data_1D88 # _entry.id 1D88 # _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 1D88 pdb_00001d88 10.2210/pdb1d88/pdb RCSB AHJ044 ? ? WWPDB D_1000172685 ? ? # 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 1D88 _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'-D(*GP*CP*GP*TP*)-R(*AP*)-D(*TP*AP*CP*GP*C)-3') ; 3061.004 2 ? ? ? ? 2 water nat water 18.015 94 ? ? ? ? # _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 '(DG)(DC)(DG)(DT)A(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 DG n 1 2 DC n 1 3 DG n 1 4 DT n 1 5 A 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 A 5 5 5 A 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 DG 1 11 11 DG G B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DG 3 13 13 DG G B . n B 1 4 DT 4 14 14 DT T B . n B 1 5 A 5 15 15 A 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 22 22 HOH HOH A . C 2 HOH 2 24 24 HOH HOH A . C 2 HOH 3 25 25 HOH HOH A . C 2 HOH 4 27 27 HOH HOH A . C 2 HOH 5 28 28 HOH HOH A . C 2 HOH 6 30 30 HOH HOH A . C 2 HOH 7 32 32 HOH HOH A . C 2 HOH 8 33 33 HOH HOH A . C 2 HOH 9 34 34 HOH HOH A . C 2 HOH 10 35 35 HOH HOH A . C 2 HOH 11 37 37 HOH HOH A . C 2 HOH 12 38 38 HOH HOH A . C 2 HOH 13 39 39 HOH HOH A . C 2 HOH 14 40 40 HOH HOH A . C 2 HOH 15 41 41 HOH HOH A . C 2 HOH 16 42 42 HOH HOH A . C 2 HOH 17 43 43 HOH HOH A . C 2 HOH 18 44 44 HOH HOH A . C 2 HOH 19 45 45 HOH HOH A . C 2 HOH 20 46 46 HOH HOH A . C 2 HOH 21 47 47 HOH HOH A . C 2 HOH 22 50 50 HOH HOH A . C 2 HOH 23 51 51 HOH HOH A . C 2 HOH 24 53 53 HOH HOH A . C 2 HOH 25 55 55 HOH HOH A . C 2 HOH 26 59 59 HOH HOH A . C 2 HOH 27 67 67 HOH HOH A . C 2 HOH 28 69 69 HOH HOH A . C 2 HOH 29 70 70 HOH HOH A . C 2 HOH 30 71 71 HOH HOH A . C 2 HOH 31 74 74 HOH HOH A . C 2 HOH 32 75 75 HOH HOH A . C 2 HOH 33 76 76 HOH HOH A . C 2 HOH 34 77 77 HOH HOH A . C 2 HOH 35 79 79 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 85 85 HOH HOH A . C 2 HOH 40 88 88 HOH HOH A . C 2 HOH 41 91 91 HOH HOH A . C 2 HOH 42 93 93 HOH HOH A . C 2 HOH 43 95 95 HOH HOH A . C 2 HOH 44 96 96 HOH HOH A . C 2 HOH 45 98 98 HOH HOH A . C 2 HOH 46 99 99 HOH HOH A . C 2 HOH 47 100 100 HOH HOH A . C 2 HOH 48 102 102 HOH HOH A . C 2 HOH 49 108 108 HOH HOH A . C 2 HOH 50 111 111 HOH HOH A . C 2 HOH 51 112 112 HOH HOH A . C 2 HOH 52 113 113 HOH HOH A . C 2 HOH 53 114 114 HOH HOH A . D 2 HOH 1 21 21 HOH HOH B . D 2 HOH 2 23 23 HOH HOH B . D 2 HOH 3 26 26 HOH HOH B . D 2 HOH 4 29 29 HOH HOH B . D 2 HOH 5 31 31 HOH HOH B . D 2 HOH 6 36 36 HOH HOH B . D 2 HOH 7 48 48 HOH HOH B . D 2 HOH 8 49 49 HOH HOH B . D 2 HOH 9 52 52 HOH HOH B . D 2 HOH 10 54 54 HOH HOH B . D 2 HOH 11 56 56 HOH HOH B . D 2 HOH 12 57 57 HOH HOH B . D 2 HOH 13 58 58 HOH HOH B . D 2 HOH 14 60 60 HOH HOH B . D 2 HOH 15 61 61 HOH HOH B . D 2 HOH 16 62 62 HOH HOH B . D 2 HOH 17 63 63 HOH HOH B . D 2 HOH 18 64 64 HOH HOH B . D 2 HOH 19 65 65 HOH HOH B . D 2 HOH 20 66 66 HOH HOH B . D 2 HOH 21 68 68 HOH HOH B . D 2 HOH 22 72 72 HOH HOH B . D 2 HOH 23 73 73 HOH HOH B . D 2 HOH 24 78 78 HOH HOH B . D 2 HOH 25 80 80 HOH HOH B . D 2 HOH 26 84 84 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 92 92 HOH HOH B . D 2 HOH 32 94 94 HOH HOH B . D 2 HOH 33 97 97 HOH HOH B . D 2 HOH 34 101 101 HOH HOH B . D 2 HOH 35 103 103 HOH HOH B . D 2 HOH 