data_1DNF # _entry.id 1DNF # _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 1DNF pdb_00001dnf 10.2210/pdb1dnf/pdb RCSB ZDFB12 ? ? WWPDB D_1000172858 ? ? # 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 1990-10-15 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' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_conn_type 7 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.value' 10 4 'Structure model' '_struct_conn.conn_type_id' 11 4 'Structure model' '_struct_conn.id' 12 4 'Structure model' '_struct_conn.pdbx_dist_value' 13 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 14 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 15 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 16 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 17 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 18 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 19 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 20 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 21 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 22 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 23 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 24 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 25 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 26 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 27 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 28 4 'Structure model' '_struct_conn_type.id' 29 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 30 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 31 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1DNF _pdbx_database_status.recvd_initial_deposition_date 1988-12-12 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Coll, M.' 1 'Saal, D.' 2 'Frederick, C.A.' 3 'Aymami, J.' 4 'Rich, A.' 5 'Wang, A.H.-J.' 6 # 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 'Effects of 5-fluorouracil/guanine wobble base pairs in Z-DNA: molecular and crystal structure of d(CGCGFG).' 'Nucleic Acids Res.' 17 911 923 1989 NARHAD UK 0305-1048 0389 ? 2922276 10.1093/nar/17.3.911 1 '5-Fluorodeoxyuridine as an Alternative to the Synthesis of Mixed Hybridization Probes for the Detection of Specific Gene Sequences' Proc.Natl.Acad.Sci.USA 85 1735 1739 1988 PNASA6 US 0027-8424 0040 ? ? ? 2 ;5-Fluoro-2'-Deoxyuridine Incorporation in L1210 DNA ; J.Biol.Chem. 256 8885 8888 1981 JBCHA3 US 0021-9258 0071 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Coll, M.' 1 ? primary 'Saal, D.' 2 ? primary 'Frederick, C.A.' 3 ? primary 'Aymami, J.' 4 ? primary 'Rich, A.' 5 ? primary 'Wang, A.H.' 6 ? 1 'Habener, J.F.' 7 ? 1 'Vo, C.D.' 8 ? 1 'Le, D.B.' 9 ? 1 'Gryan, G.P.' 10 ? 1 'Ercolani, L.' 11 ? 1 'Wang, A.H.-J.' 12 ? 2 'Kufe, D.W.' 13 ? 2 'Major, P.P.' 14 ? 2 'Egan, E.M.' 15 ? 