data_1D87 # _entry.id 1D87 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.385 _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 1D87 pdb_00001d87 10.2210/pdb1d87/pdb RCSB AHJ043 ? ? WWPDB D_1000172684 ? ? # 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 1993-07-15 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-07 # _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' 'Structure summary' # 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' struct_keywords # 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' '_struct_keywords.text' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1D87 _pdbx_database_status.recvd_initial_deposition_date 1992-08-28 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _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 'Egli, M.' 1 'Usman, N.' 2 'Rich, A.' 3 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;Conformational influence of the ribose 2'-hydroxyl group: crystal structures of DNA-RNA chimeric duplexes. ; Biochemistry 32 3221 3237 1993 BICHAW US 0006-2960 0033 ? 7681688 10.1021/bi00064a004 1 'Large Scale Chemical Synthesis, Purification and Crystallization of RNA-DNA Chimeras' 'Nucleic Acids Res.' 20 6695 6699 1992 NARHAD UK 0305-1048 0389 ? ? ? 2 'Crystal Structure of an Okazaki Fragment at 2 Angstroms Resolution' Proc.Natl.Acad.Sci.USA 89 534 538 1992 PNASA6 US 0027-8424 0040 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Egli, M.' 1 ? primary 'Usman, N.' 2 ? primary 'Rich, A.' 3 ? 1 'Usman, N.' 4 ? 1 'Egli, M.' 5 ? 1 'Rich, A.' 6 ? 2 'Egli, M.' 7 ? 2 'Usman, N.' 8 ? 2 'Zhang, S.' 9 ? 2 'Rich, A.' 10 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA/RNA (5'-R(*GP*)-D(*CP*GP*TP*AP*TP*AP*CP*GP*C)-3') ; 3061.005 2 ? ? ? ? 2 water nat water 18.015 110 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code 'G(DC)(DG)(DT)(DA)(DT)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTATACGC _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 G n 1 2 DC n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 DT 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 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 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 G 1 1 1 G 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 DT 6 6 6 DT T 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 G 1 11 11 G 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 DT 6 16 16 DT T 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 21 21 HOH HOH A . C 2 HOH 2 22 22 HOH HOH A . C 2 HOH 3 23 23 HOH HOH A . C 2 HOH 4 24 24 HOH HOH A . C 2 HOH 5 25 25 HOH HOH A . C 2 HOH 6 26 26 HOH HOH A . C 2 HOH 7 29 29 HOH HOH A . C 2 HOH 8 30 30 HOH HOH A . C 2 HOH 9 31 31 HOH HOH A . C 2 HOH 10 34 34 HOH HOH A . C 2 HOH 11 35 35 HOH HOH A . C 2 HOH 12 36 36 HOH HOH A . C 2 HOH 13 38 38 HOH HOH A . C 2 HOH 14 39 39 HOH HOH A . C 2 HOH 15 40 40 HOH HOH A . C 2 HOH 16 44 44 HOH HOH A . C 2 HOH 17 46 46 HOH HOH A . C 2 HOH 18 47 47 HOH HOH A . C 2 HOH 19 48 48 HOH HOH A . C 2 HOH 20 49 49 HOH HOH A . C 2 HOH 21 51 51 HOH HOH A . C 2 HOH 22 60 60 HOH HOH A . C 2 HOH 23 62 62 HOH HOH A . C 2 HOH 24 63 63 HOH HOH A . C 2 HOH 25 66 66 HOH HOH A . C 2 HOH 26 69 69 HOH HOH A . C 2 HOH 27 71 71 HOH HOH A . C 2 HOH 28 73 73 HOH HOH A . C 2 HOH 29 74 74 HOH HOH A . C 2 HOH 30 75 75 HOH HOH A . C 2 HOH 31 76 76 HOH HOH A . C 2 HOH 32 77 77 HOH HOH A . C 2 HOH 33 78 78 HOH HOH A . C 2 HOH 34 79 79 HOH HOH A . C 2 HOH 35 