36 104 104 HOH HOH B . D 2 HOH 37 105 105 HOH HOH B . D 2 HOH 38 106 106 HOH HOH B . D 2 HOH 39 107 107 HOH HOH B . D 2 HOH 40 109 109 HOH HOH B . D 2 HOH 41 110 110 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 1D88 _cell.length_a 25.250 _cell.length_b 45.730 _cell.length_c 45.830 _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 1D88 _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 1D88 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 43.08 _exptl_crystal.density_Matthews 2.16 _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 1D88 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 2.000 _reflns.d_resolution_low ? _reflns.d_resolution_high 2.000 _reflns.number_obs 2285 _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 1D88 _refine.ls_number_reflns_obs 2285 _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 2.000 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1950000 _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 94 _refine_hist.number_atoms_total 500 _refine_hist.d_res_high 2.000 _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 1D88 _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 1D88 _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 1D88 _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 1D88 _struct_ref.pdbx_db_accession 1D88 _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 1D88 A 1 ? 10 ? 1D88 1 ? 10 ? 1 10 2 1 1D88 B 1 ? 10 ? 1D88 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 DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 B DT 6 N3 ? ? A A 5 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 B DT 6 O4 ? ? A A 5 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B A 5 N1 ? ? A DT 6 B A 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B A 5 N6 ? ? A DT 6 B A 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O2 _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 DC _pdbx_validate_close_contact.auth_seq_id_1 20 _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_2 109 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.15 # 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 38 ? ? 1_555 O A HOH 113 ? ? 2_454 1.64 2 1 O A HOH 41 ? ? 1_555 O A HOH 85 ? ? 2_454 2.01 3 1 "O3'" A DC 10 ? ? 1_555 N2 B DG 19 ? ? 3_555 2.13 4 1 N2 B DG 11 ? ? 1_555 O2 B DC 18 ? ? 3_555 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 DG 1 ? ? N1 A DG 1 ? ? 1.344 1.391 -0.047 0.007 N 2 1 C2 A DG 1 ? ? N2 A DG 1 ? ? 1.230 1.341 -0.111 0.010 N 3 1 "O3'" A DC 2 ? ? "C3'" A DC 2 ? ? 1.375 1.419 -0.044 0.006 N 4 1 "C4'" A DG 3 ? ? "C3'" A DG 3 ? ? 1.603 1.529 0.074 0.010 N 5 1 "C2'" A DG 3 ? ? "C1'" A DG 3 ? ? 1.582 1.519 0.063 0.010 N 6 1 "O3'" A DG 3 ? ? "C3'" A DG 3 ? ? 1.379 1.419 -0.040 0.006 N 7 1 C6 A DG 3 ? ? N1 A DG 3 ? ? 1.345 1.391 -0.046 0.007 N 8 1 C8 A DG 3 ? ? N9 A DG 3 ? ? 1.320 1.374 -0.054 0.007 N 9 1 C2 A DG 3 ? ? N2 A DG 3 ? ? 1.226 1.341 -0.115 0.010 N 10 1 P A DT 4 ? ? "O5'" A DT 4 ? ? 1.662 1.593 0.069 0.010 N 11 1 "C5'" A A 5 ? ? "C4'" A A 5 ? ? 1.458 1.508 -0.050 0.007 N 12 1 "O3'" A DT 6 ? ? "C3'" A DT 6 ? ? 1.357 1.419 -0.062 0.006 N 13 1 "C4'" A DA 7 ? ? "C3'" A DA 7 ? ? 1.597 1.529 0.068 0.010 N 14 1 "O3'" A DA 7 ? ? "C3'" A DA 7 ? ? 1.341 1.419 -0.078 0.006 N 15 1 "C2'" A DC 8 ? ? "C1'" A DC 8 ? ? 