2 'Loh, E.' 16 ? # 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*(UFP)P*G)-3') ; 1829.180 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 water nat water 18.015 58 ? ? ? ? # _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)(UFP)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGNG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 water 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 UFP 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 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 UFP 'DNA linking' . "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 F N2 O8 P' 326.172 # 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 UFP 5 5 5 UFP +U 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 UFP 5 11 11 UFP +U 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 MG 1 13 13 MG MG A . D 3 HOH 1 15 15 HOH HOH A . D 3 HOH 2 16 16 HOH HOH A . D 3 HOH 3 19 19 HOH HOH A . D 3 HOH 4 21 21 HOH HOH A . D 3 HOH 5 23 23 HOH HOH A . D 3 HOH 6 24 24 HOH HOH A . D 3 HOH 7 27 27 HOH HOH A . D 3 HOH 8 28 28 HOH HOH A . D 3 HOH 9 31 31 HOH HOH A . D 3 HOH 10 40 40 HOH HOH A . D 3 HOH 11 41 41 HOH HOH A . D 3 HOH 12 44 44 HOH HOH A . D 3 HOH 13 46 46 HOH HOH A . D 3 HOH 14 54 54 HOH HOH A . D 3 HOH 15 59 59 HOH HOH A . D 3 HOH 16 63 63 HOH HOH A . D 3 HOH 17 66 66 HOH HOH A . E 3 HOH 1 14 14 HOH HOH B . E 3 HOH 2 17 17 HOH HOH B . E 3 HOH 3 18 18 HOH HOH B . E 3 HOH 4 20 20 HOH HOH B . E 3 HOH 5 22 22 HOH HOH B . E 3 HOH 6 25 25 HOH HOH B . E 3 HOH 7 26 26 HOH HOH B . E 3 HOH 8 29 29 HOH HOH B . E 3 HOH 9 30 30 HOH HOH B . E 3 HOH 10 32 32 HOH HOH B . E 3 HOH 11 33 33 HOH HOH B . E 3 HOH 12 34 34 HOH HOH B . E 3 HOH 13 35 35 HOH HOH B . E 3 HOH 14 36 36 HOH HOH B . E 3 HOH 15 37 37 HOH HOH B . E 3 HOH 16 38 38 HOH HOH B . E 3 HOH 17 39 39 HOH HOH B . E 3 HOH 18 42 42 HOH HOH B . E 3 HOH 19 43 43 HOH HOH B . E 3 HOH 20 45 45 HOH HOH B . E 3 HOH 21 47 47 HOH HOH B . E 3 HOH 22 48 48 HOH HOH B . E 3 HOH 23 49 49 HOH HOH B . E 3 HOH 24 50 50 HOH HOH B . E 3 HOH 25 51 51 HOH HOH B . E 3 HOH 26 52 52 HOH HOH B . E 3 HOH 27 53 53 HOH HOH B . E 3 HOH 28 55 55 HOH HOH B . E 3 HOH 29 56 56 HOH HOH B . E 3 HOH 30 57 57 HOH HOH B . E 3 HOH 31 58 58 HOH HOH B . E 3 HOH 32 60 60 HOH HOH B . E 3 HOH 33 61 61 HOH HOH B . E 3 HOH 34 62 62 HOH HOH B . E 3 HOH 35 64 64 HOH HOH B . E 3 HOH 36 65 65 HOH HOH B . E 3 HOH 37 67 67 HOH HOH B . E 3 HOH 38 68 68 HOH HOH B . E 3 HOH 39 69 69 HOH HOH B . E 3 HOH 40 70 70 HOH HOH B . E 3 HOH 41 71 71 HOH HOH B . # _software.name NUCLSQ _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 1DNF _cell.length_a 17.360 _cell.length_b 31.150 _cell.length_c 45.400 _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 1DNF _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 1DNF _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 26.69 _exptl_crystal.density_Matthews 1.68 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 9.00 _exptl_crystal_grow.pdbx_details 'pH 9.00, VAPOR DIFFUSION' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 BIS-TRIS-PROPANE ? ? ? 