 3ME N1 N N N 9 3ME C6 C N N 10 3ME C2 C N N 11 3ME O2 O N N 12 3ME N3 N N N 13 3ME C4 C N N 14 3ME O4 O N N 15 3ME C5 C N N 16 3ME C5A C N N 17 3ME "C2'" C N R 18 3ME "O2'" O N N 19 3ME "CB'" C N N 20 3ME "CC'" C N N 21 3ME "OD'" O N N 22 3ME "CE'" C N N 23 3ME "CF'" C N N 24 3ME "NG'" N N N 25 3ME "CI'" C N N 26 3ME "CJ'" C N N 27 3ME "C3'" C N R 28 3ME "O3'" O N N 29 3ME HO2 H N N 30 3ME "H5'1" H N N 31 3ME "H5'2" H N N 32 3ME "H4'" H N N 33 3ME "H1'" H N N 34 3ME HC6 H N N 35 3ME HN3 H N N 36 3ME H5A1 H N N 37 3ME H5A2 H N N 38 3ME H5A3 H N N 39 3ME "H2'" H N N 40 3ME "HB'1" H N N 41 3ME "HB'2" H N N 42 3ME "HC'1" H N N 43 3ME "HC'2" H N N 44 3ME "HE'1" H N N 45 3ME "HE'2" H N N 46 3ME "HF'1" H N N 47 3ME "HF'2" H N N 48 3ME "HI'1" H N N 49 3ME "HI'2" H N N 50 3ME "HI'3" H N N 51 3ME "HJ'1" H N N 52 3ME "HJ'2" H N N 53 3ME "HJ'3" H N N 54 3ME "H3'" H N N 55 3ME "HO3'" H N N 56 3ME OXT O N N 57 3ME HXT H N N 58 DA OP3 O N N 59 DA P P N N 60 DA OP1 O N N 61 DA OP2 O N N 62 DA "O5'" O N N 63 DA "C5'" C N N 64 DA "C4'" C N R 65 DA "O4'" O N N 66 DA "C3'" C N S 67 DA "O3'" O N N 68 DA "C2'" C N N 69 DA "C1'" C N R 70 DA N9 N Y N 71 DA C8 C Y N 72 DA N7 N Y N 73 DA C5 C Y N 74 DA C6 C Y N 75 DA N6 N N N 76 DA N1 N Y N 77 DA C2 C Y N 78 DA N3 N Y N 79 DA C4 C Y N 80 DA HOP3 H N N 81 DA HOP2 H N N 82 DA "H5'" H N N 83 DA "H5''" H N N 84 DA "H4'" H N N 85 DA "H3'" H N N 86 DA "HO3'" H N N 87 DA "H2'" H N N 88 DA "H2''" H N N 89 DA "H1'" H N N 90 DA H8 H N N 91 DA H61 H N N 92 DA H62 H N N 93 DA H2 H N N 94 DC OP3 O N N 95 DC P P N N 96 DC OP1 O N N 97 DC OP2 O N N 98 DC "O5'" O N N 99 DC "C5'" C N N 100 DC "C4'" C N R 101 DC "O4'" O N N 102 DC "C3'" C N S 103 DC "O3'" O N N 104 DC "C2'" C N N 105 DC "C1'" C N R 106 DC N1 N N N 107 DC C2 C N N 108 DC O2 O N N 109 DC N3 N N N 110 DC C4 C N N 111 DC N4 N N N 112 DC C5 C N N 113 DC C6 C N N 114 DC HOP3 H N N 115 DC HOP2 H N N 116 DC "H5'" H N N 117 DC "H5''" H N N 118 DC "H4'" H N N 119 DC "H3'" H N N 120 DC "HO3'" H N N 121 DC "H2'" H N N 122 DC "H2''" H N N 123 DC "H1'" H N N 124 DC H41 H N N 125 DC H42 H N N 126 DC H5 H N N 127 DC H6 H N N 128 DG OP3 O N N 129 DG P P N N 130 DG OP1 O N N 131 DG OP2 O N N 132 DG "O5'" O N N 133 DG "C5'" C N N 134 DG "C4'" C N R 135 DG "O4'" O N N 136 DG "C3'" C N S 137 DG "O3'" O N N 138 DG "C2'" C N N 139 DG "C1'" C N R 140 DG N9 N Y N 141 DG C8 C Y N 142 DG N7 N Y N 143 DG C5 C Y N 144 DG C6 C N N 145 DG O6 O N N 146 DG N1 N N N 147 DG C2 C N N 148 DG N2 N N N 149 DG N3 N N N 150 DG C4 C Y N 151 DG HOP3 H N N 152 DG HOP2 H N N 153 DG "H5'" H N N 154 DG "H5''" H N N 155 DG "H4'" H N N 156 DG "H3'" H N N 157 DG "HO3'" H N N 158 DG "H2'" H N N 159 DG "H2''" H N N 160 DG "H1'" H N N 161 DG H8 H N N 162 DG H1 H N N 163 DG H21 H N N 164 DG H22 H N N 165 DT OP3 O N N 166 DT P P N N 167 DT OP1 O N N 168 DT OP2 O N N 169 DT "O5'" O N N 170 DT "C5'" C N N 171 DT "C4'" C N R 172 DT "O4'" O N N 173 DT "C3'" C