data_420D # _entry.id 420D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 420D pdb_0000420d 10.2210/pdb420d/pdb RCSB AR0006 ? ? WWPDB D_1000179219 ? ? # 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 1999-01-13 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-28 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 17 4 'Structure model' '_pdbx_struct_conn_angle.value' 18 4 'Structure model' '_struct_conn.pdbx_dist_value' 19 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 20 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 25 4 'Structure model' '_struct_conn.ptnr1_symmetry' 26 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 27 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 31 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 32 4 'Structure model' '_struct_conn.ptnr2_symmetry' 33 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 34 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 35 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 420D _pdbx_database_status.recvd_initial_deposition_date 1998-08-13 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Pan, B.' 1 'Mitra, S.N.' 2 'Sundaralingam, M.' 3 # _citation.id primary _citation.title 'Crystal structure of an RNA 16-mer duplex R(GCAGAGUUAAAUCUGC)2 with nonadjacent G(syn).A+(anti) mispairs.' _citation.journal_abbrev Biochemistry _citation.journal_volume 38 _citation.page_first 2826 _citation.page_last 2831 _citation.year 1999 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10052954 _citation.pdbx_database_id_DOI 10.1021/bi982122y # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pan, B.' 1 ? primary 'Mitra, S.N.' 2 ? primary 'Sundaralingam, M.' 3 ? # 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 ;RNA (5'-R(*GP*CP*AP*GP*AP*GP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3') ; 5122.103 2 ? ? ? ? 2 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 3 water nat water 18.015 56 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GCAGAGUUAAAUCUGC _entity_poly.pdbx_seq_one_letter_code_can GCAGAGUUAAAUCUGC _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 'SODIUM ION' NA 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 C n 1 3 A n 1 4 G n 1 5 A n 1 6 G n 1 7 U n 1 8 U n 1 9 A n 1 10 A n 1 11 A n 1 12 U n 1 13 C n 1 14 U n 1 15 G n 1 16 C 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 G 1 1 1 G G A . n A 1 2 C 2 2 2 C C A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 G 6 6 6 G G A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 A 11 11 11 A A A . n A 1 12 U 12 12 12 U U A . n A 1 13 C 13 13 13 C C A . n A 1 14 U 14 14 14 U U A . n A 1 15 G 15 15 15 G G A . n A 1 16 C 16 16 16 C C A . n B 1 1 G 1 17 17 G G B . n B 1 2 C 2 18 18 C C B . n B 1 3 A 3 19 19 A A B . n B 1 4 G 4 20 20 G G B . n B 1 5 A 5 21 21 A A B . n B 1 6 G 6 22 22 G G B . n B 1 7 U 7 23 23 U U B . n B 1 8 U 8 24 24 U U B . n B 1 9 A 9 25 25 A A B . n B 1 10 A 10 26 26 A A B . n B 1 11 A 11 27 27 A A B . n B 1 12 U 12 28 28 U U B . n B 1 13 C 13 29 29 C C B . n B 1 14 U 14 30 30 U U B . n B 1 15 G 15 31 31 G G B . n B 1 16 C 16 32 32 C 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 NA 1 89 89 NA NA A . D 3 HOH 1 36 36 HOH HOH A . D 3 HOH 2 39 39 HOH HOH A . D 3 HOH 