1.592 1.519 0.073 0.010 N 16 1 "O3'" A DC 8 ? ? "C3'" A DC 8 ? ? 1.376 1.419 -0.043 0.006 N 17 1 C6 A DG 9 ? ? N1 A DG 9 ? ? 1.342 1.391 -0.049 0.007 N 18 1 C2 A DG 9 ? ? N2 A DG 9 ? ? 1.230 1.341 -0.111 0.010 N 19 1 N3 A DC 10 ? ? C4 A DC 10 ? ? 1.384 1.335 0.049 0.007 N 20 1 "C2'" B DG 11 ? ? "C1'" B DG 11 ? ? 1.594 1.519 0.075 0.010 N 21 1 C6 B DG 11 ? ? N1 B DG 11 ? ? 1.332 1.391 -0.059 0.007 N 22 1 C2 B DG 11 ? ? N2 B DG 11 ? ? 1.234 1.341 -0.107 0.010 N 23 1 N3 B DC 12 ? ? C4 B DC 12 ? ? 1.377 1.335 0.042 0.007 N 24 1 "O3'" B DG 13 ? ? "C3'" B DG 13 ? ? 1.374 1.419 -0.045 0.006 N 25 1 C6 B DG 13 ? ? N1 B DG 13 ? ? 1.340 1.391 -0.051 0.007 N 26 1 C2 B DG 13 ? ? N2 B DG 13 ? ? 1.236 1.341 -0.105 0.010 N 27 1 P B A 15 ? ? "O5'" B A 15 ? ? 1.660 1.593 0.067 0.010 N 28 1 "O3'" B DT 16 ? ? "C3'" B DT 16 ? ? 1.381 1.419 -0.038 0.006 N 29 1 "C2'" B DC 18 ? ? "C1'" B DC 18 ? ? 1.589 1.519 0.070 0.010 N 30 1 N3 B DC 18 ? ? C4 B DC 18 ? ? 1.392 1.335 0.057 0.007 N 31 1 C6 B DG 19 ? ? N1 B DG 19 ? ? 1.335 1.391 -0.056 0.007 N 32 1 C8 B DG 19 ? ? N9 B DG 19 ? ? 1.324 1.374 -0.050 0.007 N 33 1 C2 B DG 19 ? ? N2 B DG 19 ? ? 1.237 1.341 -0.104 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 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 112.68 108.30 4.38 0.30 N 2 1 C6 A DG 1 ? ? N1 A DG 1 ? ? C2 A DG 1 ? ? 118.77 125.10 -6.33 0.60 N 3 1 N1 A DG 1 ? ? C2 A DG 1 ? ? N3 A DG 1 ? ? 128.96 123.90 5.06 0.60 N 4 1 C5 A DG 1 ? ? C6 A DG 1 ? ? N1 A DG 1 ? ? 117.55 111.50 6.05 0.50 N 5 1 N1 A DG 1 ? ? C2 A DG 1 ? ? N2 A DG 1 ? ? 124.85 116.20 8.65 0.90 N 6 1 N3 A DG 1 ? ? C2 A DG 1 ? ? N2 A DG 1 ? ? 106.18 119.90 -13.72 0.70 N 7 1 C5 A DG 1 ? ? C6 A DG 1 ? ? O6 A DG 1 ? ? 124.05 128.60 -4.55 0.60 N 8 1 "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? 98.56 104.50 -5.94 0.40 N 9 1 "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? "C2'" A DC 2 ? ? 97.17 102.20 -5.03 0.70 N 10 1 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 125.07 119.90 5.17 0.50 N 11 1 N3 A DC 2 ? ? C4 A DC 2 ? ? C5 A DC 2 ? ? 116.25 121.90 -5.65 0.40 N 12 1 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 125.52 118.90 6.62 0.60 N 13 1 C5 A DC 2 ? ? C4 A DC 2 ? ? N4 A DC 2 ? ? 124.70 120.20 4.50 0.70 N 14 1 "O5'" A DG 3 ? ? P A DG 3 ? ? OP1 A DG 3 ? ? 98.72 105.70 -6.98 0.90 N 15 1 "O4'" A DG 3 ? ? "C4'" A DG 3 ? ? "C3'" A DG 3 ? ? 101.47 104.50 -3.03 0.40 N 16 1 "C5'" A DG 3 ? ? "C4'" A DG 3 ? ? "O4'" A DG 3 ? ? 119.48 109.80 9.68 1.10 N 17 1 "C1'" A DG 3 ? ? "O4'" A DG 3 ? ? "C4'" A DG 3 ? ? 115.64 110.30 5.34 0.70 N 18 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 116.57 108.30 8.27 0.30 N 19 1 C6 A DG 3 ? ? N1 A DG 3 ? ? C2 A DG 3 ? ? 119.71 125.10 -5.39 0.60 N 20 1 N1 A DG 3 ? ? C2 A DG 3 ? ? N3 A DG 3 ? ? 128.11 123.90 4.21 0.60 N 21 1 C5 A DG 3 ? ? C6 A DG 3 ? ? N1 A DG 3 ? ? 117.89 111.50 6.39 0.50 N 22 1 N1 A DG 3 ? ? C2 A DG 3 ? ? N2 A DG 3 ? ? 122.43 116.20 6.23 0.90 N 23 1 N3 A DG 3 ? ? C2 A DG 3 ? ? N2 A DG 3 ? ? 109.46 119.90 -10.44 0.70 N 24 1 C5 A DG 3 ? ? C6 A DG 3 ? ? O6 A DG 3 ? ? 122.00 128.60 -6.60 0.60 N 25 1 "O5'" A DT 4 ? ? P A DT 4 ? ? OP2 A DT 4 ? ? 99.35 105.70 -6.35 0.90 N 26 1 P A DT 4 ? ? "O5'" A DT 4 ? ? "C5'" A DT 4 ? ? 