80 80 HOH HOH A . C 2 HOH 36 81 81 HOH HOH A . C 2 HOH 37 82 82 HOH HOH A . C 2 HOH 38 83 83 HOH HOH A . C 2 HOH 39 84 84 HOH HOH A . C 2 HOH 40 88 88 HOH HOH A . C 2 HOH 41 93 93 HOH HOH A . C 2 HOH 42 95 95 HOH HOH A . C 2 HOH 43 96 96 HOH HOH A . C 2 HOH 44 97 97 HOH HOH A . C 2 HOH 45 98 98 HOH HOH A . C 2 HOH 46 99 99 HOH HOH A . C 2 HOH 47 101 101 HOH HOH A . C 2 HOH 48 110 110 HOH HOH A . C 2 HOH 49 111 111 HOH HOH A . C 2 HOH 50 112 112 HOH HOH A . C 2 HOH 51 113 113 HOH HOH A . C 2 HOH 52 114 114 HOH HOH A . C 2 HOH 53 115 115 HOH HOH A . C 2 HOH 54 116 116 HOH HOH A . C 2 HOH 55 119 119 HOH HOH A . C 2 HOH 56 121 121 HOH HOH A . C 2 HOH 57 122 122 HOH HOH A . C 2 HOH 58 123 123 HOH HOH A . C 2 HOH 59 124 124 HOH HOH A . C 2 HOH 60 126 126 HOH HOH A . C 2 HOH 61 130 130 HOH HOH A . D 2 HOH 1 27 27 HOH HOH B . D 2 HOH 2 28 28 HOH HOH B . D 2 HOH 3 32 32 HOH HOH B . D 2 HOH 4 33 33 HOH HOH B . D 2 HOH 5 37 37 HOH HOH B . D 2 HOH 6 41 41 HOH HOH B . D 2 HOH 7 42 42 HOH HOH B . D 2 HOH 8 43 43 HOH HOH B . D 2 HOH 9 45 45 HOH HOH B . D 2 HOH 10 50 50 HOH HOH B . D 2 HOH 11 52 52 HOH HOH B . D 2 HOH 12 53 53 HOH HOH B . D 2 HOH 13 54 54 HOH HOH B . D 2 HOH 14 55 55 HOH HOH B . D 2 HOH 15 56 56 HOH HOH B . D 2 HOH 16 57 57 HOH HOH B . D 2 HOH 17 58 58 HOH HOH B . D 2 HOH 18 59 59 HOH HOH B . D 2 HOH 19 61 61 HOH HOH B . D 2 HOH 20 64 64 HOH HOH B . D 2 HOH 21 65 65 HOH HOH B . D 2 HOH 22 67 67 HOH HOH B . D 2 HOH 23 68 68 HOH HOH B . D 2 HOH 24 70 70 HOH HOH B . D 2 HOH 25 72 72 HOH HOH B . D 2 HOH 26 85 85 HOH HOH B . D 2 HOH 27 86 86 HOH HOH B . D 2 HOH 28 87 87 HOH HOH B . D 2 HOH 29 89 89 HOH HOH B . D 2 HOH 30 90 90 HOH HOH B . D 2 HOH 31 91 91 HOH HOH B . D 2 HOH 32 92 92 HOH HOH B . D 2 HOH 33 94 94 HOH HOH B . D 2 HOH 34 100 100 HOH HOH B . D 2 HOH 35 102 102 HOH HOH B . D 2 HOH 36 103 103 HOH HOH B . D 2 HOH 37 104 104 HOH HOH B . D 2 HOH 38 105 105 HOH HOH B . D 2 HOH 39 106 106 HOH HOH B . D 2 HOH 40 107 107 HOH HOH B . D 2 HOH 41 108 108 HOH HOH B . D 2 HOH 42 109 109 HOH HOH B . D 2 HOH 43 117 117 HOH HOH B . D 2 HOH 44 118 118 HOH HOH B . D 2 HOH 45 120 120 HOH HOH B . D 2 HOH 46 125 125 HOH HOH B . D 2 HOH 47 127 127 HOH HOH B . D 2 HOH 48 128 128 HOH HOH B . D 2 HOH 49 129 129 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal PROLSQ refinement '(MODIFIED BY G.J.QUIGLEY)' ? 1 MODIFIED refinement 'BY G.J.QUIGLEY' ? 2 # _cell.entry_id 1D87 _cell.length_a 27.500 _cell.length_b 44.230 _cell.length_c 44.610 _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 1D87 _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 1D87 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 44.49 _exptl_crystal.density_Matthews 2.22 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 291.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.00 _exptl_crystal_grow.pdbx_details 'pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 291.00K' _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 'NA CACODYLATE' ? ? ? 1 3 1 MGCL2 ? ? ? 1 4 1 SPERMINE ? ? ? 1 5 2 WATER ? ? ? 1 6 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 273.