1 4 1 MGCL2 ? ? ? 1 5 1 SPERMINE ? ? ? 1 6 2 WATER ? ? ? 1 7 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 293.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type 'NICOLET P3' _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 M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _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 ? _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 1DNF _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 2.000 _reflns.d_resolution_low ? _reflns.d_resolution_high 1.500 _reflns.number_obs 2770 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 1DNF _refine.ls_number_reflns_obs 2770 _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 1.500 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.172 _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.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _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 3 _refine_hist.number_atoms_solvent 58 _refine_hist.number_atoms_total 301 _refine_hist.d_res_high 1.500 _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 n_bond_d 0.028 ? ? ? 'X-RAY DIFFRACTION' ? n_angle_d 0.037 ? ? ? 'X-RAY DIFFRACTION' ? n_planar_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_hb_or_metal_coord ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_angle_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_angle_it ? ? ? ? '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 ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_plane_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_chiral_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_singtor_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? n_multtor_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? n_xhyhbond_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1DNF _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 1DNF _struct.title 'EFFECTS OF 5-FLUOROURACIL/GUANINE WOBBLE BASE PAIRS IN Z-DNA. MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGFG)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1DNF _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Z-DNA, DOUBLE HELIX, MODIFIED, MISMATCHED, 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 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1DNF _struct_ref.pdbx_db_accession 1DNF _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 1DNF A 1 ? 6 ? 1DNF 1 ? 6 ? 1 6 2 1 1DNF B 1 ? 6 ? 1DNF 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,E # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DG 4 "O3'" ? ? ? 1_555 A UFP 5 P ? ? A DG 4 A UFP 5 1_555 ? ? ? ? ? ? ? 1.626 ? ? covale2 covale one ? A UFP 5 "O3'" ? ? ? 1_555 A DG 6 P ? ? A UFP 5 A DG 6 1_555 ? ? ? ? ? ? ? 1.577 ? ? covale3 covale both ? B DG 4 "O3'" ? ? ? 1_555 B UFP 5 P ? ? B DG 10 B UFP 11 1_555 ? ? ? ? ? ? ? 1.593 ? ? covale4 covale one ? B UFP 5 "O3'" ? ? ? 