data_223D # _entry.id 223D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 223D pdb_0000223d 10.2210/pdb223d/pdb RCSB ZDFB43 ? ? WWPDB D_1000177596 ? ? # 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 1995-12-09 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-04-04 5 'Structure model' 1 4 2024-02-14 6 'Structure model' 1 5 2024-04-03 # _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 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 6 'Structure model' 'Refinement description' # 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' diffrn_source 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' struct_conn 6 6 'Structure model' pdbx_initial_refinement_model # 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' '_diffrn_source.type' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 223D _pdbx_database_status.recvd_initial_deposition_date 1995-08-01 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Moore, M.H.' 1 'Van Meervelt, L.' 2 'Salisbury, S.A.' 3 'Kong Thoo Lin, P.' 4 'Brown, D.M.' 5 # 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 ;Direct observation of two base-pairing modes of a cytosine-thymine analogue with guanine in a DNA Z-form duplex: significance for base analogue mutagenesis. ; J.Mol.Biol. 251 665 673 1995 JMOBAK UK 0022-2836 0070 ? 7666418 10.1006/jmbi.1995.0463 1 'To Wobble or Not to Wobble: Modified Bases Incorporated Into DNA' 'Nucleosides and Nucleotides' 14 1057 1059 1995 NUNUD5 US 0732-8311 0653 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Moore, M.H.' 1 ? primary 'Van Meervelt, L.' 2 ? primary 'Salisbury, S.A.' 3 ? primary 'Lin, P.K.' 4 ? primary 'Brown, D.M.' 5 ? 1 'Van Meervelt, L.' 6 ? 1 'Moore, M.H.' 7 ? 1 'Kong Thoo Lin, P.' 8 ? 1 'Brown, D.M.' 9 ? # 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 (5'-D(*CP*GP*CP*GP*(C46)P*G)-3') ; 1852.242 2 ? ? ? ? 2 water nat water 18.015 51 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DG)(C46)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGCG _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 DC n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 C46 n 1 6 DG n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight C46 'DNA linking' n "6H,8H-3,4-DIHYDROPYRIMIDO[4,5-C][1,2]OXAZIN-7-0NE(CYTIDINE)-5'-MONOPHOSPHATE" ? 'C11 H16 N3 O8 P' 349.234 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 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 DC 1 1 1 DC C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 C46 5 5 5 C46 +C A . n A 1 6 DG 6 6 6 DG G A . n B 1 1 DC 1 7 7 DC C B . n B 1 2 DG 2 8 8 DG G B . n B 1 3 DC 3 9 9 DC C B . n B 1 4 DG 4 10 10 DG G B . n B 1 5 C46 5 11 11 C46 +C B . n B 1 6 DG 6 12 12 DG G B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 13 13 HOH HOH A . C 2 HOH 2 15 15 HOH HOH A . C 2 HOH 3 18 18 HOH HOH A . C 2 HOH 4 20 20 HOH HOH A . C 2 HOH 5 21 21 HOH HOH A . C 2 HOH 6 30 30 HOH HOH A . C 2 HOH 7 31 31 HOH HOH A . C 2 HOH 8 32 32 HOH HOH A . C 2 HOH 9 33 33 HOH HOH A . C 2 HOH 10 34 34 HOH HOH A . C 2 HOH 11 36 36 HOH HOH A . C 2 HOH 12 41 41 HOH HOH A . C 2 HOH 13 45 45 HOH HOH A . C 2 HOH 14 46 46 HOH HOH A . C 2 HOH 15 50 50 HOH HOH A . C 2 HOH 16 52 52 HOH HOH A . C 2 HOH 17 53 53 HOH HOH A . C 2 HOH 18 55 55 HOH HOH A . C 