3 41 41 HOH HOH A . D 3 HOH 4 42 42 HOH HOH A . D 3 HOH 5 43 43 HOH HOH A . D 3 HOH 6 48 48 HOH HOH A . D 3 HOH 7 49 49 HOH HOH A . D 3 HOH 8 51 51 HOH HOH A . D 3 HOH 9 52 52 HOH HOH A . D 3 HOH 10 54 54 HOH HOH A . D 3 HOH 11 55 55 HOH HOH A . D 3 HOH 12 57 57 HOH HOH A . D 3 HOH 13 58 58 HOH HOH A . D 3 HOH 14 59 59 HOH HOH A . D 3 HOH 15 61 61 HOH HOH A . D 3 HOH 16 63 63 HOH HOH A . D 3 HOH 17 64 64 HOH HOH A . D 3 HOH 18 65 65 HOH HOH A . D 3 HOH 19 67 67 HOH HOH A . D 3 HOH 20 73 73 HOH HOH A . D 3 HOH 21 75 75 HOH HOH A . D 3 HOH 22 78 78 HOH HOH A . D 3 HOH 23 80 80 HOH HOH A . D 3 HOH 24 83 83 HOH HOH A . D 3 HOH 25 87 87 HOH HOH A . E 3 HOH 1 33 33 HOH HOH B . E 3 HOH 2 34 34 HOH HOH B . E 3 HOH 3 35 35 HOH HOH B . E 3 HOH 4 37 37 HOH HOH B . E 3 HOH 5 38 38 HOH HOH B . E 3 HOH 6 40 40 HOH HOH B . E 3 HOH 7 44 44 HOH HOH B . E 3 HOH 8 45 45 HOH HOH B . E 3 HOH 9 46 46 HOH HOH B . E 3 HOH 10 47 47 HOH HOH B . E 3 HOH 11 50 50 HOH HOH B . E 3 HOH 12 53 53 HOH HOH B . E 3 HOH 13 56 56 HOH HOH B . E 3 HOH 14 60 60 HOH HOH B . E 3 HOH 15 62 62 HOH HOH B . E 3 HOH 16 66 66 HOH HOH B . E 3 HOH 17 68 68 HOH HOH B . E 3 HOH 18 69 69 HOH HOH B . E 3 HOH 19 70 70 HOH HOH B . E 3 HOH 20 71 71 HOH HOH B . E 3 HOH 21 72 72 HOH HOH B . E 3 HOH 22 74 74 HOH HOH B . E 3 HOH 23 76 76 HOH HOH B . E 3 HOH 24 77 77 HOH HOH B . E 3 HOH 25 79 79 HOH HOH B . E 3 HOH 26 81 81 HOH HOH B . E 3 HOH 27 82 82 HOH HOH B . E 3 HOH 28 84 84 HOH HOH B . E 3 HOH 29 85 85 HOH HOH B . E 3 HOH 30 86 86 HOH HOH B . E 3 HOH 31 88 88 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR refinement 3.1 ? 1 R-AXIS 'data reduction' 'IIC V. 2.1' ? 2 MSC 'data scaling' . ? 3 # _cell.entry_id 420D _cell.length_a 42.530 _cell.length_b 42.530 _cell.length_c 128.060 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 420D _symmetry.space_group_name_H-M 'H 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting trigonal _symmetry.Int_Tables_number 146 # _exptl.entry_id 420D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.18 _exptl_crystal.density_percent_sol 43.47 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'pH 7.00, VAPOR DIFFUSION' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 KCL ? ? ? 1 3 1 CACL2 ? ? ? 1 4 1 'NA HEPES' ? ? ? 1 5 1 'PEG 400' ? ? ? 1 6 2 WATER ? ? ? 1 7 2 'PEG 400' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 293.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IIC' _diffrn_detector.pdbx_collection_date 1997-05-27 _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 GRAPHITE _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 420D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 21.270 _reflns.d_resolution_high 1.820 _reflns.number_obs 7377 _reflns.number_all ? _reflns.percent_possible_obs 87.000 _reflns.pdbx_Rmerge_I_obs 0.0730000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 2.800 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 420D _refine.ls_number_reflns_obs 5433 _refine.ls_number_reflns_all 5433 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.000 _refine.ls_d_res_high 1.900 _refine.ls_percent_reflns_obs 80.800 _refine.ls_R_factor_obs 0.1970000 _refine.ls_R_factor_all 0.2070000 _refine.ls_R_factor_R_work 0.1970000 _refine.ls_R_factor_R_free 