1_555 B DG 6 P ? ? B UFP 11 B DG 12 1_555 ? ? ? ? ? ? ? 1.542 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 13 A HOH 15 1_555 ? ? ? ? ? ? ? 1.942 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 13 A HOH 16 1_555 ? ? ? ? ? ? ? 2.038 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 13 A HOH 19 4_456 ? ? ? ? ? ? ? 1.921 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 13 B HOH 14 4_456 ? ? ? ? ? ? ? 2.070 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 13 B HOH 17 4_456 ? ? ? ? ? ? ? 1.959 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 13 B HOH 18 4_456 ? ? ? ? ? ? ? 2.035 ? ? 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 DC 3 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 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 ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? D HOH . ? A HOH 15 ? 1_555 MG ? C MG . ? A MG 13 ? 1_555 O ? D HOH . ? A HOH 16 ? 1_555 89.2 ? 2 O ? D HOH . ? A HOH 15 ? 1_555 MG ? C MG . ? A MG 13 ? 1_555 O ? D HOH . ? A HOH 19 ? 4_456 98.1 ? 3 O ? D HOH . ? A HOH 16 ? 1_555 MG ? C MG . ? A MG 13 ? 1_555 O ? D HOH . ? A HOH 19 ? 4_456 91.7 ? 4 O ? D HOH . ? A HOH 15 ? 1_555 MG ? C MG . ? A MG 13 ? 1_555 O ? E HOH . ? B HOH 14 ? 4_456 176.0 ? 5 O ? D HOH . ? A HOH 16 ? 1_555 MG ? C MG . ? A MG 13 ? 1_555 O ? E HOH . ? B HOH 14 ? 4_456 89.5 ? 6 O ? D HOH . ? A HOH 19 ? 4_456 MG ? C MG . ? A MG 13 ? 1_555 O ? E HOH . ? B HOH 14 ? 4_456 85.7 ? 7 O ? D HOH . ? A HOH 15 ? 1_555 MG ? C MG . ? A MG 13 ? 1_555 O ? E HOH . ? B HOH 17 ? 4_456 90.2 ? 8 O ? D HOH . ? A HOH 16 ? 1_555 MG ? C MG . ? A MG 13 ? 1_555 O ? E HOH . ? B HOH 17 ? 4_456 178.3 ? 9 O ? D HOH . ? A HOH 19 ? 4_456 MG ? C MG . ? A MG 13 ? 1_555 O ? E HOH . ? B HOH 17 ? 4_456 89.9 ? 10 O ? E HOH . ? B HOH 14 ? 4_456 MG ? C MG . ? A MG 13 ? 1_555 O ? E HOH . ? B HOH 17 ? 4_456 91.0 ? 11 O ? D HOH . ? A HOH 15 ? 1_555 MG ? C MG . ? A MG 13 ? 1_555 O ? E HOH . ? B HOH 18 ? 4_456 88.6 ? 12 O ? D HOH . ? A HOH 16 ? 1_555 MG ? C MG . ? A MG 13 ? 1_555 O ? E HOH . ? B HOH 18 ? 4_456 88.6 ? 13 O ? D HOH . ? A HOH 19 ? 4_456 MG ? C MG . ? A MG 13 ? 1_555 O ? E HOH . ? B HOH 18 ? 4_456 173.2 ? 14 O ? E HOH . ? B HOH 14 ? 4_456 MG ? C MG . ? A MG 13 ? 1_555 O ? E HOH . ? B HOH 18 ? 4_456 87.6 ? 15 O ? E HOH . ? B HOH 17 ? 4_456 MG ? C MG . ? A MG 13 ? 1_555 O ? E HOH . ? B HOH 18 ? 4_456 89.8 ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id MG _struct_site.pdbx_auth_seq_id 13 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE MG A 13' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 HOH D . ? HOH A 15 . ? 1_555 ? 2 AC1 6 HOH D . ? HOH A 16 . ? 1_555 ? 3 AC1 6 HOH D . ? HOH A 19 . ? 4_456 ? 4 AC1 6 HOH E . ? HOH B 14 . ? 4_456 ? 5 AC1 6 HOH E . ? HOH B 17 . ? 4_456 ? 6 AC1 6 HOH E . ? HOH B 18 . ? 