2 HOH 19 56 56 HOH HOH A . C 2 HOH 20 58 58 HOH HOH A . C 2 HOH 21 59 59 HOH HOH A . C 2 HOH 22 60 60 HOH HOH A . C 2 HOH 23 63 63 HOH HOH A . D 2 HOH 1 14 14 HOH HOH B . D 2 HOH 2 16 16 HOH HOH B . D 2 HOH 3 17 17 HOH HOH B . D 2 HOH 4 19 19 HOH HOH B . D 2 HOH 5 22 22 HOH HOH B . D 2 HOH 6 23 23 HOH HOH B . D 2 HOH 7 24 24 HOH HOH B . D 2 HOH 8 25 25 HOH HOH B . D 2 HOH 9 26 26 HOH HOH B . D 2 HOH 10 27 27 HOH HOH B . D 2 HOH 11 28 28 HOH HOH B . D 2 HOH 12 29 29 HOH HOH B . D 2 HOH 13 35 35 HOH HOH B . D 2 HOH 14 37 37 HOH HOH B . D 2 HOH 15 38 38 HOH HOH B . D 2 HOH 16 39 39 HOH HOH B . D 2 HOH 17 40 40 HOH HOH B . D 2 HOH 18 42 42 HOH HOH B . D 2 HOH 19 43 43 HOH HOH B . D 2 HOH 20 44 44 HOH HOH B . D 2 HOH 21 47 47 HOH HOH B . D 2 HOH 22 48 48 HOH HOH B . D 2 HOH 23 49 49 HOH HOH B . D 2 HOH 24 51 51 HOH HOH B . D 2 HOH 25 54 54 HOH HOH B . D 2 HOH 26 57 57 HOH HOH B . D 2 HOH 27 61 61 HOH HOH B . D 2 HOH 28 62 62 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MERLOT phasing . ? 1 NUCLSQ refinement . ? 2 # _cell.entry_id 223D _cell.length_a 18.230 _cell.length_b 30.630 _cell.length_c 43.780 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 223D _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # _exptl.entry_id 223D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.65 _exptl_crystal.density_percent_sol 25.44 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 277.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.50 _exptl_crystal_grow.pdbx_details 'pH 6.50, VAPOR DIFFUSION, temperature 277.00K' _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 2 WATER ? ? ? 1 5 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 292.00 _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 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _refine.entry_id 223D _refine.ls_number_reflns_obs 2798 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 4.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.000 _refine.ls_d_res_high 1.700 _refine.ls_percent_reflns_obs 100.000 _refine.ls_R_factor_obs 0.179 _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 ZDF002 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _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.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_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 240 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 51 _refine_hist.number_atoms_total 297 _refine_hist.d_res_high 1.700 _refine_hist.d_res_low 8.000 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function n_bond_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_planar_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_hb_or_metal_coord ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_it 4.790 7.500 ? ? 'X-RAY DIFFRACTION' ? n_sugar_angle_it 5.740 7.500 ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_it 10.380 7.500 ? ? 'X-RAY DIFFRACTION' ? n_phos_angle_it 7.710 7.500 ? ? 'X-RAY DIFFRACTION' ? n_bond_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_dihedral_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_impr_tor ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_d 0.041 0.025 ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_angle_d 0.076 0.050 ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_d 0.071 0.025 ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_angle_d 0.048 0.025 ? ? 