0.2960000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.000 _refine.ls_number_reflns_R_free 569 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ISOTROPIC _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 420D _refine_analyze.Luzzati_coordinate_error_obs 0.29 _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 678 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 56 _refine_hist.number_atoms_total 735 _refine_hist.d_res_high 1.900 _refine_hist.d_res_low 8.000 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function x_bond_d 0.005 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 0.90 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 420D _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 420D _struct.title 'CRYSTAL STRUCTURE OF A 16-MER RNA DUPLEX WITH NON-ADJACENT A(ANTI).G(SYN) MISMATCHES' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 420D _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'A-RNA STRUCTURE, MISMATCH A RNA, RNA' # 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 420D _struct_ref.pdbx_db_accession 420D _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 420D A 1 ? 16 ? 420D 1 ? 16 ? 1 16 2 1 420D B 1 ? 16 ? 420D 17 ? 32 ? 17 32 # _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 # 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 metalc1 metalc ? ? A U 14 OP1 ? ? ? 3_565 C NA . NA ? ? A U 14 A NA 89 1_555 ? ? ? ? ? ? ? 2.587 ? ? metalc2 metalc ? ? A U 14 OP1 ? ? ? 2_665 C NA . NA ? ? A U 14 A NA 89 1_555 ? ? ? ? ? ? ? 2.584 ? ? metalc3 metalc ? ? A U 14 OP1 ? ? ? 1_555 C NA . NA ? ? A U 14 A NA 89 1_555 ? ? ? ? ? ? ? 2.601 ? ? metalc4 metalc ? ? D HOH . O ? ? ? 1_555 C NA . NA ? ? A HOH 48 A NA 89 1_555 ? ? ? ? ? ? ? 2.427 ? ? metalc5 metalc ? ? D HOH . O ? ? ? 3_565 C NA . NA ? ? A HOH 48 A NA 89 1_555 ? ? ? ? ? ? ? 2.427 ? ? metalc6 metalc ? ? D HOH . O ? ? ? 2_665 C NA . NA ? ? A HOH 48 A NA 89 1_555 ? ? ? ? ? ? ? 2.412 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 16 N3 ? ? A G 1 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 16 O2 ? ? A G 1 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 16 N4 ? ? A G 1 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 15 N1 ? ? A C 2 B G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 15 O6 ? ? A C 2 B G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 15 N2 ? ? A C 2 B G 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B U 14 N3 ? ? A A 3 B U 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B U 14 O4 ? ? A A 3 B U 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 13 N3 ? ? A G 4 B C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 13 O2 ? ? A G 4 B C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 13 N4 ? ? A G 4 B C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 12 N3 ? ? A A 5 B U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 12 O4 ? ? A A 5 B U 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 O6 ? ? ? 1_555 B A 11 N6 ? ? A G 6 B A 27 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog15 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 10 N1 ? ? A U 7 B A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A U 7 O4 ? ? ? 1_555 B A 10 N6 ? ? A U 7 B A 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 8 N3 ? ? ? 