103.24 120.90 -17.66 1.60 N 27 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 100.36 108.00 -7.64 0.70 N 28 1 C4 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 124.17 119.00 5.17 0.60 N 29 1 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 117.29 122.90 -5.61 0.60 N 30 1 "O5'" A A 5 ? ? P A A 5 ? ? OP1 A A 5 ? ? 99.14 105.70 -6.56 0.90 N 31 1 "O5'" A A 5 ? ? "C5'" A A 5 ? ? "C4'" A A 5 ? ? 126.52 111.70 14.82 1.90 N 32 1 P A A 5 ? ? "O5'" A A 5 ? ? "C5'" A A 5 ? ? 110.14 120.90 -10.76 1.60 N 33 1 N9 A A 5 ? ? "C1'" A A 5 ? ? "C2'" A A 5 ? ? 104.17 112.00 -7.83 1.10 N 34 1 "C3'" A DT 6 ? ? "O3'" A DT 6 ? ? P A DA 7 ? ? 130.22 119.70 10.52 1.20 Y 35 1 "O5'" A DA 7 ? ? P A DA 7 ? ? OP1 A DA 7 ? ? 97.79 105.70 -7.91 0.90 N 36 1 P A DA 7 ? ? "O5'" A DA 7 ? ? "C5'" A DA 7 ? ? 111.04 120.90 -9.86 1.60 N 37 1 "O4'" A DA 7 ? ? "C4'" A DA 7 ? ? "C3'" A DA 7 ? ? 101.14 104.50 -3.36 0.40 N 38 1 "C4'" A DA 7 ? ? "C3'" A DA 7 ? ? "C2'" A DA 7 ? ? 97.36 102.20 -4.84 0.70 N 39 1 "C3'" A DA 7 ? ? "C2'" A DA 7 ? ? "C1'" A DA 7 ? ? 97.59 102.40 -4.81 0.80 N 40 1 "O4'" A DA 7 ? ? "C1'" A DA 7 ? ? N9 A DA 7 ? ? 110.21 108.30 1.91 0.30 N 41 1 "C3'" A DA 7 ? ? "O3'" A DA 7 ? ? P A DC 8 ? ? 137.20 119.70 17.50 1.20 Y 42 1 "O5'" A DC 8 ? ? P A DC 8 ? ? OP1 A DC 8 ? ? 98.78 105.70 -6.92 0.90 N 43 1 "O4'" A DC 8 ? ? "C4'" A DC 8 ? ? "C3'" A DC 8 ? ? 99.19 104.50 -5.31 0.40 N 44 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 112.15 108.30 3.85 0.30 N 45 1 C2 A DC 8 ? ? N3 A DC 8 ? ? C4 A DC 8 ? ? 125.07 119.90 5.17 0.50 N 46 1 N3 A DC 8 ? ? C4 A DC 8 ? ? C5 A DC 8 ? ? 116.91 121.90 -4.99 0.40 N 47 1 N1 A DC 8 ? ? C2 A DC 8 ? ? O2 A DC 8 ? ? 124.64 118.90 5.74 0.60 N 48 1 C5 A DC 8 ? ? C4 A DC 8 ? ? N4 A DC 8 ? ? 126.36 120.20 6.16 0.70 N 49 1 "O5'" A DG 9 ? ? P A DG 9 ? ? OP1 A DG 9 ? ? 99.15 105.70 -6.55 0.90 N 50 1 C6 A DG 9 ? ? N1 A DG 9 ? ? C2 A DG 9 ? ? 118.03 125.10 -7.07 0.60 N 51 1 N1 A DG 9 ? ? C2 A DG 9 ? ? N3 A DG 9 ? ? 130.29 123.90 6.39 0.60 N 52 1 C2 A DG 9 ? ? N3 A DG 9 ? ? C4 A DG 9 ? ? 108.61 111.90 -3.29 0.50 N 53 1 C5 A DG 9 ? ? C6 A DG 9 ? ? N1 A DG 9 ? ? 117.57 111.50 6.07 0.50 N 54 1 N3 A DG 9 ? ? C2 A DG 9 ? ? N2 A DG 9 ? ? 109.79 119.90 -10.11 0.70 N 55 1 C5 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 122.77 128.60 -5.83 0.60 N 56 1 "O5'" A DC 10 ? ? P A DC 10 ? ? OP1 A DC 10 ? ? 98.89 105.70 -6.81 0.90 N 57 1 C2 A DC 10 ? ? N3 A DC 10 ? ? C4 A DC 10 ? ? 124.12 119.90 4.22 0.50 N 58 1 N3 A DC 10 ? ? C4 A DC 10 ? ? C5 A DC 10 ? ? 118.05 121.90 -3.85 0.40 N 59 1 N1 A DC 10 ? ? C2 A DC 10 ? ? O2 A DC 10 ? ? 125.42 118.90 6.52 0.60 N 60 1 C6 B DG 11 ? ? N1 B DG 11 ? ? C2 B DG 11 ? ? 119.45 125.10 -5.65 0.60 N 61 1 N1 B DG 11 ? ? C2 B DG 11 ? ? N3 B DG 11 ? ? 129.22 123.90 5.32 0.60 N 62 1 C5 B DG 11 ? ? C6 B DG 11 ? ? N1 B DG 11 ? ? 117.26 111.50 5.76 0.50 N 63 1 N3 B DG 11 ? ? C2 B DG 11 ? ? N2 B DG 11 ? ? 109.84 119.90 -10.06 0.70 N 64 1 C5 B DG 11 ? ? C6 B DG 11 ? ? O6 B DG 11 ? ? 123.54 128.60 -5.06 0.60 N 65 1 "O5'" B DC 12 ? ? P B DC 12 ? ? OP1 B DC 12 ? ? 99.87 105.70 -5.83 0.90 N 66 1 "O4'" B DC 12 ? ? "C1'" B DC 12 ? ? N1 B DC 12 ? ? 111.45 108.30 3.15 0.30 N 67 1 C2 B DC 12 ? ? N3 B DC 12 ? ? C4 B DC 12 ? ? 124.13 119.90 4.23 0.50 N 68 1 N3 B DC 12 ? ? C4 B DC 12 ? ? C5 B DC 12 ? ? 116.54 121.90 -5.36 0.40 N 69 1 C5 B DC 12 ? ? C6 B DC 12 ? ? N1 B DC 12 ? ? 