'X-RAY DIFFRACTION' ? n_plane_restr 0.044 0.030 ? ? 'X-RAY DIFFRACTION' ? n_chiral_restr 0.138 0.100 ? ? 'X-RAY DIFFRACTION' ? n_singtor_nbd 0.145 0.063 ? ? 'X-RAY DIFFRACTION' ? n_multtor_nbd 0.278 0.063 ? ? 'X-RAY DIFFRACTION' ? n_xhyhbond_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 223D _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 223D _struct.title ;DIRECT OBSERVATION OF TWO BASE-PAIRING MODES OF A CYTOSINE-THYMINE ANALOGUE WITH GUANINE IN A DNA Z-FORM DUPLEX: SIGNIFICANCE FOR BASE ANALOGUE MUTAGENESIS ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 223D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Z-DNA, DOUBLE HELIX, MODIFIED, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 223D _struct_ref.pdbx_db_accession 223D _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 223D A 1 ? 6 ? 223D 1 ? 6 ? 1 6 2 1 223D B 1 ? 6 ? 223D 7 ? 12 ? 7 12 # _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 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DG 4 "O3'" ? ? ? 1_555 A C46 5 P ? ? A DG 4 A C46 5 1_555 ? ? ? ? ? ? ? 1.577 ? ? covale2 covale one ? A C46 5 "O3'" ? ? ? 1_555 A DG 6 P ? ? A C46 5 A DG 6 1_555 ? ? ? ? ? ? ? 1.590 ? ? covale3 covale both ? B DG 4 "O3'" ? ? ? 1_555 B C46 5 P ? ? B DG 10 B C46 11 1_555 ? ? ? ? ? ? ? 1.595 ? ? covale4 covale one ? B C46 5 "O3'" ? ? ? 1_555 B DG 6 P ? ? B C46 11 B DG 12 1_555 ? ? ? ? ? ? ? 1.584 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B C46 5 O2 ? ? A DG 2 B C46 11 1_555 ? ? ? ? ? ? 'DG-C46 PAIR' ? ? ? hydrog5 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C46 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A C46 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C46 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A C46 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C46 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A C46 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 "O4'" A DC 1 ? ? "C4'" A DC 1 ? ? 1.345 1.446 -0.101 0.010 N 2 1 N3 A DC 1 ? ? C4 A DC 1 ? ? 1.400 1.335 0.065 0.007 N 3 1 "O3'" A DC 1 ? ? P A DG 2 ? ? 1.680 1.607 0.073 0.012 Y 4 1 P A DG 2 ? ? "O5'" A DG 2 ? ? 1.693 1.593 0.100 0.010 N 5 1 "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? 1.597 1.529 0.068 0.010 N 6 1 "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? 1.351 1.446 -0.095 0.010 N 7 1 C2 A DG 2 ? ? N2 A DG 2 ? ? 1.414 1.341 0.073 0.010 N 8 1 "C3'" A DC 3 ? ? "C2'" A DC 3 ? ? 1.599 1.518 0.081 0.012 N 9 1 C4 A DC 3 ? ? C5 A DC 3 ? ? 1.376 1.425 -0.049 0.008 N 10 1 P A DG 4 ? ? "O5'" A DG 4 ? ? 1.660 1.593 0.067 0.010 N 11 1 "O3'" A DG 4 ? ? "C3'" A DG 4 ? ? 1.383 1.419 -0.036 0.006 N 12 1 C2 A DG 4 ? ? N3 A DG 4 ? ? 1.390 1.323 0.067 0.008 N 13 1 N9 A DG 4 ? ? C4 A DG 4 ? ? 1.427 1.375 0.052 0.008 N 14 1 P A DG 6 ? ? "O5'" A DG 6 ? ? 1.663 1.593 0.070 0.010 N 15 1 "C3'" B DC 7 ? ? "C2'" B DC 7 ? ? 1.690 1.518 0.172 0.012 N 16 1 "O3'" B DC 7 ? ? "C3'" B DC 7 ? ? 1.371 1.419 -0.048 0.006 N 17 1 C4 B DC 7 ? ? C5 B DC 7 ? ? 1.480 1.425 0.055 0.008 N 18 1 "O3'" B DC 7 ? ? P B DG 8 ? ? 1.717 1.607 0.110 0.012 Y 19 1 P B DG 8 ? ? OP2 B DG 8 ? ? 1.365 1.485 -0.120 0.017 N 20 1 P B DG 8 ? ? "O5'" B DG 8 ? ? 