N S 174 DT "O3'" O N N 175 DT "C2'" C N N 176 DT "C1'" C N R 177 DT N1 N N N 178 DT C2 C N N 179 DT O2 O N N 180 DT N3 N N N 181 DT C4 C N N 182 DT O4 O N N 183 DT C5 C N N 184 DT C7 C N N 185 DT C6 C N N 186 DT HOP3 H N N 187 DT HOP2 H N N 188 DT "H5'" H N N 189 DT "H5''" H N N 190 DT "H4'" H N N 191 DT "H3'" H N N 192 DT "HO3'" H N N 193 DT "H2'" H N N 194 DT "H2''" H N N 195 DT "H1'" H N N 196 DT H3 H N N 197 DT H71 H N N 198 DT H72 H N N 199 DT H73 H N N 200 DT H6 H N N 201 HOH O O N N 202 HOH H1 H N N 203 HOH H2 H N N 204 # 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 3ME P OP1 doub N N 1 3ME P OP2 sing N N 2 3ME P "O5'" sing N N 3 3ME OP2 HO2 sing N N 4 3ME "O5'" "C5'" sing N N 5 3ME "C5'" "C4'" sing N N 6 3ME "C5'" "H5'1" sing N N 7 3ME "C5'" "H5'2" sing N N 8 3ME "C4'" "O4'" sing N N 9 3ME "C4'" "C3'" sing N N 10 3ME "C4'" "H4'" sing N N 11 3ME "O4'" "C1'" sing N N 12 3ME "C1'" N1 sing N N 13 3ME "C1'" "C2'" sing N N 14 3ME "C1'" "H1'" sing N N 15 3ME N1 C6 sing N N 16 3ME N1 C2 sing N N 17 3ME C6 C5 doub N N 18 3ME C6 HC6 sing N N 19 3ME C2 O2 doub N N 20 3ME C2 N3 sing N N 21 3ME N3 C4 sing N N 22 3ME N3 HN3 sing N N 23 3ME C4 O4 doub N N 24 3ME C4 C5 sing N N 25 3ME C5 C5A sing N N 26 3ME C5A H5A1 sing N N 27 3ME C5A H5A2 sing N N 28 3ME C5A H5A3 sing N N 29 3ME "C2'" "O2'" sing N N 30 3ME "C2'" "C3'" sing N N 31 3ME "C2'" "H2'" sing N N 32 3ME "O2'" "CB'" sing N N 33 3ME "CB'" "CC'" sing N N 34 3ME "CB'" "HB'1" sing N N 35 3ME "CB'" "HB'2" sing N N 36 3ME "CC'" "OD'" sing N N 37 3ME "CC'" "HC'1" sing N N 38 3ME "CC'" "HC'2" sing N N 39 3ME "OD'" "CE'" sing N N 40 3ME "CE'" "CF'" sing N N 41 3ME "CE'" "HE'1" sing N N 42 3ME "CE'" "HE'2" sing N N 43 3ME "CF'" "NG'" sing N N 44 3ME "CF'" "HF'1" sing N N 45 3ME "CF'" "HF'2" sing N N 46 3ME "NG'" "CI'" sing N N 47 3ME "NG'" "CJ'" sing N N 48 3ME "CI'" "HI'1" sing N N 49 3ME "CI'" "HI'2" sing N N 50 3ME "CI'" "HI'3" sing N N 51 3ME "CJ'" "HJ'1" sing N N 52 3ME "CJ'" "HJ'2" sing N N 53 3ME "CJ'" "HJ'3" sing N N 54 3ME "C3'" "O3'" sing N N 55 3ME "C3'" "H3'" sing N N 56 3ME "O3'" "HO3'" sing N N 57 3ME P OXT sing N N 58 3ME OXT HXT sing N N 59 DA OP3 P sing N N 60 DA OP3 HOP3 sing N N 61 DA P OP1 doub N N 62 DA P OP2 sing N N 63 DA P "O5'" sing N N 64 DA OP2 HOP2 sing N N 65 DA "O5'" "C5'" sing N N 66 DA "C5'" "C4'" sing N N 67 DA "C5'" "H5'" sing N N 68 DA "C5'" "H5''" sing N N 69 DA "C4'" "O4'" sing N N 70 DA "C4'" "C3'" sing N N 71 DA "C4'" "H4'" sing N N 72 DA "O4'" "C1'" sing N N 73 DA "C3'" "O3'" sing N N 74 DA "C3'" "C2'" sing N N 75 DA "C3'" "H3'" sing N N 76 DA "O3'" "HO3'" sing N N 77 DA "C2'" "C1'" sing N N 78 DA "C2'" "H2'" sing N N 79 DA "C2'" "H2''" sing N N 80 DA "C1'" N9 sing N N 81 DA "C1'" "H1'" sing N N 82 DA N9 C8 sing Y N 83 DA N9 C4 sing Y N 84 DA C8 N7 doub Y N 85 DA C8 H8 sing N N 86 DA N7 C5 sing Y N 87 DA C5 C6 sing Y N 88 DA C5 C4 doub Y N 89 DA C6 N6 sing N N 90 DA C6 N1 doub Y N 