data_1D48 # _entry.id 1D48 # _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 1D48 pdb_00001d48 10.2210/pdb1d48/pdb RCSB ZDF029 ? ? WWPDB D_1000172652 ? ? # 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 1992-04-15 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' 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' '_struct_site.pdbx_auth_asym_id' 4 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1D48 _pdbx_database_status.recvd_initial_deposition_date 1991-09-11 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Egli, M.' 1 'Williams, L.D.' 2 'Gao, Q.' 3 'Rich, A.' 4 # _citation.id primary _citation.title 'Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-A resolution.' _citation.journal_abbrev Biochemistry _citation.journal_volume 30 _citation.page_first 11388 _citation.page_last 11402 _citation.year 1991 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 1742278 _citation.pdbx_database_id_DOI 10.1021/bi00112a005 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Egli, M.' 1 ? primary 'Williams, L.D.' 2 ? primary 'Gao, Q.' 3 ? primary 'Rich, A.' 4 ? # 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*CP*G)-3') ; 1810.205 2 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 3 water nat water 18.015 47 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGCG _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 SPERMINE SPM 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 DC 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 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 # 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 DC 5 5 5 DC 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 DC 5 11 11 DC 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 SPM 1 13 13 SPM SPM A . D 3 HOH 1 14 14 HOH HOH A . D 3 HOH 2 15 15 HOH HOH A . D 3 HOH 3 18 18 HOH HOH A . D 3 HOH 4 19 19 HOH HOH A . D 3 HOH 5 20 20 HOH HOH A . D 3 HOH 6 21 21 HOH HOH A . D 3 HOH 7 24 24 HOH HOH A . D 3 HOH 8 26 26 HOH HOH A . D 3 HOH 9 28 28 HOH HOH A . D 3 HOH 10 29 29 HOH HOH A . D 3 HOH 11 33 33 HOH HOH A . D 3 HOH 12 34 34 HOH HOH A . D 3 HOH 13 35 35 HOH HOH A . D 3 HOH 14 41 41 HOH HOH A . D 3 HOH 15 42 42 HOH HOH A . D 3 HOH 16 43 43 HOH HOH A . D 3 HOH 17 44 44 HOH HOH A . D 3 HOH 18 46 46 HOH HOH A . D 3 HOH 19 56 56 HOH HOH A . D 3 HOH 20 57 57 HOH HOH A . E 3 HOH 1 16 16 HOH HOH B . E 3 HOH 2 17 17 HOH HOH B . E 3 HOH 3 22 22 HOH HOH B . E 3 HOH 4 23 23 HOH HOH B . E 3 HOH 5 25 25 HOH HOH B . E 3 HOH 6 27 27 HOH HOH B . E 3 HOH 7 30 30 HOH HOH B . E 3 HOH 8 31 31 HOH HOH B . E 3 HOH 9 32 32 HOH HOH B . E 3 HOH 10 36 36 HOH HOH B . E 3 HOH 11 37 37 HOH HOH B . E 3 HOH 12 38 38 HOH HOH B . E 3 HOH 13 39 39 HOH HOH B . E 3 HOH 14 40 40 HOH HOH B . E 3 HOH 15 45 45 HOH HOH B . E 3 HOH 16 47 47 HOH HOH B . E 3 HOH 17 48 48 HOH HOH B . E 3 HOH 18 49 49 HOH HOH B . E 3 HOH 19 50 50 HOH HOH B . E 3 HOH 20 51 51 HOH HOH B . E 3 HOH 21 52 52 HOH HOH B . E 3 HOH 22 53 53 HOH HOH B . E 3 HOH 23 54 54 HOH HOH B . E 3 HOH 24 55 55 HOH HOH B . E 3 HOH 25 58 58 HOH HOH B . E 3 HOH 26 59 59 HOH HOH B . E 3 HOH 27 60 60 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 1D48 _cell.length_a 18.405 _cell.length_b 30.768 _cell.length_c 43.152 _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 1D48 _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 1D48 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.69 _exptl_crystal.density_percent_sol 27.11 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details 'ROOM TEMPERATURE' _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'pH 7.00, VAPOR DIFFUSION, SITTING DROP' _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 SPERMINE ? ? ? 