4_456 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 47 _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 71 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.74 # 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 OP2 B DC 9 ? ? 1_555 O A HOH 54 ? ? 2_665 2.01 2 1 O A HOH 31 ? ? 1_555 O B HOH 42 ? ? 4_556 2.14 # 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 DG 2 ? ? "C4'" A DG 2 ? ? 1.386 1.446 -0.060 0.010 N 2 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? 1.497 1.420 0.077 0.011 N 3 1 "O4'" A DC 3 ? ? "C4'" A DC 3 ? ? 1.385 1.446 -0.061 0.010 N 4 1 "O3'" A DC 3 ? ? "C3'" A DC 3 ? ? 1.382 1.419 -0.037 0.006 N 5 1 N3 A DC 3 ? ? C4 A DC 3 ? ? 1.387 1.335 0.052 0.007 N 6 1 "C2'" A DG 4 ? ? "C1'" A DG 4 ? ? 1.452 1.518 -0.066 0.010 N 7 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? 1.491 1.420 0.071 0.011 N 8 1 "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? 1.363 1.446 -0.083 0.010 N 9 1 N1 A DG 4 ? ? C2 A DG 4 ? ? 1.312 1.373 -0.061 0.008 N 10 1 N7 A DG 4 ? ? C8 A DG 4 ? ? 1.251 1.305 -0.054 0.006 N 11 1 "O4'" A DG 6 ? ? "C4'" A DG 6 ? ? 1.385 1.446 -0.061 0.010 N 12 1 N7 A DG 6 ? ? C8 A DG 6 ? ? 1.260 1.305 -0.045 0.006 N 13 1 C2 B DC 7 ? ? O2 B DC 7 ? ? 1.156 1.240 -0.084 0.009 N 14 1 C5 B DC 7 ? ? C6 B DC 7 ? ? 1.408 1.339 0.069 0.008 N 15 1 "C3'" B DG 8 ? ? "C2'" B DG 8 ? ? 1.457 1.516 -0.059 0.008 N 16 1 N3 B DG 8 ? ? C4 B DG 8 ? ? 1.286 1.350 -0.064 0.007 N 17 1 C4 B DG 8 ? ? C5 B DG 8 ? ? 1.426 1.379 0.047 0.007 N 18 1 C6 B DG 8 ? ? N1 B DG 8 ? ? 1.347 1.391 -0.044 0.007 N 19 1 C6 B DG 8 ? ? O6 B DG 8 ? ? 1.300 1.237 0.063 0.009 N 20 1 "O3'" B DG 8 ? ? P B DC 9 ? ? 1.458 1.607 -0.149 0.012 Y 21 1 P B DC 9 ? ? OP2 B DC 9 ? ? 1.781 1.485 0.296 0.017 N 22 1 N1 B DC 9 ? ? C6 B DC 9 ? ? 1.411 1.367 0.044 0.006 N 23 1 "O4'" B DG 10 ? ? "C4'" B DG 10 ? ? 1.364 1.446 -0.082 0.010 N 24 1 N1 B DG 10 ? ? C2 B DG 10 ? ? 1.320 1.373 -0.053 0.008 N 25 1 "O3'" B DG 12 ? ? "C3'" B DG 12 ? ? 1.526 1.435 0.091 0.013 N 26 1 C6 B DG 12 ? ? N1 B DG 12 ? ? 1.348 1.391 -0.043 0.007 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 DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.96 108.30 3.66 0.30 N 2 1 N1 A DC 1 ? ? C2 A DC 1 ? ? O2 A DC 1 ? ? 128.09 118.90 9.19 0.60 N 3 1 N3 A DC 1 ? ? C2 A DC 1 ? ? O2 A DC 1 ? ? 114.10 121.90 -7.80 0.70 N 4 1 "O5'" A DG 2 ? ? "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 103.69 109.40 -5.71 0.80 N 5 1 C6 A DG 2 ? ? N1 A DG 2 ? ? C2 A DG 2 ? ? 120.72 125.10 -4.38 0.60 N 6 1 C2 A DG 2 ? ? N3 A DG 2 ? ? C4 A DG 2 ? ? 117.26 111.90 5.36 0.50 N 7 1 N3 A DG 2 ? ? C4 A DG 2 ? ? C5 A DG 2 ? ? 124.68 128.60 -3.92 0.50 N 8 1 C5 A DG 2 ? ? C6 A DG 2 ? ? N1 A DG 2 ? ? 115.89 111.50 4.39 0.50 N 9 1 N1 A DG 2 ? ? C6 A DG 2 ? ? O6 A DG 2 ? ? 114.40 119.90 -5.50 0.60 N 10 1 "O5'" A DG 4 ? ? "C5'" A DG 4 ? ? "C4'" A DG 4 ? ? 96.70 109.40 -12.70 0.80 N 11 1 C8 A DG 4 ? ? N9 A DG 4 ? ? C4 A DG 4 ? ? 103.98 106.40 -2.42 0.40 N 12 1 N1 A DG 4 ? ? C2 A DG 4 ? ? N2 A DG 4 ? ? 