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type 'RIGAKU AFC-5R' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1D87 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 2.000 _reflns.d_resolution_low ? _reflns.d_resolution_high 2.250 _reflns.number_obs 1592 _reflns.number_all ? _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_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 1D87 _refine.ls_number_reflns_obs 1592 _refine.ls_number_reflns_all ? _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 ? _refine.ls_d_res_high 2.250 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1780000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _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 ? _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.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _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.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_diffrn_id 1 _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 406 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 110 _refine_hist.number_atoms_total 516 _refine_hist.d_res_high 2.250 _refine_hist.d_res_low . # 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 p_bond_d 0.020 ? ? ? 'X-RAY DIFFRACTION' ? p_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? p_angle_deg ? ? ? ? 'X-RAY DIFFRACTION' ? p_planar_d ? ? ? ? 'X-RAY DIFFRACTION' ? p_hb_or_metal_coord ? ? ? ? 'X-RAY DIFFRACTION' ? p_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? p_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? p_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? p_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? p_plane_restr 0.010 ? ? ? 'X-RAY DIFFRACTION' ? p_chiral_restr 0.140 ? ? ? 'X-RAY DIFFRACTION' ? p_singtor_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? p_multtor_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? p_xhyhbond_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? p_xyhbond_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? p_planar_tor ? ? ? ? 'X-RAY DIFFRACTION' ? p_staggered_tor ? ? ? ? 'X-RAY DIFFRACTION' ? p_orthonormal_tor ? ? ? ? 'X-RAY DIFFRACTION' ? p_transverse_tor ? ? ? ? 'X-RAY DIFFRACTION' ? p_special_tor ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1D87 _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 1D87 _struct.title ;CONFORMATIONAL INFLUENCE OF THE RIBOSE 2'-HYDROXYL GROUP: CRYSTAL STRUCTURES OF DNA-RNA CHIMERIC DUPLEXES ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1D87 _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' _struct_keywords.text 'A-DNA/RNA, DOUBLE HELIX, DNA-RNA HYBRID COMPLEX, DNA-RNA HYBRID' # 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 1D87 _struct_ref.pdbx_db_accession 1D87 _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 1D87 A 1 ? 10 ? 1D87 1 ? 10 ? 1 10 2 1 1D87 B 1 ? 10 ? 1D87 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 hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A G 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A G 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A G 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 DT 4 N3 ? ? ? 1_555 B DC 8 O2 ? ? A DT 4 B DC 18 1_555 ? ? ? ? ? ? 'DT-DC MISPAIR' ? ? ? hydrog13 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 6 N3 ? ? A DA 5 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 5 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DT 4 N3 ? ? A DC 8 B DT 14 1_555 ? ? ? ? ? ? 'DC-DT MISPAIR' ? ? ? hydrog23 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B G 1 N1 ? ? A DC 10 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B G 1 O6 ? ? A DC 10 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B G 1 N2 ? ? A DC 10 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 34 ? ? 