1 3 2 WATER ? ? ? 1 4 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details 'ROOM TEMPERATURE' _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 1D48 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 2.000 _reflns.d_resolution_low ? _reflns.d_resolution_high 1.000 _reflns.number_obs 8200 _reflns.number_all 10900 _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.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 1D48 _refine.ls_number_reflns_obs 8183 _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 1.000 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1850000 _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.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 14 _refine_hist.number_atoms_solvent 47 _refine_hist.number_atoms_total 301 _refine_hist.d_res_high 1.000 _refine_hist.d_res_low . # _database_PDB_matrix.entry_id 1D48 _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 1D48 _struct.title 'STRUCTURE OF THE PURE-SPERMINE FORM OF Z-DNA (MAGNESIUM FREE) AT 1 ANGSTROM RESOLUTION' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1D48 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Z-DNA, DOUBLE HELIX, 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 1D48 _struct_ref.pdbx_db_accession 1D48 _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 1D48 A 1 ? 6 ? 1D48 1 ? 6 ? 1 6 2 1 1D48 B 1 ? 6 ? 1D48 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 # 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 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 DC 5 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id SPM _struct_site.pdbx_auth_seq_id 13 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 11 _struct_site.details 'BINDING SITE FOR RESIDUE SPM 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 11 DG A 2 ? DG A 2 . ? 1_555 ? 2 AC1 11 DC A 3 ? DC A 3 . ? 1_555 ? 3 AC1 11 DG A 4 ? DG A 4 . ? 1_555 ? 4 AC1 11 HOH D . ? HOH A 21 . ? 1_555 ? 5 AC1 11 HOH D . ? HOH A 29 . ? 4_566 ? 6 AC1 11 DG B 2 ? DG B 8 . ? 1_555 ? 7 AC1 11 DC B 3 ? DC B 9 . ? 4_556 ? 8 AC1 11 DG B 4 ? DG B 10 . ? 1_655 ? 9 AC1 11 DG B 4 ? DG B 10 . ? 4_556 ? 10 AC1 11 DC B 5 ? DC B 11 . ? 1_655 ? 11 AC1 11 DG B 6 ? DG B 12 . ? 1_655 ? # 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 "O3'" A DC 1 ? ? "C3'" A DC 1 ? ? 1.367 1.419 -0.052 0.006 N 2 1 N3 A DC 1 ? ? C4 A DC 1 ? ? 1.378 1.335 0.043 0.007 N 3 1 P A DG 2 ? ? OP2 A DG 2 ? ? 1.371 1.485 -0.114 0.017 N 4 1 "C3'" A DG 2 ? ? "C2'" A DG 2 ? ? 1.455 1.516 -0.061 0.008 N 5 1 "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? 1.374 1.446 -0.072 0.010 N 6 1 C6 A DG 2 ? ? N1 A DG 2 ? ? 1.343 1.391 -0.048 0.007 N 7 1 C2 A DG 2 ? ? N2 A DG 2 ? ? 1.250 1.341 -0.091 0.010 N 8 1 C6 A DG 2 ? ? O6 A DG 2 ? ? 1.294 1.237 0.057 0.009 N 9 1 "C2'" A DC 3 ? ? "C1'" A DC 3 ? ? 1.588 1.519 0.069 0.010 N 10 1 N3 A DC 3 ? ? C4 A DC 3 ? ? 1.383 1.335 0.048 0.007 N 11 1 "C2'" A DG 4 ? ? "C1'" A DG 4 ? ? 1.596 1.519 0.077 0.010 N 12 1 C6 A DG 4 ? ? N1 A DG 4 ? ? 1.337 1.391 -0.054 0.007 N 13 1 C5 A DG 4 ? ? N7 A DG 4 ? ? 