1.710 1.593 0.117 0.010 N 21 1 "C4'" B DG 8 ? ? "C3'" B DG 8 ? ? 1.591 1.529 0.062 0.010 N 22 1 "C3'" B DG 8 ? ? "C2'" B DG 8 ? ? 1.422 1.516 -0.094 0.008 N 23 1 "C2'" B DG 8 ? ? "C1'" B DG 8 ? ? 1.441 1.518 -0.077 0.010 N 24 1 "O4'" B DG 8 ? ? "C4'" B DG 8 ? ? 1.335 1.446 -0.111 0.010 N 25 1 C2 B DG 8 ? ? N3 B DG 8 ? ? 1.391 1.323 0.068 0.008 N 26 1 C6 B DG 8 ? ? N1 B DG 8 ? ? 1.330 1.391 -0.061 0.007 N 27 1 C5 B DG 8 ? ? N7 B DG 8 ? ? 1.428 1.388 0.040 0.006 N 28 1 C8 B DG 8 ? ? N9 B DG 8 ? ? 1.329 1.374 -0.045 0.007 N 29 1 N9 B DG 8 ? ? C4 B DG 8 ? ? 1.436 1.375 0.061 0.008 N 30 1 P B DC 9 ? ? "O5'" B DC 9 ? ? 1.676 1.593 0.083 0.010 N 31 1 "O4'" B DC 9 ? ? "C4'" B DC 9 ? ? 1.362 1.446 -0.084 0.010 N 32 1 C2 B DC 9 ? ? N3 B DC 9 ? ? 1.280 1.353 -0.073 0.008 N 33 1 P B DG 10 ? ? "O5'" B DG 10 ? ? 1.663 1.593 0.070 0.010 N 34 1 "O4'" B DG 10 ? ? "C4'" B DG 10 ? ? 1.360 1.446 -0.086 0.010 N 35 1 "O3'" B DG 10 ? ? "C3'" B DG 10 ? ? 1.354 1.419 -0.065 0.006 N 36 1 N3 B DG 10 ? ? C4 B DG 10 ? ? 1.400 1.350 0.050 0.007 N 37 1 N7 B DG 10 ? ? C8 B DG 10 ? ? 1.348 1.305 0.043 0.006 N 38 1 C6 B DG 10 ? ? O6 B DG 10 ? ? 1.300 1.237 0.063 0.009 N 39 1 "O4'" B DG 12 ? ? "C4'" B DG 12 ? ? 1.351 1.446 -0.095 0.010 N 40 1 N9 B DG 12 ? ? C4 B DG 12 ? ? 1.430 1.375 0.055 0.008 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 "O5'" A DC 1 ? ? "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? 98.09 109.40 -11.31 0.80 N 2 1 "O4'" A DC 1 ? ? "C4'" A DC 1 ? ? "C3'" A DC 1 ? ? 99.42 104.50 -5.08 0.40 N 3 1 "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? "O4'" A DC 1 ? ? 128.39 109.80 18.59 1.10 N 4 1 "C1'" A DC 1 ? ? "O4'" A DC 1 ? ? "C4'" A DC 1 ? ? 118.64 110.30 8.34 0.70 N 5 1 "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? "C1'" A DC 1 ? ? 95.28 102.40 -7.12 0.80 N 6 1 N3 A DC 1 ? ? C4 A DC 1 ? ? C5 A DC 1 ? ? 118.70 121.90 -3.20 0.40 N 7 1 C5 A DC 1 ? ? C6 A DC 1 ? ? N1 A DC 1 ? ? 124.06 121.00 3.06 0.50 N 8 1 C5 A DC 1 ? ? C4 A DC 1 ? ? N4 A DC 1 ? ? 126.56 120.20 6.36 0.70 N 9 1 OP1 A DG 2 ? ? P A DG 2 ? ? OP2 A DG 2 ? ? 129.38 119.60 9.78 1.50 N 10 1 "O5'" A DG 2 ? ? "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 99.54 109.40 -9.86 0.80 N 11 1 "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? "O4'" A DG 2 ? ? 116.62 109.80 6.82 1.10 N 12 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? "C2'" A DG 2 ? ? 111.25 106.80 4.45 0.50 N 13 1 C6 A DG 2 ? ? N1 A DG 2 ? ? C2 A DG 2 ? ? 120.43 125.10 -4.67 0.60 N 14 1 N1 A DG 2 ? ? C2 A DG 2 ? ? N3 A DG 2 ? ? 128.46 123.90 4.56 0.60 N 15 1 C2 A DG 2 ? ? N3 A DG 2 ? ? C4 A DG 2 ? ? 108.80 111.90 -3.10 0.50 N 16 1 N3 A DG 2 ? ? C4 A DG 2 ? ? C5 A DG 2 ? ? 131.81 128.60 3.21 0.50 N 17 1 C4 A DG 2 ? ? C5 A DG 2 ? ? C6 A DG 2 ? ? 113.74 118.80 -5.06 0.60 N 18 1 C5 A DG 2 ? ? C6 A DG 2 ? ? N1 A DG 2 ? ? 116.35 111.50 4.85 0.50 N 19 1 C4 A DG 2 ? ? C5 A DG 2 ? ? N7 A DG 2 ? ? 113.38 110.80 2.58 0.40 N 20 1 N1 A DG 2 ? ? C2 A DG 2 ? ? N2 A DG 2 ? ? 103.59 116.20 -12.61 0.90 N 21 1 N3 A DG 2 ? ? C2 A DG 2 ? ? N2 A DG 2 ? ? 127.54 119.90 7.64 0.70 N 22 1 C5 A DG 2 ? ? C6 A DG 2 ? ? O6 A DG 2 ? ? 123.07 128.60 -5.53 0.60 N 23 1 "O4'" A DC 3 ? ? "C4'" A DC 3 ? ? "C3'" A DC 3 ? ? 97.87 104.50 -6.63 0.40 N 24 1 "C5'" A DC 3 ? ? "C4'" A DC 3 ? ? "O4'" A DC 3 ? ? 