122.94 116.20 6.74 0.90 N 13 1 N3 A DG 4 ? ? C2 A DG 4 ? ? N2 A DG 4 ? ? 111.68 119.90 -8.22 0.70 N 14 1 "C3'" A DG 4 ? ? "O3'" A DG 4 ? ? P A UFP 5 ? ? 128.61 119.70 8.91 1.20 Y 15 1 C6 A DG 6 ? ? N1 A DG 6 ? ? C2 A DG 6 ? ? 117.31 125.10 -7.79 0.60 N 16 1 N1 A DG 6 ? ? C2 A DG 6 ? ? N3 A DG 6 ? ? 129.22 123.90 5.32 0.60 N 17 1 C5 A DG 6 ? ? C6 A DG 6 ? ? N1 A DG 6 ? ? 115.32 111.50 3.82 0.50 N 18 1 N1 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 114.85 119.90 -5.05 0.60 N 19 1 C6 B DC 7 ? ? N1 B DC 7 ? ? C2 B DC 7 ? ? 125.59 120.30 5.29 0.40 N 20 1 N1 B DC 7 ? ? C2 B DC 7 ? ? N3 B DC 7 ? ? 114.65 119.20 -4.55 0.70 N 21 1 N1 B DC 7 ? ? C2 B DC 7 ? ? O2 B DC 7 ? ? 124.05 118.90 5.15 0.60 N 22 1 "C3'" B DC 7 ? ? "O3'" B DC 7 ? ? P B DG 8 ? ? 127.95 119.70 8.25 1.20 Y 23 1 N1 B DG 8 ? ? C2 B DG 8 ? ? N3 B DG 8 ? ? 119.23 123.90 -4.67 0.60 N 24 1 C2 B DG 8 ? ? N3 B DG 8 ? ? C4 B DG 8 ? ? 118.85 111.90 6.95 0.50 N 25 1 N3 B DG 8 ? ? C4 B DG 8 ? ? C5 B DG 8 ? ? 124.64 128.60 -3.96 0.50 N 26 1 C5 B DG 8 ? ? C6 B DG 8 ? ? N1 B DG 8 ? ? 117.13 111.50 5.63 0.50 N 27 1 N3 B DG 8 ? ? C4 B DG 8 ? ? N9 B DG 8 ? ? 130.99 126.00 4.99 0.60 N 28 1 C6 B DG 8 ? ? C5 B DG 8 ? ? N7 B DG 8 ? ? 134.65 130.40 4.25 0.60 N 29 1 N1 B DG 8 ? ? C2 B DG 8 ? ? N2 B DG 8 ? ? 121.85 116.20 5.65 0.90 N 30 1 N1 B DG 8 ? ? C6 B DG 8 ? ? O6 B DG 8 ? ? 113.86 119.90 -6.04 0.60 N 31 1 "C3'" B DG 8 ? ? "O3'" B DG 8 ? ? P B DC 9 ? ? 132.94 119.70 13.24 1.20 Y 32 1 "O3'" B DG 8 ? ? P B DC 9 ? ? "O5'" B DC 9 ? ? 121.78 104.00 17.78 1.90 Y 33 1 "O3'" B DG 8 ? ? P B DC 9 ? ? OP1 B DC 9 ? ? 120.98 110.50 10.48 1.10 Y 34 1 OP1 B DC 9 ? ? P B DC 9 ? ? OP2 B DC 9 ? ? 91.09 119.60 -28.51 1.50 N 35 1 "O5'" B DC 9 ? ? P B DC 9 ? ? OP2 B DC 9 ? ? 90.95 105.70 -14.75 0.90 N 36 1 "O5'" B DC 9 ? ? "C5'" B DC 9 ? ? "C4'" B DC 9 ? ? 103.85 109.40 -5.55 0.80 N 37 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 101.03 105.90 -4.87 0.80 N 38 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 111.58 108.30 3.28 0.30 N 39 1 C6 B DC 9 ? ? N1 B DC 9 ? ? C2 B DC 9 ? ? 117.66 120.30 -2.64 0.40 N 40 1 N3 B DC 9 ? ? C4 B DC 9 ? ? C5 B DC 9 ? ? 118.82 121.90 -3.08 0.40 N 41 1 "C3'" B DG 12 ? ? "C2'" B DG 12 ? ? "C1'" B DG 12 ? ? 96.64 102.40 -5.76 0.80 N 42 1 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 110.53 108.30 2.23 0.30 N 43 1 C2 B DG 12 ? ? N3 B DG 12 ? ? C4 B DG 12 ? ? 115.44 111.90 3.54 0.50 N 44 1 C5 B DG 12 ? ? C6 B DG 12 ? ? N1 B DG 12 ? ? 115.60 111.50 4.10 0.50 N 45 1 C4 B DG 12 ? ? C5 B DG 12 ? ? N7 B DG 12 ? ? 113.89 110.80 3.09 0.40 N 46 1 N3 B DG 12 ? ? C4 B DG 12 ? ? N9 B DG 12 ? ? 129.96 126.00 3.96 0.60 N 47 1 C5 B DG 12 ? ? C6 B DG 12 ? ? O6 B DG 12 ? ? 