1_555 O B HOH 127 ? ? 1_655 1.52 2 1 O A HOH 35 ? ? 1_555 O B HOH 117 ? ? 1_655 1.65 3 1 O A HOH 24 ? ? 1_555 O B HOH 52 ? ? 1_655 1.75 4 1 O A HOH 63 ? ? 1_555 O B HOH 104 ? ? 4_565 1.81 5 1 O2 A DT 4 ? ? 1_555 N2 B G 11 ? ? 2_664 1.98 6 1 O A HOH 35 ? ? 1_555 O B HOH 54 ? ? 1_655 2.15 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 C6 A G 1 ? ? N1 A G 1 ? ? 1.335 1.391 -0.056 0.007 N 2 1 C2 A G 1 ? ? N2 A G 1 ? ? 1.237 1.341 -0.104 0.010 N 3 1 "O3'" A DC 2 ? ? "C3'" A DC 2 ? ? 1.369 1.419 -0.050 0.006 N 4 1 N3 A DC 2 ? ? C4 A DC 2 ? ? 1.382 1.335 0.047 0.007 N 5 1 "O3'" A DG 3 ? ? "C3'" A DG 3 ? ? 1.351 1.419 -0.068 0.006 N 6 1 C6 A DG 3 ? ? N1 A DG 3 ? ? 1.332 1.391 -0.059 0.007 N 7 1 C2 A DG 3 ? ? N2 A DG 3 ? ? 1.249 1.341 -0.092 0.010 N 8 1 "C4'" A DT 4 ? ? "C3'" A DT 4 ? ? 1.599 1.529 0.070 0.010 N 9 1 "C2'" A DT 4 ? ? "C1'" A DT 4 ? ? 1.583 1.519 0.064 0.010 N 10 1 "O3'" A DT 4 ? ? "C3'" A DT 4 ? ? 1.336 1.419 -0.083 0.006 N 11 1 "O3'" A DA 5 ? ? "C3'" A DA 5 ? ? 1.347 1.419 -0.072 0.006 N 12 1 P A DA 7 ? ? "O5'" A DA 7 ? ? 1.664 1.593 0.071 0.010 N 13 1 "C4'" A DA 7 ? ? "C3'" A DA 7 ? ? 1.594 1.529 0.065 0.010 N 14 1 "C2'" A DA 7 ? ? "C1'" A DA 7 ? ? 1.646 1.519 0.127 0.010 N 15 1 "O3'" A DA 7 ? ? "C3'" A DA 7 ? ? 1.334 1.419 -0.085 0.006 N 16 1 "O3'" A DC 8 ? ? "C3'" A DC 8 ? ? 1.368 1.419 -0.051 0.006 N 17 1 "C2'" A DG 9 ? ? "C1'" A DG 9 ? ? 1.601 1.519 0.082 0.010 N 18 1 "O3'" A DG 9 ? ? "C3'" A DG 9 ? ? 1.377 1.419 -0.042 0.006 N 19 1 C6 A DG 9 ? ? N1 A DG 9 ? ? 1.342 1.391 -0.049 0.007 N 20 1 C2 A DG 9 ? ? N2 A DG 9 ? ? 1.228 1.341 -0.113 0.010 N 21 1 N3 A DC 10 ? ? C4 A DC 10 ? ? 1.384 1.335 0.049 0.007 N 22 1 C6 B G 11 ? ? N1 B G 11 ? ? 1.332 1.391 -0.059 0.007 N 23 1 C2 B G 11 ? ? N2 B G 11 ? ? 1.233 1.341 -0.108 0.010 N 24 1 P B DC 12 ? ? "O5'" B DC 12 ? ? 1.660 1.593 0.067 0.010 N 25 1 "C3'" B DC 12 ? ? "C2'" B DC 12 ? ? 1.450 1.516 -0.066 0.008 N 26 1 N3 B DC 12 ? ? C4 B DC 12 ? ? 1.387 1.335 0.052 0.007 N 27 1 C6 B DG 13 ? ? N1 B DG 13 ? ? 1.332 1.391 -0.059 0.007 N 28 1 C2 B DG 13 ? ? N2 B DG 13 ? ? 1.231 1.341 -0.110 0.010 N 29 1 "O3'" B DT 14 ? ? "C3'" B DT 14 ? ? 1.329 1.419 -0.090 0.006 N 30 1 N3 B DC 18 ? ? C4 B DC 18 ? ? 1.383 1.335 0.048 0.007 N 31 1 "C3'" B DG 19 ? ? "C2'" B DG 19 ? ? 1.466 1.516 -0.050 0.008 N 32 1 "O4'" B DG 19 ? ? "C4'" B DG 19 ? ? 1.380 1.446 -0.066 0.010 N 33 1 C6 B DG 19 ? ? N1 B DG 19 ? ? 1.335 1.391 -0.056 0.007 N 34 1 C2 B DG 19 ? ? N2 B DG 19 ? ? 1.227 1.341 -0.114 0.010 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 C6 A G 1 ? ? N1 A G 1 ? ? C2 A G 1 ? ? 119.35 125.10 -5.75 0.60 N 2 1 N1 A G 1 ? ? C2 A G 1 ? ? N3 A G 1 ? ? 128.91 123.90 5.01 0.60 N 3 1 C5 A G 1 ? ? C6 A G 1 ? ? N1 A G 1 ? ? 116.92 111.50 5.42 0.50 N 4 1 N3 A G 1 ? ? C2 A G 1 ? ? N2 A G 1 ? ? 111.02 119.90 -8.88 0.70 N 5 1 C5 A G 1 ? ? C6 A G 1 ? ? O6 A G 1 ? ? 122.81 128.60 -5.79 0.60 N 6 1 "O5'" A DC 2 ? ? P A DC 2 ? ? OP1 A DC 2 ? ? 95.72 105.70 -9.98 0.90 N 7 1 "O5'" A DC 2 ? ? "C5'" A DC 2 ? ? "C4'" A DC 2 ? ? 104.26 109.40 -5.14 0.80 N 8 1 P A DC 2 ? ? "O5'" A DC 2 ? ? "C5'" A DC 2 ? ? 111.09 120.90 -9.81 1.60 N 9 1 "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? 100.14 104.50 -4.36 0.40 N 10 1 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 124.73 119.90 4.83 0.50 N 11 1 N3 A DC 2 ? ? C4 A DC 2 ? ? C5 A DC 2 ? ? 116.84 121.90 -5.06 0.40 N 12 1 C5 A DC 2 ? ? C6 A DC 2 ? ? N1 A DC 2 ? ? 