128.01 109.80 18.21 1.10 N 25 1 "C1'" A DC 3 ? ? "O4'" A DC 3 ? ? "C4'" A DC 3 ? ? 119.29 110.30 8.99 0.70 N 26 1 "C3'" A DC 3 ? ? "C2'" A DC 3 ? ? "C1'" A DC 3 ? ? 95.82 102.40 -6.58 0.80 N 27 1 N1 A DC 3 ? ? C2 A DC 3 ? ? N3 A DC 3 ? ? 114.61 119.20 -4.59 0.70 N 28 1 "O5'" A DG 4 ? ? "C5'" A DG 4 ? ? "C4'" A DG 4 ? ? 98.64 109.40 -10.76 0.80 N 29 1 "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? "C3'" A DG 4 ? ? 111.16 106.00 5.16 0.60 N 30 1 "C1'" A DG 4 ? ? "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? 101.03 110.10 -9.07 1.00 N 31 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? "C2'" A DG 4 ? ? 111.07 106.80 4.27 0.50 N 32 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 101.90 108.00 -6.10 0.70 N 33 1 C6 A DG 4 ? ? N1 A DG 4 ? ? C2 A DG 4 ? ? 120.65 125.10 -4.45 0.60 N 34 1 C5 A DG 4 ? ? C6 A DG 4 ? ? N1 A DG 4 ? ? 115.79 111.50 4.29 0.50 N 35 1 "C3'" A DG 4 ? ? "O3'" A DG 4 ? ? P A C46 5 ? ? 137.72 119.70 18.02 1.20 Y 36 1 "C3'" A DG 6 ? ? "C2'" A DG 6 ? ? "C1'" A DG 6 ? ? 97.53 102.40 -4.87 0.80 N 37 1 C5 A DG 6 ? ? C6 A DG 6 ? ? N1 A DG 6 ? ? 115.13 111.50 3.63 0.50 N 38 1 N7 A DG 6 ? ? C8 A DG 6 ? ? N9 A DG 6 ? ? 116.49 113.10 3.39 0.50 N 39 1 C8 A DG 6 ? ? N9 A DG 6 ? ? C4 A DG 6 ? ? 103.71 106.40 -2.69 0.40 N 40 1 N3 A DG 6 ? ? C2 A DG 6 ? ? N2 A DG 6 ? ? 114.74 119.90 -5.16 0.70 N 41 1 C5 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 123.60 128.60 -5.00 0.60 N 42 1 "O4'" B DC 7 ? ? "C4'" B DC 7 ? ? "C3'" B DC 7 ? ? 96.12 104.50 -8.38 0.40 N 43 1 "C5'" B DC 7 ? ? "C4'" B DC 7 ? ? "C3'" B DC 7 ? ? 103.10 114.10 -11.00 1.80 N 44 1 "C5'" B DC 7 ? ? "C4'" B DC 7 ? ? "O4'" B DC 7 ? ? 128.12 109.80 18.32 1.10 N 45 1 "C1'" B DC 7 ? ? "O4'" B DC 7 ? ? "C4'" B DC 7 ? ? 124.15 110.30 13.85 0.70 N 46 1 "C4'" B DC 7 ? ? "C3'" B DC 7 ? ? "O3'" B DC 7 ? ? 126.58 112.30 14.28 2.00 N 47 1 "C4'" B DC 7 ? ? "C3'" B DC 7 ? ? "C2'" B DC 7 ? ? 96.35 102.20 -5.85 0.70 N 48 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? "C2'" B DC 7 ? ? 95.27 105.90 -10.63 0.80 N 49 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 110.90 108.30 2.60 0.30 N 50 1 C4 B DC 7 ? ? C5 B DC 7 ? ? C6 B DC 7 ? ? 112.53 117.40 -4.87 0.50 N 51 1 C5 B DC 7 ? ? C6 B DC 7 ? ? N1 B DC 7 ? ? 124.78 121.00 3.78 0.50 N 52 1 OP1 B DG 8 ? ? P B DG 8 ? ? OP2 B DG 8 ? ? 135.51 119.60 15.91 1.50 N 53 1 "O5'" B DG 8 ? ? P B DG 8 ? ? OP1 B DG 8 ? ? 100.21 105.70 -5.49 0.90 N 54 1 "O5'" B DG 8 ? ? "C5'" B DG 8 ? ? "C4'" B DG 8 ? ? 97.86 109.40 -11.54 0.80 N 55 1 "O4'" B DG 8 ? ? "C4'" B DG 8 ? ? "C3'" B DG 8 ? ? 111.59 106.00 5.59 0.60 N 56 1 "C4'" B DG 8 ? ? "C3'" B DG 8 ? ? "C2'" B DG 8 ? ? 94.35 102.20 -7.85 0.70 N 57 1 "C3'" B DG 8 ? ? "C2'" B DG 8 ? ? "C1'" B DG 8 ? ? 112.02 102.50 9.52 1.20 N 58 1 C5 B DG 8 ? ? C6 B DG 8 ? ? N1 B DG 8 ? ? 115.40 111.50 3.90 0.50 N 59 1 C5 B DG 8 ? ? N7 B DG 8 ? ? C8 B DG 8 ? ? 101.12 104.30 -3.18 0.50 N 60 1 N7 B DG 8 ? ? C8 B DG 8 ? ? N9 B DG 8 ? ? 119.29 113.10 6.19 0.50 N 61 1 C8 B DG 8 ? ? N9 B DG 8 ? ? C4 B DG 8 ? ? 103.66 106.40 -2.74 0.40 N 62 1 N1 B DG 8 ? ? C2 B DG 8 ? ? N2 B DG 8 ? ? 122.65 116.20 6.45 0.90 N 63 1 N3 B DG 8 ? ? C2 B DG 8 ? ? N2 B DG 8 ? ? 113.81 119.90 -6.09 0.70 N 64 1 C5 B DG 8 ? ? C6 B DG 8 ? ? O6 B DG 8 ? ? 