1_555 B A 9 N1 ? ? A U 8 B A 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A U 8 O4 ? ? ? 1_555 B A 9 N6 ? ? A U 8 B A 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 8 N3 ? ? A A 9 B U 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 9 N6 ? ? ? 1_555 B U 8 O4 ? ? A A 9 B U 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 7 N3 ? ? A A 10 B U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 7 O4 ? ? A A 10 B U 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A A 11 N6 ? ? ? 1_555 B G 6 O6 ? ? A A 11 B G 22 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog24 hydrog ? ? A U 12 N3 ? ? ? 1_555 B A 5 N1 ? ? A U 12 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A U 12 O4 ? ? ? 1_555 B A 5 N6 ? ? A U 12 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 13 B G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 13 B G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 13 B G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A U 14 N3 ? ? ? 1_555 B A 3 N1 ? ? A U 14 B A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 14 O4 ? ? ? 1_555 B A 3 N6 ? ? A U 14 B A 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 15 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 15 B C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 15 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 15 B C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 15 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 15 B C 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 16 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 16 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 16 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 16 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 16 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 16 B G 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference 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 OP1 ? A U 14 ? A U 14 ? 3_565 NA ? C NA . ? A NA 89 ? 1_555 OP1 ? A U 14 ? A U 14 ? 2_665 113.3 ? 2 OP1 ? A U 14 ? A U 14 ? 3_565 NA ? C NA . ? A NA 89 ? 1_555 OP1 ? A U 14 ? A U 14 ? 1_555 112.7 ? 3 OP1 ? A U 14 ? A U 14 ? 2_665 NA ? C NA . ? A NA 89 ? 1_555 OP1 ? A U 14 ? A U 14 ? 1_555 112.8 ? 4 OP1 ? A U 14 ? A U 14 ? 3_565 NA ? C NA . ? A NA 89 ? 1_555 O ? D HOH . ? A HOH 48 ? 1_555 162.1 ? 5 OP1 ? A U 14 ? A U 14 ? 2_665 NA ? C NA . ? A NA 89 ? 1_555 O ? D HOH . ? A HOH 48 ? 1_555 82.0 ? 6 OP1 ? A U 14 ? A U 14 ? 1_555 NA ? C NA . ? A NA 89 ? 1_555 O ? D HOH . ? A HOH 48 ? 1_555 66.4 ? 7 OP1 ? A U 14 ? A U 14 ? 3_565 NA ? C NA . ? A NA 89 ? 1_555 O ? D HOH . ? A HOH 48 ? 3_565 66.6 ? 8 OP1 ? A U 14 ? A U 14 ? 2_665 NA ? C NA . ? A NA 89 ? 1_555 O ? D HOH . ? A HOH 48 ? 3_565 162.6 ? 9 OP1 ? A U 14 ? A U 14 ? 1_555 NA ? C NA . ? A NA 89 ? 1_555 O ? D HOH . ? A HOH 48 ? 3_565 81.6 ? 10 O ? D HOH . ? A HOH 48 ? 1_555 NA ? C NA . ? A NA 89 ? 1_555 O ? D HOH . ? A HOH 48 ? 3_565 95.9 ? 11 OP1 ? A U 14 ? A U 14 ? 3_565 NA ? C NA . ? A NA 89 ? 1_555 O ? D HOH . ? A HOH 48 ? 2_665 82.2 ? 12 OP1 ? A U 14 ? A U 14 ? 2_665 NA ? C NA . ? A NA 89 ? 1_555 O ? D HOH . ? A HOH 48 ? 2_665 66.9 ? 13 OP1 ? A U 14 ? A U 14 ? 1_555 NA ? C NA . ? A NA 89 ? 1_555 O ? D HOH . ? A HOH 48 ? 