124.21 121.00 3.21 0.50 N 13 1 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 124.69 118.90 5.79 0.60 N 14 1 C5 A DC 2 ? ? C4 A DC 2 ? ? N4 A DC 2 ? ? 125.01 120.20 4.81 0.70 N 15 1 "C3'" A DC 2 ? ? "O3'" A DC 2 ? ? P A DG 3 ? ? 127.62 119.70 7.92 1.20 Y 16 1 "O5'" A DG 3 ? ? P A DG 3 ? ? OP1 A DG 3 ? ? 96.56 105.70 -9.14 0.90 N 17 1 "O4'" A DG 3 ? ? "C4'" A DG 3 ? ? "C3'" A DG 3 ? ? 101.66 104.50 -2.84 0.40 N 18 1 C6 A DG 3 ? ? N1 A DG 3 ? ? C2 A DG 3 ? ? 119.29 125.10 -5.81 0.60 N 19 1 N1 A DG 3 ? ? C2 A DG 3 ? ? N3 A DG 3 ? ? 128.83 123.90 4.93 0.60 N 20 1 C5 A DG 3 ? ? C6 A DG 3 ? ? N1 A DG 3 ? ? 117.48 111.50 5.98 0.50 N 21 1 N3 A DG 3 ? ? C2 A DG 3 ? ? N2 A DG 3 ? ? 112.06 119.90 -7.84 0.70 N 22 1 C5 A DG 3 ? ? C6 A DG 3 ? ? O6 A DG 3 ? ? 122.95 128.60 -5.65 0.60 N 23 1 "O5'" A DT 4 ? ? P A DT 4 ? ? OP2 A DT 4 ? ? 95.75 105.70 -9.95 0.90 N 24 1 "O5'" A DT 4 ? ? "C5'" A DT 4 ? ? "C4'" A DT 4 ? ? 103.33 109.40 -6.07 0.80 N 25 1 P A DT 4 ? ? "O5'" A DT 4 ? ? "C5'" A DT 4 ? ? 109.03 120.90 -11.87 1.60 N 26 1 "O4'" A DT 4 ? ? "C4'" A DT 4 ? ? "C3'" A DT 4 ? ? 99.79 104.50 -4.71 0.40 N 27 1 "C4'" A DT 4 ? ? "C3'" A DT 4 ? ? "C2'" A DT 4 ? ? 97.39 102.20 -4.81 0.70 N 28 1 C4 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 124.43 119.00 5.43 0.60 N 29 1 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 116.34 122.90 -6.56 0.60 N 30 1 "O5'" A DA 5 ? ? P A DA 5 ? ? OP1 A DA 5 ? ? 99.22 105.70 -6.48 0.90 N 31 1 "O4'" A DA 5 ? ? "C4'" A DA 5 ? ? "C3'" A DA 5 ? ? 101.57 104.50 -2.93 0.40 N 32 1 "C4'" A DA 5 ? ? "C3'" A DA 5 ? ? "C2'" A DA 5 ? ? 96.79 102.20 -5.41 0.70 N 33 1 "C3'" A DA 5 ? ? "C2'" A DA 5 ? ? "C1'" A DA 5 ? ? 96.03 102.40 -6.37 0.80 N 34 1 "C3'" A DA 5 ? ? "O3'" A DA 5 ? ? P A DT 6 ? ? 130.98 119.70 11.28 1.20 Y 35 1 "O5'" A DT 6 ? ? P A DT 6 ? ? OP1 A DT 6 ? ? 97.39 105.70 -8.31 0.90 N 36 1 C6 A DT 6 ? ? C5 A DT 6 ? ? C7 A DT 6 ? ? 118.26 122.90 -4.64 0.60 N 37 1 "O5'" A DA 7 ? ? P A DA 7 ? ? OP1 A DA 7 ? ? 97.96 105.70 -7.74 0.90 N 38 1 P A DA 7 ? ? "O5'" A DA 7 ? ? "C5'" A DA 7 ? ? 106.68 120.90 -14.22 1.60 N 39 1 "C4'" A DA 7 ? ? "C3'" A DA 7 ? ? "C2'" A DA 7 ? ? 96.30 102.20 -5.90 0.70 N 40 1 "O4'" A DA 7 ? ? "C1'" A DA 7 ? ? "C2'" A DA 7 ? ? 100.95 105.90 -4.95 0.80 N 41 1 "O4'" A DA 7 ? ? "C1'" A DA 7 ? ? N9 A DA 7 ? ? 113.23 108.30 4.93 0.30 N 42 1 "C3'" A DA 7 ? ? "O3'" A DA 7 ? ? P A DC 8 ? ? 151.41 119.70 31.71 1.20 Y 43 1 "O3'" A DA 7 ? ? P A DC 8 ? ? "O5'" A DC 8 ? ? 115.91 104.00 11.91 1.90 Y 44 1 "O5'" A DC 8 ? ? P A DC 8 ? ? OP1 A DC 8 ? ? 97.96 105.70 -7.74 0.90 N 45 1 "O4'" A DC 8 ? ? "C4'" A DC 8 ? ? "C3'" A DC 8 ? ? 100.48 104.50 -4.02 0.40 N 46 1 "C5'" A DC 8 ? ? "C4'" A DC 8 ? ? "C3'" A DC 8 ? ? 123.37 115.70 7.67 1.20 N 47 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 103.33 108.00 -4.67 0.70 N 48 1 C2 A DC 8 ? ? N3 A DC 8 ? ? C4 A DC 8 ? ? 125.14 119.90 5.24 0.50 N 49 1 N3 A DC 8 ? ? C4 A DC 8 ? ? C5 A DC 8 ? ? 117.40 121.90 -4.50 0.40 N 50 1 N1 A DC 8 ? ? C2 A DC 8 ? ? O2 A DC 8 ? ? 123.89 118.90 4.99 0.60 N 51 1 "O3'" A DC 8 ? ? P A DG 9 ? ? "O5'" A DG 9 ? ? 115.82 104.00 11.82 1.90 Y 52 1 "O5'" A DG 9 ? ? "C5'" A DG 9 ? ? "C4'" A DG 9 ? ? 99.83 109.40 -9.57 0.80 N 53 1 "O4'" A DG 9 ? ? "C4'" A DG 9 ? ? "C3'" A DG 9 ? ? 99.96 104.50 -4.54 0.40 N 54 1 "C4'" A DG 9 ? ? "C3'" A DG 9 ? ? "C2'" A DG 9 ? ? 95.09 102.20 -7.11 0.70 N 55 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 113.80 108.30 5.50 0.30 N 56 1 C6 A DG 9 ? ? N1 A DG 9 ? ? C2 A DG 9 ? ? 