123.72 128.60 -4.88 0.60 N 65 1 "C3'" B DG 8 ? ? "O3'" B DG 8 ? ? P B DC 9 ? ? 127.28 119.70 7.58 1.20 Y 66 1 "O3'" B DG 8 ? ? P B DC 9 ? ? "O5'" B DC 9 ? ? 90.73 104.00 -13.27 1.90 Y 67 1 "O3'" B DG 8 ? ? P B DC 9 ? ? OP1 B DC 9 ? ? 119.53 110.50 9.03 1.10 Y 68 1 "O5'" B DC 9 ? ? P B DC 9 ? ? OP2 B DC 9 ? ? 120.82 110.70 10.12 1.20 N 69 1 "C5'" B DC 9 ? ? "C4'" B DC 9 ? ? "C3'" B DC 9 ? ? 101.30 114.10 -12.80 1.80 N 70 1 "C5'" B DC 9 ? ? "C4'" B DC 9 ? ? "O4'" B DC 9 ? ? 122.82 109.80 13.02 1.10 N 71 1 "C3'" B DC 9 ? ? "C2'" B DC 9 ? ? "C1'" B DC 9 ? ? 95.82 102.40 -6.58 0.80 N 72 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 110.16 106.80 3.36 0.50 N 73 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 100.66 108.00 -7.34 0.70 N 74 1 C2 B DC 9 ? ? N3 B DC 9 ? ? C4 B DC 9 ? ? 128.44 119.90 8.54 0.50 N 75 1 N3 B DC 9 ? ? C4 B DC 9 ? ? C5 B DC 9 ? ? 115.27 121.90 -6.63 0.40 N 76 1 N1 B DC 9 ? ? C2 B DC 9 ? ? O2 B DC 9 ? ? 112.34 118.90 -6.56 0.60 N 77 1 N3 B DC 9 ? ? C2 B DC 9 ? ? O2 B DC 9 ? ? 129.80 121.90 7.90 0.70 N 78 1 N3 B DC 9 ? ? C4 B DC 9 ? ? N4 B DC 9 ? ? 127.93 118.00 9.93 0.70 N 79 1 "O5'" B DG 10 ? ? "C5'" B DG 10 ? ? "C4'" B DG 10 ? ? 103.08 109.40 -6.32 0.80 N 80 1 "C5'" B DG 10 ? ? "C4'" B DG 10 ? ? "C3'" B DG 10 ? ? 98.95 114.10 -15.15 1.80 N 81 1 "O4'" B DG 10 ? ? "C1'" B DG 10 ? ? "C2'" B DG 10 ? ? 113.19 106.80 6.39 0.50 N 82 1 "O4'" B DG 10 ? ? "C1'" B DG 10 ? ? N9 B DG 10 ? ? 100.69 108.00 -7.31 0.70 N 83 1 C6 B DG 10 ? ? N1 B DG 10 ? ? C2 B DG 10 ? ? 121.14 125.10 -3.96 0.60 N 84 1 N1 B DG 10 ? ? C2 B DG 10 ? ? N3 B DG 10 ? ? 130.15 123.90 6.25 0.60 N 85 1 C2 B DG 10 ? ? N3 B DG 10 ? ? C4 B DG 10 ? ? 105.65 111.90 -6.25 0.50 N 86 1 C5 B DG 10 ? ? C6 B DG 10 ? ? N1 B DG 10 ? ? 116.81 111.50 5.31 0.50 N 87 1 C5 B DG 10 ? ? N7 B DG 10 ? ? C8 B DG 10 ? ? 99.03 104.30 -5.27 0.50 N 88 1 N3 B DG 10 ? ? C2 B DG 10 ? ? N2 B DG 10 ? ? 114.77 119.90 -5.13 0.70 N 89 1 C5 B DG 10 ? ? C6 B DG 10 ? ? O6 B DG 10 ? ? 122.02 128.60 -6.58 0.60 N 90 1 "C3'" B DG 10 ? ? "O3'" B DG 10 ? ? P B C46 11 ? ? 130.17 119.70 10.47 1.20 Y 91 1 "C3'" B C46 11 ? ? "O3'" B C46 11 ? ? P B DG 12 ? ? 134.24 119.70 14.54 1.20 Y 92 1 "O5'" B DG 12 ? ? "C5'" B DG 12 ? ? "C4'" B DG 12 ? ? 99.60 109.40 -9.80 0.80 N 93 1 "O4'" B DG 12 ? ? "C4'" B DG 12 ? ? "C3'" B DG 12 ? ? 111.32 106.00 5.32 0.60 N 94 1 "C5'" B DG 12 ? ? "C4'" B DG 12 ? ? "C3'" B DG 12 ? ? 103.20 114.10 -10.90 1.80 N 95 1 N3 B DG 12 ? ? C4 B DG 12 ? ? C5 B DG 12 ? ? 124.42 128.60 -4.18 0.50 N 96 1 C4 B DG 12 ? ? C5 B DG 12 ? ? N7 B DG 12 ? ? 107.55 110.80 -3.25 0.40 N 97 1 N9 B DG 12 ? ? C4 B DG 12 ? ? C5 B DG 12 ? ? 107.82 105.40 2.42 0.40 N 98 1 N1 B DG 12 ? ? C6 B DG 12 ? ? O6 B DG 12 ? ? 114.50 119.90 -5.40 0.60 N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A C46 5 A C46 5 ? DC ? 2 B C46 5 B C46 11 ? DC ? # 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 C46 P P N N 1 C46 O1P O N N 2 C46 O2P O N N 3 C46 O3P O N N 4 C46 "O5'" O N N 5 C46 "C5'" C N N 6 C46 "C4'" C N R 7 C46 "O4'" O N N 8 C46 "C3'" C N S 9 C46 "O3'" O N N 10 C46 "C2'" C N N 11 C46 "C1'" C N R 12 C46 N1 N N N 13 C46 C2 C N N 14 C46 O2 O N N 15 C46 N3 N N N 16 C46 C4 C N N 17 C46 N4 N N N 18 C46 C5 C N N 19 C46 C6 C N N 20 C46 CM5 C N N 21 C46 O4 O N N 22 C46 C7 C N N 23 C46 H1P H N N 24 C46 H3P H N N 25 