124.59 121.00 3.59 0.50 N 70 1 N1 B DC 12 ? ? C2 B DC 12 ? ? O2 B DC 12 ? ? 123.25 118.90 4.35 0.60 N 71 1 C5 B DC 12 ? ? C4 B DC 12 ? ? N4 B DC 12 ? ? 125.49 120.20 5.29 0.70 N 72 1 "O5'" B DG 13 ? ? P B DG 13 ? ? OP1 B DG 13 ? ? 96.41 105.70 -9.29 0.90 N 73 1 P B DG 13 ? ? "O5'" B DG 13 ? ? "C5'" B DG 13 ? ? 107.81 120.90 -13.09 1.60 N 74 1 "O4'" B DG 13 ? ? "C4'" B DG 13 ? ? "C3'" B DG 13 ? ? 97.63 104.50 -6.87 0.40 N 75 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? N9 B DG 13 ? ? 115.42 108.30 7.12 0.30 N 76 1 C6 B DG 13 ? ? N1 B DG 13 ? ? C2 B DG 13 ? ? 120.30 125.10 -4.80 0.60 N 77 1 C5 B DG 13 ? ? C6 B DG 13 ? ? N1 B DG 13 ? ? 117.87 111.50 6.37 0.50 N 78 1 N1 B DG 13 ? ? C2 B DG 13 ? ? N2 B DG 13 ? ? 125.53 116.20 9.33 0.90 N 79 1 N3 B DG 13 ? ? C2 B DG 13 ? ? N2 B DG 13 ? ? 107.16 119.90 -12.74 0.70 N 80 1 C5 B DG 13 ? ? C6 B DG 13 ? ? O6 B DG 13 ? ? 122.27 128.60 -6.33 0.60 N 81 1 "C3'" B DG 13 ? ? "O3'" B DG 13 ? ? P B DT 14 ? ? 106.70 119.70 -13.00 1.20 Y 82 1 "O5'" B DT 14 ? ? P B DT 14 ? ? OP1 B DT 14 ? ? 100.10 105.70 -5.60 0.90 N 83 1 P B DT 14 ? ? "O5'" B DT 14 ? ? "C5'" B DT 14 ? ? 105.59 120.90 -15.31 1.60 N 84 1 "C3'" B DT 14 ? ? "C2'" B DT 14 ? ? "C1'" B DT 14 ? ? 96.40 102.40 -6.00 0.80 N 85 1 "O4'" B DT 14 ? ? "C1'" B DT 14 ? ? N1 B DT 14 ? ? 111.15 108.30 2.85 0.30 N 86 1 N3 B DT 14 ? ? C2 B DT 14 ? ? O2 B DT 14 ? ? 117.47 122.30 -4.83 0.60 N 87 1 N3 B DT 14 ? ? C4 B DT 14 ? ? O4 B DT 14 ? ? 116.17 119.90 -3.73 0.60 N 88 1 "O5'" B A 15 ? ? P B A 15 ? ? OP1 B A 15 ? ? 99.29 105.70 -6.41 0.90 N 89 1 P B A 15 ? ? "O5'" B A 15 ? ? "C5'" B A 15 ? ? 106.90 120.90 -14.00 1.60 N 90 1 N9 B A 15 ? ? "C1'" B A 15 ? ? "C2'" B A 15 ? ? 104.07 112.00 -7.93 1.10 N 91 1 "O4'" B A 15 ? ? "C1'" B A 15 ? ? N9 B A 15 ? ? 116.72 108.50 8.22 0.70 N 92 1 "O5'" B DT 16 ? ? P B DT 16 ? ? OP1 B DT 16 ? ? 95.42 105.70 -10.28 0.90 N 93 1 C4 B DT 16 ? ? C5 B DT 16 ? ? C7 B DT 16 ? ? 122.84 119.00 3.84 0.60 N 94 1 C6 B DT 16 ? ? C5 B DT 16 ? ? C7 B DT 16 ? ? 118.06 122.90 -4.84 0.60 N 95 1 "O5'" B DA 17 ? ? P B DA 17 ? ? OP2 B DA 17 ? ? 98.39 105.70 -7.31 0.90 N 96 1 P B DA 17 ? ? "O5'" B DA 17 ? ? "C5'" B DA 17 ? ? 110.33 120.90 -10.57 1.60 N 97 1 "O5'" B DC 18 ? ? "C5'" B DC 18 ? ? "C4'" B DC 18 ? ? 101.66 109.40 -7.74 0.80 N 98 1 "C4'" B DC 18 ? ? "C3'" B DC 18 ? ? "C2'" B DC 18 ? ? 97.49 102.20 -4.71 0.70 N 99 1 C2 B DC 18 ? ? N3 B DC 18 ? ? C4 B DC 18 ? ? 124.24 119.90 4.34 0.50 N 100 1 N3 B DC 18 ? ? C4 B DC 18 ? ? C5 B DC 18 ? ? 117.45 121.90 -4.45 0.40 N 101 1 C5 B DC 18 ? ? C6 B DC 18 ? ? N1 B DC 18 ? ? 124.27 121.00 3.27 0.50 N 102 1 N1 B DC 18 ? ? C2 B DC 18 ? ? O2 B DC 18 ? ? 124.35 118.90 5.45 0.60 N 103 1 C5 B DC 18 ? ? C4 B DC 18 ? ? N4 B DC 18 ? ? 125.52 120.20 5.32 0.70 N 104 1 "O5'" B DG 19 ? ? P B DG 19 ? ? OP2 B DG 19 ? ? 98.75 105.70 -6.95 0.90 N 105 1 "O4'" B DG 19 ? ? "C1'" B DG 19 ? ? N9 B DG 19 ? ? 114.44 108.30 6.14 0.30 N 106 1 C6 B DG 19 ? ? N1 B DG 19 ? ? C2 B DG 19 ? ? 120.41 125.10 -4.69 0.60 N 107 1 C5 B DG 19 ? ? C6 B DG 19 ? ? N1 B DG 19 ? ? 117.51 111.50 6.01 0.50 N 108 1 N1 B DG 19 ? ? C2 B DG 19 ? ? N2 B DG 19 ? ? 121.86 116.20 5.66 0.90 N 109 1 N3 B DG 19 ? ? C2 B DG 19 ? ? N2 B DG 19 ? ? 110.71 119.90 -9.19 0.70 N 110 1 C5 B DG 19 ? ? C6 B DG 19 ? ? O6 B DG 19 ? ? 