119.43 125.10 -5.67 0.60 N 57 1 N1 A DG 9 ? ? C2 A DG 9 ? ? N3 A DG 9 ? ? 129.44 123.90 5.54 0.60 N 58 1 C2 A DG 9 ? ? N3 A DG 9 ? ? C4 A DG 9 ? ? 108.74 111.90 -3.16 0.50 N 59 1 C5 A DG 9 ? ? C6 A DG 9 ? ? N1 A DG 9 ? ? 117.08 111.50 5.58 0.50 N 60 1 N3 A DG 9 ? ? C2 A DG 9 ? ? N2 A DG 9 ? ? 108.98 119.90 -10.92 0.70 N 61 1 "C3'" A DG 9 ? ? "O3'" A DG 9 ? ? P A DC 10 ? ? 129.97 119.70 10.27 1.20 Y 62 1 "O5'" A DC 10 ? ? P A DC 10 ? ? OP1 A DC 10 ? ? 98.79 105.70 -6.91 0.90 N 63 1 C2 A DC 10 ? ? N3 A DC 10 ? ? C4 A DC 10 ? ? 124.53 119.90 4.63 0.50 N 64 1 N3 A DC 10 ? ? C4 A DC 10 ? ? C5 A DC 10 ? ? 117.51 121.90 -4.39 0.40 N 65 1 C5 A DC 10 ? ? C6 A DC 10 ? ? N1 A DC 10 ? ? 125.38 121.00 4.38 0.50 N 66 1 N1 A DC 10 ? ? C2 A DC 10 ? ? O2 A DC 10 ? ? 125.54 118.90 6.64 0.60 N 67 1 C6 B G 11 ? ? N1 B G 11 ? ? C2 B G 11 ? ? 119.34 125.10 -5.76 0.60 N 68 1 N1 B G 11 ? ? C2 B G 11 ? ? N3 B G 11 ? ? 128.73 123.90 4.83 0.60 N 69 1 C5 B G 11 ? ? C6 B G 11 ? ? N1 B G 11 ? ? 117.34 111.50 5.84 0.50 N 70 1 N3 B G 11 ? ? C2 B G 11 ? ? N2 B G 11 ? ? 111.84 119.90 -8.06 0.70 N 71 1 C5 B G 11 ? ? C6 B G 11 ? ? O6 B G 11 ? ? 122.85 128.60 -5.75 0.60 N 72 1 "C3'" B G 11 ? ? "O3'" B G 11 ? ? P B DC 12 ? ? 127.77 119.70 8.07 1.20 Y 73 1 "O5'" B DC 12 ? ? P B DC 12 ? ? OP1 B DC 12 ? ? 96.65 105.70 -9.05 0.90 N 74 1 C2 B DC 12 ? ? N3 B DC 12 ? ? C4 B DC 12 ? ? 124.63 119.90 4.73 0.50 N 75 1 N3 B DC 12 ? ? C4 B DC 12 ? ? C5 B DC 12 ? ? 116.36 121.90 -5.54 0.40 N 76 1 N1 B DC 12 ? ? C2 B DC 12 ? ? O2 B DC 12 ? ? 123.86 118.90 4.96 0.60 N 77 1 C5 B DC 12 ? ? C4 B DC 12 ? ? N4 B DC 12 ? ? 125.87 120.20 5.67 0.70 N 78 1 "O4'" B DG 13 ? ? "C4'" B DG 13 ? ? "C3'" B DG 13 ? ? 93.48 104.50 -11.02 0.40 N 79 1 "C5'" B DG 13 ? ? "C4'" B DG 13 ? ? "O4'" B DG 13 ? ? 116.42 109.80 6.62 1.10 N 80 1 C6 B DG 13 ? ? N1 B DG 13 ? ? C2 B DG 13 ? ? 119.14 125.10 -5.96 0.60 N 81 1 N1 B DG 13 ? ? C2 B DG 13 ? ? N3 B DG 13 ? ? 129.73 123.90 5.83 0.60 N 82 1 C5 B DG 13 ? ? C6 B DG 13 ? ? N1 B DG 13 ? ? 117.12 111.50 5.62 0.50 N 83 1 N3 B DG 13 ? ? C2 B DG 13 ? ? N2 B DG 13 ? ? 111.97 119.90 -7.93 0.70 N 84 1 C5 B DG 13 ? ? C6 B DG 13 ? ? O6 B DG 13 ? ? 123.73 128.60 -4.87 0.60 N 85 1 "C3'" B DG 13 ? ? "O3'" B DG 13 ? ? P B DT 14 ? ? 109.43 119.70 -10.27 1.20 Y 86 1 "O4'" B DT 14 ? ? "C4'" B DT 14 ? ? "C3'" B DT 14 ? ? 101.76 104.50 -2.74 0.40 N 87 1 "C3'" B DT 14 ? ? "C2'" B DT 14 ? ? "C1'" B DT 14 ? ? 97.26 102.40 -5.14 0.80 N 88 1 "O4'" B DT 14 ? ? "C1'" B DT 14 ? ? N1 B DT 14 ? ? 111.77 108.30 3.47 0.30 N 89 1 C4 B DT 14 ? ? C5 B DT 14 ? ? C7 B DT 14 ? ? 122.74 119.00 3.74 0.60 N 90 1 C6 B DT 14 ? ? C5 B DT 14 ? ? C7 B DT 14 ? ? 119.14 122.90 -3.76 0.60 N 91 1 "C3'" B DT 14 ? ? "O3'" B DT 14 ? ? P B DA 15 ? ? 132.84 119.70 13.14 1.20 Y 92 1 "O5'" B DA 15 ? ? P B DA 15 ? ? OP1 B DA 15 ? ? 96.97 105.70 -8.73 0.90 N 93 1 P B DA 15 ? ? "O5'" B DA 15 ? ? "C5'" B DA 15 ? ? 108.65 120.90 -12.25 1.60 N 94 1 "O4'" B DA 15 ? ? "C1'" B DA 15 ? ? N9 B DA 15 ? ? 112.48 108.30 4.18 0.30 N 95 1 "O5'" B DT 16 ? ? P B DT 16 ? ? OP1 B DT 16 ? ? 97.25 105.70 -8.45 0.90 N 96 1 P B DT 16 ? ? "O5'" B DT 16 ? ? "C5'" B DT 16 ? ? 110.16 120.90 -10.74 1.60 N 97 1 "O4'" B DT 16 ? ? "C4'" B DT 16 ? ? "C3'" B DT 16 ? ? 97.70 104.50 -6.80 0.40 N 98 1 "C5'" B DT 16 ? ? "C4'" B DT 16 ? ? "C3'" B DT 16 ? ? 124.67 115.70 8.97 1.20 N 99 1 "C4'" B DT 16 ? ? "C3'" B DT 16 ? ? "C2'" B DT 16 ? ? 96.30 102.20 -5.90 0.70 N 100 1 C2 B DT 16 ? ? N3 B DT 16 ? ? C4 B DT 16 ? ? 