C46 "H5'1" H N N 26 C46 "H5'2" H N N 27 C46 "H4'" H N N 28 C46 "H3'" H N N 29 C46 HA H N N 30 C46 "H2'1" H N N 31 C46 "H2'2" H N N 32 C46 "H1'" H N N 33 C46 H4 H N N 34 C46 H6 H N N 35 C46 HM51 H N N 36 C46 HM52 H N N 37 C46 H7C1 H N N 38 C46 H7C2 H N N 39 DC OP3 O N N 40 DC P P N N 41 DC OP1 O N N 42 DC OP2 O N N 43 DC "O5'" O N N 44 DC "C5'" C N N 45 DC "C4'" C N R 46 DC "O4'" O N N 47 DC "C3'" C N S 48 DC "O3'" O N N 49 DC "C2'" C N N 50 DC "C1'" C N R 51 DC N1 N N N 52 DC C2 C N N 53 DC O2 O N N 54 DC N3 N N N 55 DC C4 C N N 56 DC N4 N N N 57 DC C5 C N N 58 DC C6 C N N 59 DC HOP3 H N N 60 DC HOP2 H N N 61 DC "H5'" H N N 62 DC "H5''" H N N 63 DC "H4'" H N N 64 DC "H3'" H N N 65 DC "HO3'" H N N 66 DC "H2'" H N N 67 DC "H2''" H N N 68 DC "H1'" H N N 69 DC H41 H N N 70 DC H42 H N N 71 DC H5 H N N 72 DC H6 H N N 73 DG OP3 O N N 74 DG P P N N 75 DG OP1 O N N 76 DG OP2 O N N 77 DG "O5'" O N N 78 DG "C5'" C N N 79 DG "C4'" C N R 80 DG "O4'" O N N 81 DG "C3'" C N S 82 DG "O3'" O N N 83 DG "C2'" C N N 84 DG "C1'" C N R 85 DG N9 N Y N 86 DG C8 C Y N 87 DG N7 N Y N 88 DG C5 C Y N 89 DG C6 C N N 90 DG O6 O N N 91 DG N1 N N N 92 DG C2 C N N 93 DG N2 N N N 94 DG N3 N N N 95 DG C4 C Y N 96 DG HOP3 H N N 97 DG HOP2 H N N 98 DG "H5'" H N N 99 DG "H5''" H N N 100 DG "H4'" H N N 101 DG "H3'" H N N 102 DG "HO3'" H N N 103 DG "H2'" H N N 104 DG "H2''" H N N 105 DG "H1'" H N N 106 DG H8 H N N 107 DG H1 H N N 108 DG H21 H N N 109 DG H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 # 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 C46 P O1P sing N N 1 C46 P O2P doub N N 2 C46 P O3P sing N N 3 C46 P "O5'" sing N N 4 C46 O1P H1P sing N N 5 C46 O3P H3P sing N N 6 C46 "O5'" "C5'" sing N N 7 C46 "C5'" "C4'" sing N N 8 C46 "C5'" "H5'1" sing N N 9 C46 "C5'" "H5'2" sing N N 10 C46 "C4'" "O4'" sing N N 11 C46 "C4'" "C3'" sing N N 12 C46 "C4'" "H4'" sing N N 13 C46 "O4'" "C1'" sing N N 14 C46 "C3'" "O3'" sing N N 15 C46 "C3'" "C2'" sing N N 16 C46 "C3'" "H3'" sing N N 17 C46 "O3'" HA sing N N 18 C46 "C2'" "C1'" sing N N 19 C46 "C2'" "H2'1" sing N N 20 C46 "C2'" "H2'2" sing N N 21 C46 "C1'" N1 sing N N 22 C46 "C1'" "H1'" sing N N 23 C46 N1 C2 sing N N 24 C46 N1 C6 sing N N 25 C46 C2 O2 doub N N 26 C46 C2 N3 sing N N 27 C46 N3 C4 doub N N 28 C46 C4 N4 sing N N 29 C46 C4 C5 sing N N 30 C46 N4 O4 sing N N 31 C46 N4 H4 sing N N 32 C46 C5 C6 doub N N 33 C46 C5 CM5 sing N N 34 C46 C6 H6 sing N N 35 C46 CM5 C7 sing N N 36 C46 CM5 HM51 sing N N 37 C46 CM5 HM52 sing N N 38 C46 O4 C7 sing N N 39 C46 C7 H7C1 sing N N 40 C46 C7 H7C2 sing N N 41 DC OP3 P sing N N 42 DC OP3 HOP3 sing N N 43 DC P OP1 doub N N 44 DC P OP2 sing N N 45 DC P "O5'" sing N N 46 DC OP2 HOP2 sing N N 47 DC "O5'" "C5'" sing N N 48 DC "C5'" "C4'" sing N N 49 DC "C5'" "H5'" sing N N 50 DC "C5'" "H5''" sing N N 51 DC "C4'" "O4'" sing N N 52 DC "C4'" "C3'" sing N N 53 DC "C4'" "H4'" sing N N 54 DC "O4'" "C1'" sing N N 55 DC "C3'" "O3'" sing N N 56 DC "C3'" "C2'" sing N N 57 DC "C3'" "H3'" sing N N 58 DC "O3'" "HO3'" sing N N 59 DC "C2'" "C1'" sing N N 60 DC "C2'" "H2'" sing N N 61 DC "C2'" "H2''" sing N N 62 DC "C1'" N1 sing N N 63 DC "C1'" "H1'" sing N N 64 DC N1 C2 sing N N 65 DC N1 C6 sing N N 66 DC C2 O2 doub N N 67 DC C2 N3 sing N N 68 DC N3 C4 doub N N 69 DC C4 N4 sing N N 70 