123.70 128.60 -4.90 0.60 N 111 1 "O5'" B DC 20 ? ? P B DC 20 ? ? OP2 B DC 20 ? ? 98.78 105.70 -6.92 0.90 N 112 1 "O4'" B DC 20 ? ? "C4'" B DC 20 ? ? "C3'" B DC 20 ? ? 102.02 104.50 -2.48 0.40 N 113 1 C2 B DC 20 ? ? N3 B DC 20 ? ? C4 B DC 20 ? ? 125.51 119.90 5.61 0.50 N 114 1 N3 B DC 20 ? ? C4 B DC 20 ? ? C5 B DC 20 ? ? 116.60 121.90 -5.30 0.40 N 115 1 N1 B DC 20 ? ? C2 B DC 20 ? ? O2 B DC 20 ? ? 122.90 118.90 4.00 0.60 N 116 1 C5 B DC 20 ? ? C4 B DC 20 ? ? N4 B DC 20 ? ? 124.48 120.20 4.28 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 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 DA OP3 O N N 38 DA P P N N 39 DA OP1 O N N 40 DA OP2 O N N 41 DA "O5'" O N N 42 DA "C5'" C N N 43 DA "C4'" C N R 44 DA "O4'" O N N 45 DA "C3'" C N S 46 DA "O3'" O N N 47 DA "C2'" C N N 48 DA "C1'" C N R 49 DA N9 N Y N 50 DA C8 C Y N 51 DA N7 N Y N 52 DA C5 C Y N 53 DA C6 C Y N 54 DA N6 N N N 55 DA N1 N Y N 56 DA C2 C Y N 57 DA N3 N Y N 58 DA C4 C Y N 59 DA HOP3 H N N 60 DA HOP2 H N N 61 DA "H5'" H N N 62 DA "H5''" H N N 63 DA "H4'" H N N 64 DA "H3'" H N N 65 DA "HO3'" H N N 66 DA "H2'" H N N 67 DA "H2''" H N N 68 DA "H1'" H N N 69 DA H8 H N N 70 DA H61 H N N 71 DA H62 H N N 72 DA H2 H N N 73 DC OP3 O N N 74 DC P P N N 75 DC OP1 O N N 76 DC OP2 O N N 77 DC "O5'" O N N 78 DC "C5'" C N N 79 DC "C4'" C N R 80 DC "O4'" O N N 81 DC "C3'" C N S 82 DC "O3'" O N N 83 DC "C2'" C N N 84 DC "C1'" C N R 85 DC N1 N N N 86 DC C2 C N N 87 DC O2 O N N 88 DC N3 N N N 89 DC C4 C N N 90 DC N4 N N N 91 DC C5 C N N 92 DC C6 C N N 93 DC HOP3 H N N 94 DC HOP2 H N N 95 DC "H5'" H N N 96 DC "H5''" H N N 97 DC "H4'" H N N 98 DC "H3'" H N N 99 DC "HO3'" H N N 100 DC "H2'" H N N 101 DC "H2''" H N N 102 DC "H1'" H N N 103 DC H41 H N N 104 DC H42 H N N 105 DC H5 H N N 106 DC H6 H N N 107 DG OP3 O N N 108 DG P P N N 109 DG OP1 O N N 110 DG OP2 O N N 111 DG "O5'" O N N 112 DG "C5'" C N N 113 DG "C4'" C N R 114 DG "O4'" O N N 115 DG "C3'" C N S 116 DG "O3'" O N N 117 DG "C2'" C N N 118 DG "C1'" C N R 119 DG N9 N Y N 120 DG C8 C Y N 121 DG N7 N Y N 122 DG C5 C Y N 123 DG C6 C N N 124 DG O6 O N N 125 DG N1 N N N 126 DG C2 C N N 127 DG N2 N N N 128 DG N3 N N N 129 DG C4 C Y N 130 DG HOP3 H N N 131 DG HOP2 H N N 132 DG "H5'" H N N 133 DG "H5''" H N N 134 DG "H4'" H N N 135 DG "H3'" H N N 136 DG "HO3'" H N N 137 DG "H2'" H N N 138 DG "H2''" H N N 139 DG "H1'" H N N 140 DG H8 H N N 141 DG H1 H N N 142 DG H21 H N N 143 DG H22 H N N 144 DT OP3 O N N 145 DT P P N N 146 DT OP1 O N N 147 DT OP2 O N N 148 DT "O5'" O N N 149 DT "C5'" C N N 150 DT "C4'" C N R 151 DT "O4'" O N N 152 DT "C3'" C N S 153 DT "O3'" O N N 154 DT "C2'" C N N 155 DT "C1'" C N R 156 DT N1 N N N 157 DT C2 C N N 158 DT O2 O N N 159 DT N3 N N N 160 DT C4 C N N 161 DT O4 O N N 162 DT C5 C N N 163 DT C7 C N N 164 DT C6 C N N 165 DT HOP3 H N N 166 DT HOP2 H N N 167 DT "H5'" H N N 168 DT "H5''" H N N 169 DT "H4'" H N N 170 DT "H3'" H N N 171 DT "HO3'" H N N 172 DT "H2'" H N N 173 DT "H2''" H N N 174 DT "H1'" H N N 175 DT H3 H N N 176 DT H71 H N N 177 DT H72 H N N 178 DT H73 H N N 179 DT H6 H N N 180 HOH O O N N 181 HOH H1 H N N 182 HOH H2 H N N 183 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 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 DA OP3 P