91 DA N6 H61 sing N N 92 DA N6 H62 sing N N 93 DA N1 C2 sing Y N 94 DA C2 N3 doub Y N 95 DA C2 H2 sing N N 96 DA N3 C4 sing Y N 97 DC OP3 P sing N N 98 DC OP3 HOP3 sing N N 99 DC P OP1 doub N N 100 DC P OP2 sing N N 101 DC P "O5'" sing N N 102 DC OP2 HOP2 sing N N 103 DC "O5'" "C5'" sing N N 104 DC "C5'" "C4'" sing N N 105 DC "C5'" "H5'" sing N N 106 DC "C5'" "H5''" sing N N 107 DC "C4'" "O4'" sing N N 108 DC "C4'" "C3'" sing N N 109 DC "C4'" "H4'" sing N N 110 DC "O4'" "C1'" sing N N 111 DC "C3'" "O3'" sing N N 112 DC "C3'" "C2'" sing N N 113 DC "C3'" "H3'" sing N N 114 DC "O3'" "HO3'" sing N N 115 DC "C2'" "C1'" sing N N 116 DC "C2'" "H2'" sing N N 117 DC "C2'" "H2''" sing N N 118 DC "C1'" N1 sing N N 119 DC "C1'" "H1'" sing N N 120 DC N1 C2 sing N N 121 DC N1 C6 sing N N 122 DC C2 O2 doub N N 123 DC C2 N3 sing N N 124 DC N3 C4 doub N N 125 DC C4 N4 sing N N 126 DC C4 C5 sing N N 127 DC N4 H41 sing N N 128 DC N4 H42 sing N N 129 DC C5 C6 doub N N 130 DC C5 H5 sing N N 131 DC C6 H6 sing N N 132 DG OP3 P sing N N 133 DG OP3 HOP3 sing N N 134 DG P OP1 doub N N 135 DG P OP2 sing N N 136 DG P "O5'" sing N N 137 DG OP2 HOP2 sing N N 138 DG "O5'" "C5'" sing N N 139 DG "C5'" "C4'" sing N N 140 DG "C5'" "H5'" sing N N 141 DG "C5'" "H5''" sing N N 142 DG "C4'" "O4'" sing N N 143 DG "C4'" "C3'" sing N N 144 DG "C4'" "H4'" sing N N 145 DG "O4'" "C1'" sing N N 146 DG "C3'" "O3'" sing N N 147 DG "C3'" "C2'" sing N N 148 DG "C3'" "H3'" sing N N 149 DG "O3'" "HO3'" sing N N 150 DG "C2'" "C1'" sing N N 151 DG "C2'" "H2'" sing N N 152 DG "C2'" "H2''" sing N N 153 DG "C1'" N9 sing N N 154 DG "C1'" "H1'" sing N N 155 DG N9 C8 sing Y N 156 DG N9 C4 sing Y N 157 DG C8 N7 doub Y N 158 DG C8 H8 sing N N 159 DG N7 C5 sing Y N 160 DG C5 C6 sing N N 161 DG C5 C4 doub Y N 162 DG C6 O6 doub N N 163 DG C6 N1 sing N N 164 DG N1 C2 sing N N 165 DG N1 H1 sing N N 166 DG C2 N2 sing N N 167 DG C2 N3 doub N N 168 DG N2 H21 sing N N 169 DG N2 H22 sing N N 170 DG N3 C4 sing N N 171 DT OP3 P sing N N 172 DT OP3 HOP3 sing N N 173 DT P OP1 doub N N 174 DT P OP2 sing N N 175 DT P "O5'" sing N N 176 DT OP2 HOP2 sing N N 177 DT "O5'" "C5'" sing N N 178 DT "C5'" "C4'" sing N N 179 DT "C5'" "H5'" sing N N 180 DT "C5'" "H5''" sing N N 181 DT "C4'" "O4'" sing N N 182 DT "C4'" "C3'" sing N N 183 DT "C4'" "H4'" sing N N 184 DT "O4'" "C1'" sing N N 185 DT "C3'" "O3'" sing N N 186 DT "C3'" "C2'" sing N N 187 DT "C3'" "H3'" sing N N 188 DT "O3'" "HO3'" sing N N 189 DT "C2'" "C1'" sing N N 190 DT "C2'" "H2'" sing N N 191 DT "C2'" "H2''" sing N N 192 DT "C1'" N1 sing N N 193 DT "C1'" "H1'" sing N N 194 DT N1 C2 sing N N 195 DT N1 C6 sing N N 196 DT C2 O2 doub N N 197 DT C2 N3 sing N N 198 DT N3 C4 sing N N 199 DT N3 H3 sing N N 200 DT C4 O4 doub N N 201 DT C4 C5 sing N N 202 DT C5 C7 sing N N 203 DT C5 C6 doub N N 204 DT C7 H71 sing N N 205 DT C7 H72 sing N N 206 DT C7 H73 sing N N 207 DT C6 H6 sing N N 208 HOH O H1 sing N N 209 