124.87 128.60 -3.73 0.60 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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DG OP3 O N N 35 DG P P N N 36 DG OP1 O N N 37 DG OP2 O N N 38 DG "O5'" O N N 39 DG "C5'" C N N 40 DG "C4'" C N R 41 DG "O4'" O N N 42 DG "C3'" C N S 43 DG "O3'" O N N 44 DG "C2'" C N N 45 DG "C1'" C N R 46 DG N9 N Y N 47 DG C8 C Y N 48 DG N7 N Y N 49 DG C5 C Y N 50 DG C6 C N N 51 DG O6 O N N 52 DG N1 N N N 53 DG C2 C N N 54 DG N2 N N N 55 DG N3 N N N 56 DG C4 C Y N 57 DG HOP3 H N N 58 DG HOP2 H N N 59 DG "H5'" H N N 60 DG "H5''" H N N 61 DG "H4'" H N N 62 DG "H3'" H N N 63 DG "HO3'" H N N 64 DG "H2'" H N N 65 DG "H2''" H N N 66 DG "H1'" H N N 67 DG H8 H N N 68 DG H1 H N N 69 DG H21 H N N 70 DG H22 H N N 71 HOH O O N N 72 HOH H1 H N N 73 HOH H2 H N N 74 MG MG MG N N 75 UFP N1 N N N 76 UFP C2 C N N 77 UFP N3 N N N 78 UFP C4 C N N 79 UFP C5 C N N 80 UFP C6 C N N 81 UFP O2 O N N 82 UFP O4 O N N 83 UFP F5 F N N 84 UFP "C1'" C N R 85 UFP "C2'" C N N 86 UFP "C3'" C N S 87 UFP "C4'" C N R 88 UFP "O3'" O N N 89 UFP "O4'" O N N 90 UFP "C5'" C N N 91 UFP "O5'" O N N 92 UFP P P N N 93 UFP O1P O N N 94 UFP O2P O N N 95 UFP O3P O N N 96 UFP HN3 H N N 97 UFP H6 H N N 98 UFP "H1'" H N N 99 UFP "H2'1" H N N 100 UFP "H2'2" H N N 101 UFP "H3'" H N N 102 UFP "H4'" H N N 103 UFP "HO3'" H N N 104 UFP "H5'1" H N N 105 UFP "H5'2" H N N 106 UFP HOP2 H N N 107 UFP HOP3 H N N 108 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DG OP3 P sing N N 36 DG OP3 HOP3 sing N N 37 DG P OP1 doub N N 38 DG P OP2 sing N N 39 DG P "O5'" sing N N 40 DG OP2 HOP2 sing N N 41 DG "O5'" "C5'" sing N N 42 DG "C5'" "C4'" sing N N 43 DG "C5'" "H5'" sing N N 44 DG "C5'" "H5''" sing N N 45 DG "C4'" "O4'" sing N N 46 DG "C4'" "C3'" sing N N 47 DG "C4'" "H4'" sing N N 48 DG "O4'" "C1'" sing N N 49 DG "C3'" "O3'" sing N N 50 DG "C3'" "C2'" sing N N 51 DG "C3'" "H3'" sing N N 52 DG "O3'" "HO3'" sing N N 53 DG "C2'" "C1'" sing N N 54 DG "C2'" "H2'" sing N N 55 DG "C2'" "H2''" sing N N 56 DG "C1'" N9 sing N N 57 DG "C1'" "H1'" sing N N 58 DG N9 C8 sing Y N 59 DG N9 C4 sing Y N 60 DG C8 N7 doub Y N 61 DG C8 H8 sing N N 62 DG N7 C5 sing Y N 63 DG C5 C6 sing N N 64 DG C5 C4 doub Y N 65 DG C6 O6 doub N N 66 DG C6 N1 sing N N 67 DG N1 C2 sing N N 68 DG N1 H1 sing N N 69 DG C2 N2 sing N N 70 DG C2 N3 doub N N 71 DG N2 H21 sing N N 72 DG N2 H22 sing N N 73 DG N3 C4 sing N N 74 HOH O H1 sing N N 75 HOH O H2 sing N N 76 UFP N1 C2 sing N N 77 UFP N1 C6 sing N N 78 UFP N1 "C1'" sing N N 79 UFP C2 N3 sing N N 80 UFP C2 O2 doub N N 81 UFP N3 C4 sing N N 82 UFP N3 HN3 sing N N 83 UFP C4 C5 sing N N 84 UFP C4 O4 doub N N 85 UFP C5 C6 doub N N 86 UFP C5 F5 sing N N 87 UFP C6 H6 sing N N 88 UFP "C1'" "C2'" sing N N 89 UFP "C1'" "O4'" sing N N 90 UFP "C1'" "H1'" sing N N 91 UFP "C2'" "C3'" sing N N 92 UFP "C2'" "H2'1" sing N N 93 UFP "C2'" "H2'2" sing N N 94 UFP "C3'" "C4'" sing N N 95 UFP "C3'" "O3'" sing N N 96 UFP "C3'" "H3'" sing N N 97 UFP "C4'" "O4'" sing N N 98 UFP "C4'" "C5'" sing N N 99 UFP "C4'" "H4'" sing N N 100 UFP "O3'" "HO3'" sing N N 101 UFP "C5'" "O5'" sing N N 102 UFP "C5'" "H5'1" sing N N 103 UFP "C5'" "H5'2" sing N N 104 UFP "O5'" P sing