sing N N 40 DA OP3 HOP3 sing N N 41 DA P OP1 doub N N 42 DA P OP2 sing N N 43 DA P "O5'" sing N N 44 DA OP2 HOP2 sing N N 45 DA "O5'" "C5'" sing N N 46 DA "C5'" "C4'" sing N N 47 DA "C5'" "H5'" sing N N 48 DA "C5'" "H5''" sing N N 49 DA "C4'" "O4'" sing N N 50 DA "C4'" "C3'" sing N N 51 DA "C4'" "H4'" sing N N 52 DA "O4'" "C1'" sing N N 53 DA "C3'" "O3'" sing N N 54 DA "C3'" "C2'" sing N N 55 DA "C3'" "H3'" sing N N 56 DA "O3'" "HO3'" sing N N 57 DA "C2'" "C1'" sing N N 58 DA "C2'" "H2'" sing N N 59 DA "C2'" "H2''" sing N N 60 DA "C1'" N9 sing N N 61 DA "C1'" "H1'" sing N N 62 DA N9 C8 sing Y N 63 DA N9 C4 sing Y N 64 DA C8 N7 doub Y N 65 DA C8 H8 sing N N 66 DA N7 C5 sing Y N 67 DA C5 C6 sing Y N 68 DA C5 C4 doub Y N 69 DA C6 N6 sing N N 70 DA C6 N1 doub Y N 71 DA N6 H61 sing N N 72 DA N6 H62 sing N N 73 DA N1 C2 sing Y N 74 DA C2 N3 doub Y N 75 DA C2 H2 sing N N 76 DA N3 C4 sing Y N 77 DC OP3 P sing N N 78 DC OP3 HOP3 sing N N 79 DC P OP1 doub N N 80 DC P OP2 sing N N 81 DC P "O5'" sing N N 82 DC OP2 HOP2 sing N N 83 DC "O5'" "C5'" sing N N 84 DC "C5'" "C4'" sing N N 85 DC "C5'" "H5'" sing N N 86 DC "C5'" "H5''" sing N N 87 DC "C4'" "O4'" sing N N 88 DC "C4'" "C3'" sing N N 89 DC "C4'" "H4'" sing N N 90 DC "O4'" "C1'" sing N N 91 DC "C3'" "O3'" sing N N 92 DC "C3'" "C2'" sing N N 93 DC "C3'" "H3'" sing N N 94 DC "O3'" "HO3'" sing N N 95 DC "C2'" "C1'" sing N N 96 DC "C2'" "H2'" sing N N 97 DC "C2'" "H2''" sing N N 98 DC "C1'" N1 sing N N 99 DC "C1'" "H1'" sing N N 100 DC N1 C2 sing N N 101 DC N1 C6 sing N N 102 DC C2 O2 doub N N 103 DC C2 N3 sing N N 104 DC N3 C4 doub N N 105 DC C4 N4 sing N N 106 DC C4 C5 sing N N 107 DC N4 H41 sing N N 108 DC N4 H42 sing N N 109 DC C5 C6 doub N N 110 DC C5 H5 sing N N 111 DC C6 H6 sing N N 112 DG OP3 P sing N N 113 DG OP3 HOP3 sing N N 114 DG P OP1 doub N N 115 DG P OP2 sing N N 116 DG P "O5'" sing N N 117 DG OP2 HOP2 sing N N 118 DG "O5'" "C5'" sing N N 119 DG "C5'" "C4'" sing N N 120 DG "C5'" "H5'" sing N N 121 DG "C5'" "H5''" sing N N 122 DG "C4'" "O4'" sing N N 123 DG "C4'" "C3'" sing N N 124 DG "C4'" "H4'" sing N N 125 DG "O4'" "C1'" sing N N 126 DG "C3'" "O3'" sing N N 127 DG "C3'" "C2'" sing N N 128 DG "C3'" "H3'" sing N N 129 DG "O3'" "HO3'" sing N N 130 DG "C2'" "C1'" sing N N 131 DG "C2'" "H2'" sing N N 132 DG "C2'" "H2''" sing N N 133 DG "C1'" N9 sing N N 134 DG "C1'" "H1'" sing N N 135 DG N9 C8 sing Y N 136 DG N9 C4 sing Y N 137 DG C8 N7 doub Y N 138 DG C8 H8 sing N N 139 DG N7 C5 sing Y N 140 DG C5 C6 sing N N 141 DG C5 C4 doub Y N 142 DG C6 O6 doub N N 143 DG C6 N1 sing N N 144 DG N1 C2 sing N N 145 DG N1 H1 sing N N 146 DG C2 N2 sing N N 147 DG C2 N3 doub N N 148 DG N2 H21 sing N N 149 DG N2 H22 sing N N 150 DG N3 C4 sing N N 151 DT OP3 P sing N N 152 DT OP3 HOP3 sing N N 153 DT P OP1 doub N N 154 DT P OP2 sing N N 155 DT P "O5'" sing N N 156 DT OP2 HOP2 sing N N 157 DT "O5'" "C5'" sing N N 158 DT "C5'" "C4'" sing N N 159 DT "C5'" "H5'" sing N N 160 DT "C5'" "H5''" sing N N 161 DT "C4'" "O4'" sing N N 162 DT "C4'" "C3'" sing N N 163 DT "C4'" "H4'" sing N N 164 DT "O4'" "C1'" sing N N 165 DT "C3'" "O3'" sing N N 166 DT "C3'" "C2'" sing N N 167 DT "C3'" "H3'" sing N N 168 DT "O3'" "HO3'" sing N N 169 DT "C2'" "C1'" sing N N 170 DT "C2'" "H2'" sing N N 171 DT "C2'" "H2''" sing N N 172 DT "C1'" N1 sing N N 173 DT "C1'" "H1'" sing N N 174 DT N1 C2 sing N N 175 DT N1 C6 sing N N 176 DT C2 O2 doub N N 177 DT C2 N3 sing N N 178 DT N3 C4 sing N N 179 DT N3 H3 sing N N 180 DT C4 O4 doub N N 181 DT C4 C5 sing N N 182 DT C5 C7 sing N N 183 DT C5 C6 doub N N 184 DT C7 H71 sing N N 185 DT C7 H72 sing N N 186 DT C7 H73 sing N N 187 DT C6 H6 sing N N 188 HOH O H1 sing N N 189 HOH O H2 sing N N 190 # _ndb_struct_conf_na.entry_id 1D88 _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 1 1_555 B DC 10 1_555 1.062 -0.262 0.522 3.102 -9.175 1.757 1 A_DG1:DC20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.140 -0.246 0.200 12.606 -27.719 -1.642 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 0.110 -0.129 0.262 -0.705 -14.053 1.684 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.079 -0.129 -0.596 3.430 -20.423 -2.949 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A A 5 1_555 B DT 6 1_555 -0.517 -0.176 0.284 -8.314 -22.622 0.894 5 A_A5:DT16_B A 5 ? B 16 ? 20 1 1 A DT 6 1_555 B A 5 1_555 -0.866 -0.221 0.041 8.556 -10.917 3.603 6 A_DT6:A15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.305 -0.095 -0.005 8.861 -14.895 12.357 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.635 -0.346 0.232 11.771 -15.292 2.399 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.165 -0.045 -0.408 -10.520 -4.067 1.175 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.294 -0.222 -0.660 7.168 -8.158 0.076 10 A_DC10:DG11_B A 10 ? B 11 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 1 1_555 B DC 10 1_555 A DC 2 1_555 B DG 9 1_555 -0.203 -1.837 3.318 5.182 -1.510 30.608 -3.134 1.395 3.324 -2.833 -9.721 31.069 1 AA_DG1DC2:DG19DC20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.256 -2.404 3.586 -2.130 9.050 29.679 -6.203 -0.882 2.728 17.147 4.036 31.070 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -1.528 -1.053 3.270 4.064 10.050 33.193 -3.173 3.122 2.650 17.035 -6.889 34.871 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 A 5 1_555 B DT 6 1_555 1.441 -1.649 3.730 -0.688 15.621 22.993 -7.158 -3.170 2.149 34.529 1.522 27.747 4 AA_DT4A5:DT16DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A A 5 1_555 B DT 6 1_555 A DT 6 1_555 B A 5 1_555 0.682 -1.211 2.866 0.564 5.989 29.233 -3.402 -1.227 2.585 11.711 -1.102 29.832 5 AA_A5DT6:A15DT16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DT 6 1_555 B A 5 1_555 A DA 7 1_555 B DT 4 1_555 0.397 -1.319 3.184 2.751 16.658 36.154 -3.674 -0.296 2.397 25.219 -4.165 39.782 6 AA_DT6DA7:DT14A15_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 0.209 -1.109 3.258 1.356 2.535 31.224 -2.522 -0.136 3.166 4.696 -2.513 31.353 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 -0.425 -1.495 3.694 3.369 17.617 30.472 -5.113 1.208 2.437 30.434 -5.821 35.251 8 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 -0.111 -1.918 3.225 2.983 6.496 31.200 -4.568 0.700 2.757 11.884 -5.457 31.989 9 AA_DG9DC10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _atom_sites.entry_id 1D88 _atom_sites.fract_transf_matrix[1][1] 0.039604 _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] 0.021868 _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] 0.021820 _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_