HOH O H2 sing N N 210 # _ndb_struct_conf_na.entry_id 1NZG _ndb_struct_conf_na.feature 'a-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 DG 1 1_555 B DC 10 1_555 -0.243 -0.168 0.271 0.799 -7.020 -2.274 1 A_DG1:DC20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.155 -0.095 -0.009 7.658 -14.705 0.675 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.373 -0.186 0.001 -8.232 -15.199 1.268 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.157 -0.136 -0.147 -3.162 -17.057 0.288 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DA 5 1_555 B 3ME 6 1_555 0.257 0.007 0.114 -2.856 -12.201 -5.065 5 A_DA5:3ME16_B A 5 ? B 16 ? 20 1 1 A 3ME 6 1_555 B DA 5 1_555 -0.005 -0.112 0.227 5.327 -13.532 6.126 6 A_3ME6:DA15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.083 -0.159 0.076 5.597 -11.520 2.212 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.229 -0.189 -0.318 10.890 -15.325 2.842 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.014 -0.171 -0.050 -5.636 -9.259 2.209 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.251 -0.085 0.002 -1.864 5.410 0.141 10 A_DC10:DG11_B A 10 ? B 11 ? 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 DG 1 1_555 B DC 10 1_555 A DC 2 1_555 B DG 9 1_555 0.351 -1.572 3.102 3.640 0.421 39.090 -2.388 -0.110 3.104 0.627 -5.426 39.254 1 AA_DG1DC2:DG19DC20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.258 -2.046 3.566 0.274 10.238 25.204 -6.858 -0.482 2.556 22.322 -0.598 27.174 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -1.109 -1.356 3.059 -1.384 6.094 37.321 -2.805 1.549 2.848 9.442 2.144 37.822 3 AA_DG3DT4:DA17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B 3ME 6 1_555 0.590 -1.560 3.193 1.461 20.125 25.883 -5.649 -0.839 1.621 38.366 -2.785 32.713 4 AA_DT4DA5:3ME16DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DA 5 1_555 B 3ME 6 1_555 A 3ME 6 1_555 B DA 5 1_555 0.871 -1.327 3.101 0.246 5.477 32.036 -3.250 -1.518 2.848 9.834 -0.442 32.489 5 AA_DA53ME6:DA153ME16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A 3ME 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.327 -1.405 3.090 0.546 12.833 30.508 -4.344 0.655 2.321 23.142 -0.985 33.042 6 AA_3ME6DA7:DT14DA15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 0.250 -1.601 3.245 3.269 4.655 31.577 -3.703 0.112 2.994 8.468 -5.947 32.072 7 AA_DA7DC8:DG13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.308 -1.836 3.621 -1.628 11.956 29.154 -5.621 0.262 2.691 22.572 3.073 31.503 8 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 0.282 -1.753 3.320 1.360 2.334 34.270 -3.330 -0.265 3.205 3.954 -2.304 34.373 9 AA_DG9DC10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _atom_sites.entry_id 1NZG _atom_sites.fract_transf_matrix[1][1] 0.039588 _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] 0.022671 _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] 0.021964 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_