123.12 127.20 -4.08 0.60 N 101 1 "O5'" B DA 17 ? ? P B DA 17 ? ? OP2 B DA 17 ? ? 97.57 105.70 -8.13 0.90 N 102 1 "O5'" B DC 18 ? ? P B DC 18 ? ? OP1 B DC 18 ? ? 95.64 105.70 -10.06 0.90 N 103 1 C2 B DC 18 ? ? N3 B DC 18 ? ? C4 B DC 18 ? ? 125.00 119.90 5.10 0.50 N 104 1 N3 B DC 18 ? ? C4 B DC 18 ? ? C5 B DC 18 ? ? 116.99 121.90 -4.91 0.40 N 105 1 C5 B DC 18 ? ? C6 B DC 18 ? ? N1 B DC 18 ? ? 124.93 121.00 3.93 0.50 N 106 1 N1 B DC 18 ? ? C2 B DC 18 ? ? O2 B DC 18 ? ? 125.74 118.90 6.84 0.60 N 107 1 "O5'" B DG 19 ? ? P B DG 19 ? ? OP2 B DG 19 ? ? 98.89 105.70 -6.81 0.90 N 108 1 P B DG 19 ? ? "O5'" B DG 19 ? ? "C5'" B DG 19 ? ? 106.10 120.90 -14.80 1.60 N 109 1 "C5'" B DG 19 ? ? "C4'" B DG 19 ? ? "O4'" B DG 19 ? ? 117.30 109.80 7.50 1.10 N 110 1 "O4'" B DG 19 ? ? "C1'" B DG 19 ? ? N9 B DG 19 ? ? 110.12 108.30 1.82 0.30 N 111 1 C6 B DG 19 ? ? N1 B DG 19 ? ? C2 B DG 19 ? ? 119.73 125.10 -5.37 0.60 N 112 1 N1 B DG 19 ? ? C2 B DG 19 ? ? N3 B DG 19 ? ? 129.67 123.90 5.77 0.60 N 113 1 C2 B DG 19 ? ? N3 B DG 19 ? ? C4 B DG 19 ? ? 108.59 111.90 -3.31 0.50 N 114 1 C5 B DG 19 ? ? C6 B DG 19 ? ? N1 B DG 19 ? ? 116.87 111.50 5.37 0.50 N 115 1 N3 B DG 19 ? ? C2 B DG 19 ? ? N2 B DG 19 ? ? 110.88 119.90 -9.02 0.70 N 116 1 C5 B DG 19 ? ? C6 B DG 19 ? ? O6 B DG 19 ? ? 124.42 128.60 -4.18 0.60 N 117 1 "O5'" B DC 20 ? ? P B DC 20 ? ? OP2 B DC 20 ? ? 97.18 105.70 -8.52 0.90 N 118 1 "O4'" B DC 20 ? ? "C1'" B DC 20 ? ? "C2'" B DC 20 ? ? 100.86 105.90 -5.04 0.80 N 119 1 N1 B DC 20 ? ? "C1'" B DC 20 ? ? "C2'" B DC 20 ? ? 123.98 114.30 9.68 1.40 N 120 1 C6 B DC 20 ? ? N1 B DC 20 ? ? C2 B DC 20 ? ? 117.73 120.30 -2.57 0.40 N 121 1 C2 B DC 20 ? ? N3 B DC 20 ? ? C4 B DC 20 ? ? 125.88 119.90 5.98 0.50 N 122 1 N3 B DC 20 ? ? C4 B DC 20 ? ? C5 B DC 20 ? ? 116.59 121.90 -5.31 0.40 N 123 1 C5 B DC 20 ? ? C6 B DC 20 ? ? N1 B DC 20 ? ? 126.55 121.00 5.55 0.50 N 124 1 N1 B DC 20 ? ? C2 B DC 20 ? ? O2 B DC 20 ? ? 123.62 118.90 4.72 0.60 N 125 1 N3 B DC 20 ? ? C4 B DC 20 ? ? N4 B DC 20 ? ? 122.53 118.00 4.53 0.70 N # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TR isotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TR isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix 'X-RAY DIFFRACTION' # 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 G OP3 O N N 144 G P P N N 145 G OP1 O N N 146 G OP2 O N N 147 G "O5'" O N N 148 G "C5'" C N N 149 G "C4'" C N R 150 G "O4'" O N N 151 G "C3'" C N S 152 G "O3'" O N N 153 G "C2'" C N R 154 G "O2'" O N N 155 G "C1'" C N R 156 G N9 N Y N 157 G C8 C Y N 158 G N7 N Y N 159 G C5 C Y N 160 G C6 C N N 161 G O6 O N N 162 G N1 N N N 163 G C2 C N N 164 G N2 N N N 165 G N3 N N N 166 G C4 C Y N 167 G HOP3 H N N 168 G HOP2 H N N 169 G "H5'" H N N 170 G "H5''" H N N 171 G "H4'" H N N 172 G "H3'" H N N 173 G "HO3'" H N N 174 G "H2'" H N N 175 G "HO2'" H N N 176 G "H1'" H N N 177 G H8 H N N 178 G H1 H N N 179 G H21 H N N 180 G H22 H N N 181 HOH O O N N 182 HOH H1 H N N 183 HOH H2 H N N 184 # 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 G OP3 P sing N N 150 G OP3 HOP3 sing N N 151 G P OP1 doub N N 152 G P OP2 sing N N 153 G P "O5'" sing N N 154 G OP2 HOP2 sing N N 155 G "O5'" "C5'" sing N N 156 G "C5'" "C4'" sing N N 157 G "C5'" "H5'" sing N N 158 G "C5'" "H5''" sing N N 159 G "C4'" "O4'" sing N N 160 G "C4'" "C3'" sing N N 161 G "C4'" "H4'" sing N N 162 G "O4'" "C1'" sing N N 163 G "C3'" "O3'" sing N N 164 G "C3'" "C2'" sing N N 165 G "C3'" "H3'" sing N N 166 G "O3'" "HO3'" sing N N 167 G "C2'" "O2'" sing N N 168 G "C2'" "C1'" sing N N 169 G "C2'" "H2'" sing N N 170 G "O2'" "HO2'" sing N N 171 G "C1'" N9 sing N N 172 G "C1'" "H1'" sing N N 173 G N9 C8 sing Y N 174 G N9 C4 sing Y N 175 G C8 N7 doub Y N 176 G C8 H8 sing N N 177 G N7 C5 sing Y N 178 G C5 C6 sing N N 179 G C5 C4 doub Y N 180 G C6 O6 doub N N 181 G C6 N1 sing N N 182 G N1 C2 sing N N 183 G N1 H1 sing N N 184 G C2 N2 sing N N 185 G C2 N3 doub N N 186 G N2 H21 sing N N 187 G N2 H22 sing N N 188 G N3 C4 sing N N 189 HOH O H1 sing N N 190 HOH O H2 sing N N 191 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1D87 'double helix' 1D87 '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 G 1 1_555 B DC 10 1_555 0.517 -0.253 -0.139 -3.059 -19.256 -2.373 1 A_G1:DC20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.044 -0.043 0.006 0.437 -16.241 2.997 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 0.354 -0.078 -0.448 -13.184 -11.151 -3.372 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -1.095 -0.219 -0.551 4.287 -16.958 -1.750 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DA 5 1_555 B DT 6 1_555 1.331 0.076 0.683 4.207 -10.276 -15.461 5 A_DA5:DT16_B A 5 ? B 16 ? 20 1 1 A DT 6 1_555 B DA 5 1_555 -1.205 -0.001 0.014 9.419 6.512 -4.498 6 A_DT6:DA15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.693 -0.123 -0.928 -9.066 -27.165 -0.148 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 1.386 -0.815 -0.420 8.246 -10.975 -4.451 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.472 -0.030 0.090 -11.369 -17.203 3.164 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B G 1 1_555 0.137 -0.282 0.548 -3.416 17.271 0.118 10 A_DC10:G11_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 G 1 1_555 B DC 10 1_555 A DC 2 1_555 B DG 9 1_555 1.255 -1.488 3.214 -1.720 8.741 28.521 -4.535 -2.761 2.576 17.220 3.389 29.852 1 AA_G1DC2: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 -0.271 -1.195 4.125 1.053 -0.717 29.169 -2.173 0.826 4.141 -1.423 -2.089 29.196 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 -0.994 -2.006 2.644 2.711 8.499 34.985 -4.115 1.885 2.037 13.861 -4.422 36.071 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 DT 6 1_555 0.544 -1.521 3.663 -5.948 15.287 34.433 -4.313 -1.604 2.652 24.197 9.414 38.033 4 AA_DT4DA5:DT16DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DA 5 1_555 B DT 6 1_555 A DT 6 1_555 B DA 5 1_555 0.344 -2.562 3.307 6.000 7.895 21.501 -8.592 0.940 2.251 19.859 -15.091 23.653 5 AA_DA5DT6:DA15DT16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DT 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 0.870 -1.203 3.828 7.887 19.970 36.454 -3.978 -0.300 2.938 29.039 -11.469 42.122 6 AA_DT6DA7: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 0.818 -1.933 2.803 0.373 4.427 34.767 -3.757 -1.313 2.553 7.371 -0.621 35.041 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 0.096 -1.201 3.826 0.163 4.262 22.856 -4.649 -0.173 3.547 10.635 -0.408 23.246 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 G 1 1_555 -0.900 -1.084 3.407 -9.201 8.507 38.306 -2.580 0.222 3.228 12.560 13.586 40.230 9 AA_DG9DC10:G11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _atom_sites.entry_id 1D87 _atom_sites.fract_transf_matrix[1][1] 0.036364 _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] 0.022609 _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] 0.022417 _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_