2_665 162.1 ? 14 O ? D HOH . ? A HOH 48 ? 1_555 NA ? C NA . ? A NA 89 ? 1_555 O ? D HOH . ? A HOH 48 ? 2_665 96.3 ? 15 O ? D HOH . ? A HOH 48 ? 3_565 NA ? C NA . ? A NA 89 ? 1_555 O ? D HOH . ? A HOH 48 ? 2_665 96.3 ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id NA _struct_site.pdbx_auth_seq_id 89 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE NA A 89' # 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 U A 14 ? U A 14 . ? 3_565 ? 2 AC1 6 U A 14 ? U A 14 . ? 1_555 ? 3 AC1 6 U A 14 ? U A 14 . ? 2_665 ? 4 AC1 6 HOH D . ? HOH A 48 . ? 1_555 ? 5 AC1 6 HOH D . ? HOH A 48 . ? 2_665 ? 6 AC1 6 HOH D . ? HOH A 48 . ? 3_565 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 "O3'" _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 A _pdbx_validate_close_contact.auth_seq_id_1 21 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 88 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.02 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A NA 89 ? C NA . 2 1 A HOH 73 ? D HOH . 3 1 B HOH 72 ? E HOH . # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 NA NA NA N N 114 U OP3 O N N 115 U P P N N 116 U OP1 O N N 117 U OP2 O N N 118 U "O5'" O N N 119 U "C5'" C N N 120 U "C4'" C N R 121 U "O4'" O N N 122 U "C3'" C N S 123 U "O3'" O N N 124 U "C2'" C N R 125 U "O2'" O N N 126 U "C1'" C N R 127 U N1 N N N 128 U C2 C N N 129 U O2 O N N 130 U N3 N N N 131 U C4 C N N 132 U O4 O N N 133 U C5 C N N 134 U C6 C N N 135 U HOP3 H N N 136 U HOP2 H N N 137 U "H5'" H N N 138 U "H5''" H N N 139 U "H4'" H N N 140 U "H3'" H N N 141 U "HO3'" H N N 142 U "H2'" H N N 143 U "HO2'" H N N 144 U "H1'" H N N 145 U H3 H N N 146 U H5 H N N 147 U H6 H N N 148 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 420D 'double helix' 420D 'a-form double helix' 420D '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 G 1 1_555 B C 16 1_555 -0.865 -0.255 0.294 -1.724 -17.416 0.985 1 A_G1:C32_B A 1 ? B 32 ? 19 1 1 A C 2 1_555 B G 15 1_555 0.455 -0.375 0.232 2.418 -16.782 1.960 2 A_C2:G31_B A 2 ? B 31 ? 19 1 1 A A 3 1_555 B U 14 1_555 0.502 -0.212 0.126 -1.736 -14.380 1.786 3 A_A3:U30_B A 3 ? B 30 ? 20 1 1 A G 4 1_555 B C 13 1_555 -0.117 -0.259 -0.035 -3.972 -13.860 -1.698 4 A_G4:C29_B A 4 ? B 29 ? 19 1 1 A A 5 1_555 B U 12 1_555 0.219 -0.098 -0.049 -3.038 -12.091 4.305 5 A_A5:U28_B A 5 ? B 28 ? 20 1 1 A G 6 1_555 B A 11 1_555 0.211 -4.493 -0.672 7.463 19.677 87.495 6 A_G6:A27_B A 6 ? B 27 ? ? ? 1 A U 7 1_555 B A 10 1_555 0.078 -0.202 0.263 -6.905 -10.640 4.109 7 A_U7:A26_B A 7 ? B 26 ? 20 1 1 A U 8 1_555 B A 9 1_555 0.000 -0.242 -0.052 -3.448 -10.136 4.481 8 A_U8:A25_B A 8 ? B 25 ? 20 1 1 A A 9 1_555 B U 8 1_555 0.340 -0.260 0.120 1.881 -4.304 6.153 9 A_A9:U24_B A 9 ? B 24 ? 20 1 1 A A 10 1_555 B U 7 1_555 -0.126 -0.231 0.179 7.785 -11.395 3.491 10 A_A10:U23_B A 10 ? B 23 ? 20 1 1 A A 11 1_555 B G 6 1_555 0.005 4.450 0.504 -7.891 -16.216 -82.747 11 A_A11:G22_B A 11 ? B 22 ? ? ? 1 A U 12 1_555 B A 5 1_555 -0.120 0.062 -0.166 6.725 -15.939 4.942 12 A_U12:A21_B A 12 ? B 21 ? 20 1 1 A C 13 1_555 B G 4 1_555 0.587 -0.323 -0.227 4.900 -10.714 -2.088 13 A_C13:G20_B A 13 ? B 20 ? 19 1 1 A U 14 1_555 B A 3 1_555 -0.196 -0.294 0.293 -2.358 -9.552 1.304 14 A_U14:A19_B A 14 ? B 19 ? 