N N 105 UFP P O1P doub N N 106 UFP P O2P sing N N 107 UFP P O3P sing N N 108 UFP O2P HOP2 sing N N 109 UFP O3P HOP3 sing N N 110 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1DNF 'double helix' 1DNF '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 -0.320 -0.128 0.062 5.622 4.267 2.206 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DC 3 1_555 B DG 4 1_555 -0.326 -0.132 0.141 2.663 -0.518 0.445 2 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 3 1_555 0.166 -0.172 0.178 -1.465 1.348 3.518 3 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 0.165 -0.112 0.299 -4.906 -5.202 0.256 4 A_DG6:DC7_B A 6 ? B 7 ? 19 1 # _ndb_struct_na_base_pair_step.model_number 1 _ndb_struct_na_base_pair_step.i_label_asym_id_1 A _ndb_struct_na_base_pair_step.i_label_comp_id_1 DC _ndb_struct_na_base_pair_step.i_label_seq_id_1 3 _ndb_struct_na_base_pair_step.i_symmetry_1 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_1 B _ndb_struct_na_base_pair_step.j_label_comp_id_1 DG _ndb_struct_na_base_pair_step.j_label_seq_id_1 4 _ndb_struct_na_base_pair_step.j_symmetry_1 1_555 _ndb_struct_na_base_pair_step.i_label_asym_id_2 A _ndb_struct_na_base_pair_step.i_label_comp_id_2 DG _ndb_struct_na_base_pair_step.i_label_seq_id_2 4 _ndb_struct_na_base_pair_step.i_symmetry_2 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_2 B _ndb_struct_na_base_pair_step.j_label_comp_id_2 DC _ndb_struct_na_base_pair_step.j_label_seq_id_2 3 _ndb_struct_na_base_pair_step.j_symmetry_2 1_555 _ndb_struct_na_base_pair_step.shift -0.059 _ndb_struct_na_base_pair_step.slide 5.283 _ndb_struct_na_base_pair_step.rise 3.740 _ndb_struct_na_base_pair_step.tilt -0.738 _ndb_struct_na_base_pair_step.roll -4.773 _ndb_struct_na_base_pair_step.twist -8.961 _ndb_struct_na_base_pair_step.x_displacement -16.453 _ndb_struct_na_base_pair_step.y_displacement -2.393 _ndb_struct_na_base_pair_step.helical_rise 5.762 _ndb_struct_na_base_pair_step.inclination 28.031 _ndb_struct_na_base_pair_step.tip -4.333 _ndb_struct_na_base_pair_step.helical_twist -10.178 _ndb_struct_na_base_pair_step.step_number 1 _ndb_struct_na_base_pair_step.step_name AA_DC3DG4:DC9DG10_BB _ndb_struct_na_base_pair_step.i_auth_asym_id_1 A _ndb_struct_na_base_pair_step.i_auth_seq_id_1 3 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_1 B _ndb_struct_na_base_pair_step.j_auth_seq_id_1 10 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.i_auth_asym_id_2 A _ndb_struct_na_base_pair_step.i_auth_seq_id_2 4 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_2 B _ndb_struct_na_base_pair_step.j_auth_seq_id_2 9 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 ? # _atom_sites.entry_id 1DNF _atom_sites.fract_transf_matrix[1][1] 0.057604 _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] 0.032103 _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] 0.022026 _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 F MG N O P # loop_