DC C4 C5 sing N N 71 DC N4 H41 sing N N 72 DC N4 H42 sing N N 73 DC C5 C6 doub N N 74 DC C5 H5 sing N N 75 DC C6 H6 sing N N 76 DG OP3 P sing N N 77 DG OP3 HOP3 sing N N 78 DG P OP1 doub N N 79 DG P OP2 sing N N 80 DG P "O5'" sing N N 81 DG OP2 HOP2 sing N N 82 DG "O5'" "C5'" sing N N 83 DG "C5'" "C4'" sing N N 84 DG "C5'" "H5'" sing N N 85 DG "C5'" "H5''" sing N N 86 DG "C4'" "O4'" sing N N 87 DG "C4'" "C3'" sing N N 88 DG "C4'" "H4'" sing N N 89 DG "O4'" "C1'" sing N N 90 DG "C3'" "O3'" sing N N 91 DG "C3'" "C2'" sing N N 92 DG "C3'" "H3'" sing N N 93 DG "O3'" "HO3'" sing N N 94 DG "C2'" "C1'" sing N N 95 DG "C2'" "H2'" sing N N 96 DG "C2'" "H2''" sing N N 97 DG "C1'" N9 sing N N 98 DG "C1'" "H1'" sing N N 99 DG N9 C8 sing Y N 100 DG N9 C4 sing Y N 101 DG C8 N7 doub Y N 102 DG C8 H8 sing N N 103 DG N7 C5 sing Y N 104 DG C5 C6 sing N N 105 DG C5 C4 doub Y N 106 DG C6 O6 doub N N 107 DG C6 N1 sing N N 108 DG N1 C2 sing N N 109 DG N1 H1 sing N N 110 DG C2 N2 sing N N 111 DG C2 N3 doub N N 112 DG N2 H21 sing N N 113 DG N2 H22 sing N N 114 DG N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 # _ndb_struct_conf_na.entry_id 223D _ndb_struct_conf_na.feature 'z-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 6 1_555 -0.165 -0.127 0.402 5.396 5.418 2.356 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B C46 5 1_555 2.593 -0.758 0.118 -2.450 6.923 -2.325 2 A_DG2:C4611_B A 2 ? B 11 ? ? 1 1 A DC 3 1_555 B DG 4 1_555 -0.413 -0.076 0.187 6.027 0.078 1.392 3 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 3 1_555 0.272 -0.065 0.014 -9.525 -3.406 1.451 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A C46 5 1_555 B DG 2 1_555 -0.633 -0.288 0.177 1.429 2.210 3.346 5 A_C465:DG8_B A 5 ? B 8 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 0.189 -0.162 0.395 -0.394 -2.347 1.878 6 A_DG6:DC7_B A 6 ? B 7 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 6 1_555 A DG 2 1_555 B C46 5 1_555 0.031 5.263 3.795 6.457 4.301 -2.143 -43.420 9.113 -1.826 -41.342 62.070 -8.048 1 AA_DC1DG2:C4611DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B C46 5 1_555 A DC 3 1_555 B DG 4 1_555 0.274 -0.007 3.340 -4.351 -6.705 -63.051 0.308 0.064 3.335 6.385 -4.143 -63.504 2 AA_DG2DC3:DG10C4611_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DC 3 1_555 B DG 4 1_555 A DG 4 1_555 B DC 3 1_555 0.006 5.493 3.939 0.009 -1.247 -7.482 -36.070 0.085 4.787 9.471 0.068 -7.585 3 AA_DC3DG4:DC9DG10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DG 4 1_555 B DC 3 1_555 A C46 5 1_555 B DG 2 1_555 0.208 -1.277 3.265 0.988 -2.473 -49.182 1.715 0.323 3.197 2.969 1.186 -49.250 4 AA_DG4C465:DG8DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A C46 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 -0.290 5.364 3.764 -2.719 2.672 -8.639 -37.613 -6.880 1.846 -16.710 -17.005 -9.441 5 AA_C465DG6:DC7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ? # _pdbx_initial_refinement_model.accession_code 1DCG _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details ZDF002 # _atom_sites.entry_id 223D _atom_sites.fract_transf_matrix[1][1] 0.054855 _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] 0.032648 _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] 0.022841 _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_