20 1 1 A G 15 1_555 B C 2 1_555 -0.692 -0.178 0.113 -4.956 -16.932 5.567 15 A_G15:C18_B A 15 ? B 18 ? 19 1 1 A C 16 1_555 B G 1 1_555 0.906 -0.218 0.289 0.901 -12.103 0.471 16 A_C16:G17_B A 16 ? B 17 ? 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 G 1 1_555 B C 16 1_555 A C 2 1_555 B G 15 1_555 -0.205 -1.056 3.245 0.051 1.490 39.118 -1.752 0.311 3.204 2.224 -0.075 39.146 1 AA_G1C2:G31C32_BB A 1 ? B 32 ? A 2 ? B 31 ? 1 A C 2 1_555 B G 15 1_555 A A 3 1_555 B U 14 1_555 0.150 -1.527 3.316 0.717 6.918 34.869 -3.482 -0.144 2.971 11.404 -1.182 35.535 2 AA_C2A3:U30G31_BB A 2 ? B 31 ? A 3 ? B 30 ? 1 A A 3 1_555 B U 14 1_555 A G 4 1_555 B C 13 1_555 -0.271 -2.094 3.326 1.620 10.468 26.496 -6.398 0.883 2.326 21.764 -3.369 28.500 3 AA_A3G4:C29U30_BB A 3 ? B 30 ? A 4 ? B 29 ? 1 A G 4 1_555 B C 13 1_555 A A 5 1_555 B U 12 1_555 0.113 -1.549 3.332 -1.138 14.156 31.671 -4.614 -0.351 2.434 24.458 1.967 34.635 4 AA_G4A5:U28C29_BB A 4 ? B 29 ? A 5 ? B 28 ? 1 A A 5 1_555 B U 12 1_555 A G 6 1_555 B A 11 1_555 0.212 3.369 -1.291 165.697 -16.627 -127.211 -1.715 -0.172 -1.103 8.383 83.542 -174.023 5 AA_A5G6:A27U28_BB A 5 ? B 28 ? A 6 ? B 27 ? 1 A G 6 1_555 B A 11 1_555 A U 7 1_555 B A 10 1_555 0.120 -3.869 -2.409 138.554 -105.562 119.266 -2.203 -0.411 -0.847 -53.022 -69.594 177.061 6 AA_G6U7:A26A27_BB A 6 ? B 27 ? A 7 ? B 26 ? 1 A U 7 1_555 B A 10 1_555 A U 8 1_555 B A 9 1_555 -0.143 -1.606 3.177 2.667 6.265 28.308 -4.454 0.820 2.741 12.580 -5.356 29.099 7 AA_U7U8:A25A26_BB A 7 ? B 26 ? A 8 ? B 25 ? 1 A U 8 1_555 B A 9 1_555 A A 9 1_555 B U 8 1_555 0.155 -1.047 3.239 -1.960 5.006 33.113 -2.609 -0.580 3.039 8.712 3.411 33.535 8 AA_U8A9:U24A25_BB A 8 ? B 25 ? A 9 ? B 24 ? 1 A A 9 1_555 B U 8 1_555 A A 10 1_555 B U 7 1_555 0.004 -1.718 3.128 0.789 6.246 25.681 -5.244 0.178 2.642 13.790 -1.742 26.429 9 AA_A9A10:U23U24_BB A 9 ? B 24 ? A 10 ? B 23 ? 1 A A 10 1_555 B U 7 1_555 A A 11 1_555 B G 6 1_555 0.935 -3.321 2.986 4.407 9.310 75.828 -2.922 -0.644 2.668 7.542 -3.570 76.420 10 AA_A10A11:G22U23_BB A 10 ? B 23 ? A 11 ? B 22 ? 1 A A 11 1_555 B G 6 1_555 A U 12 1_555 B A 5 1_555 -1.134 0.970 3.206 4.923 9.491 -11.878 -10.049 -0.679 2.162 -37.394 19.396 -15.969 11 AA_A11U12:A21G22_BB A 11 ? B 22 ? A 12 ? B 21 ? 1 A U 12 1_555 B A 5 1_555 A C 13 1_555 B G 4 1_555 -0.314 -1.471 3.440 -0.221 15.371 33.281 -4.380 0.471 2.541 25.231 0.362 36.568 12 AA_U12C13:G20A21_BB A 12 ? B 21 ? A 13 ? B 20 ? 1 A C 13 1_555 B G 4 1_555 A U 14 1_555 B A 3 1_555 0.205 -2.185 3.482 -3.291 9.833 24.777 -7.089 -1.239 2.407 21.739 7.275 26.828 13 AA_C13U14:A19G20_BB A 13 ? B 20 ? A 14 ? B 19 ? 1 A U 14 1_555 B A 3 1_555 A G 15 1_555 B C 2 1_555 -0.037 -1.569 3.178 1.260 6.750 33.277 -3.687 0.250 2.812 11.633 -2.172 33.958 14 AA_U14G15:C18A19_BB A 14 ? B 19 ? A 15 ? B 18 ? 1 A G 15 1_555 B C 2 1_555 A C 16 1_555 B G 1 1_555 0.056 -1.059 3.246 -0.577 0.714 39.890 -1.633 -0.148 3.227 1.046 0.845 39.900 15 AA_G15C16:G17C18_BB A 15 ? B 18 ? A 16 ? B 17 ? # _atom_sites.entry_id 420D _atom_sites.fract_transf_matrix[1][1] 0.023513 _atom_sites.fract_transf_matrix[1][2] 0.013575 _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] 0.027150 _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] 0.007809 _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 NA O P # loop_