1.350 1.388 -0.038 0.006 N 14 1 C8 A DG 4 ? ? N9 A DG 4 ? ? 1.332 1.374 -0.042 0.007 N 15 1 C2 A DG 4 ? ? N2 A DG 4 ? ? 1.266 1.341 -0.075 0.010 N 16 1 C6 A DG 6 ? ? N1 A DG 6 ? ? 1.322 1.391 -0.069 0.007 N 17 1 C2 A DG 6 ? ? N2 A DG 6 ? ? 1.248 1.341 -0.093 0.010 N 18 1 N3 B DC 7 ? ? C4 B DC 7 ? ? 1.380 1.335 0.045 0.007 N 19 1 "C5'" B DG 8 ? ? "C4'" B DG 8 ? ? 1.571 1.512 0.059 0.007 N 20 1 C6 B DG 8 ? ? N1 B DG 8 ? ? 1.343 1.391 -0.048 0.007 N 21 1 N7 B DG 8 ? ? C8 B DG 8 ? ? 1.345 1.305 0.040 0.006 N 22 1 C8 B DG 8 ? ? N9 B DG 8 ? ? 1.328 1.374 -0.046 0.007 N 23 1 C2 B DG 8 ? ? N2 B DG 8 ? ? 1.253 1.341 -0.088 0.010 N 24 1 "C2'" B DC 9 ? ? "C1'" B DC 9 ? ? 1.599 1.519 0.080 0.010 N 25 1 N3 B DC 9 ? ? C4 B DC 9 ? ? 1.380 1.335 0.045 0.007 N 26 1 P B DG 10 ? ? "O5'" B DG 10 ? ? 1.654 1.593 0.061 0.010 N 27 1 C6 B DG 10 ? ? N1 B DG 10 ? ? 1.338 1.391 -0.053 0.007 N 28 1 C2 B DG 10 ? ? N2 B DG 10 ? ? 1.251 1.341 -0.090 0.010 N 29 1 N3 B DC 11 ? ? C4 B DC 11 ? ? 1.381 1.335 0.046 0.007 N 30 1 C6 B DG 12 ? ? N1 B DG 12 ? ? 1.342 1.391 -0.049 0.007 N 31 1 C2 B DG 12 ? ? N2 B DG 12 ? ? 1.262 1.341 -0.079 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 C2 A DC 1 ? ? N3 A DC 1 ? ? C4 A DC 1 ? ? 124.48 119.90 4.58 0.50 N 2 1 N3 A DC 1 ? ? C4 A DC 1 ? ? C5 A DC 1 ? ? 116.57 121.90 -5.33 0.40 N 3 1 N1 A DC 1 ? ? C2 A DC 1 ? ? O2 A DC 1 ? ? 125.12 118.90 6.22 0.60 N 4 1 C5 A DC 1 ? ? C4 A DC 1 ? ? N4 A DC 1 ? ? 125.11 120.20 4.91 0.70 N 5 1 C6 A DG 2 ? ? N1 A DG 2 ? ? C2 A DG 2 ? ? 119.33 125.10 -5.77 0.60 N 6 1 N1 A DG 2 ? ? C2 A DG 2 ? ? N3 A DG 2 ? ? 128.32 123.90 4.42 0.60 N 7 1 C5 A DG 2 ? ? C6 A DG 2 ? ? N1 A DG 2 ? ? 118.09 111.50 6.59 0.50 N 8 1 N3 A DG 2 ? ? C2 A DG 2 ? ? N2 A DG 2 ? ? 111.03 119.90 -8.87 0.70 N 9 1 C5 A DG 2 ? ? C6 A DG 2 ? ? O6 A DG 2 ? ? 121.62 128.60 -6.98 0.60 N 10 1 N3 A DC 3 ? ? C4 A DC 3 ? ? C5 A DC 3 ? ? 119.20 121.90 -2.70 0.40 N 11 1 N1 A DC 3 ? ? C2 A DC 3 ? ? O2 A DC 3 ? ? 123.06 118.90 4.16 0.60 N 12 1 N1 A DG 4 ? ? C2 A DG 4 ? ? N3 A DG 4 ? ? 127.59 123.90 3.69 0.60 N 13 1 C5 A DG 4 ? ? C6 A DG 4 ? ? N1 A DG 4 ? ? 115.46 111.50 3.96 0.50 N 14 1 N3 A DG 4 ? ? C2 A DG 4 ? ? N2 A DG 4 ? ? 113.58 119.90 -6.32 0.70 N 15 1 C5 A DG 4 ? ? C6 A DG 4 ? ? O6 A DG 4 ? ? 124.46 128.60 -4.14 0.60 N 16 1 C2 A DC 5 ? ? N3 A DC 5 ? ? C4 A DC 5 ? ? 126.44 119.90 6.54 0.50 N 17 1 N3 A DC 5 ? ? C4 A DC 5 ? ? C5 A DC 5 ? ? 116.35 121.90 -5.55 0.40 N 18 1 N1 A DC 5 ? ? C2 A DC 5 ? ? O2 A DC 5 ? ? 123.98 118.90 5.08 0.60 N 19 1 C6 A DG 6 ? ? N1 A DG 6 ? ? C2 A DG 6 ? ? 120.92 125.10 -4.18 0.60 N 20 1 C5 A DG 6 ? ? C6 A DG 6 ? ? N1 A DG 6 ? ? 116.92 111.50 5.42 0.50 N 21 1 C4 A DG 6 ? ? C5 A DG 6 ? ? N7 A DG 6 ? ? 114.31 110.80 3.51 0.40 N 22 1 N3 A DG 6 ? ? C2 A DG 6 ? ? N2 A DG 6 ? ? 113.19 119.90 -6.71 0.70 N 23 1 C5 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 123.70 128.60 -4.90 0.60 N 24 1 N3 B DC 7 ? ? C4 B DC 7 ? ? C5 B DC 7 ? ? 118.45 121.90 -3.45 0.40 N 25 1 "O5'" B DG 8 ? ? "C5'" B DG 8 ? ? "C4'" B DG 8 ? ? 102.64 109.40 -6.76 0.80 N 26 1 C6 B DG 8 ? ? N1 B DG 8 ? ? C2 B DG 8 ? ? 119.98 125.10 -5.12 0.60 N 27 1 N1 B DG 8 ? ? C2 B DG 8 ? ? N3 B DG 8 ? ? 129.01 123.90 5.11 0.60 N 28 1 C2 B DG 8 ? ? N3 B DG 8 ? ? C4 B DG 8 ? ? 108.57 111.90 -3.33 0.50 N 29 1 C5 B DG 8 ? ? C6 B DG 8 ? ? N1 B DG 8 ? ? 117.15 111.50 5.65 0.50 N 30 1 N3 B DG 8 ? ? C2 B DG 8 ? ? N2 B DG 8 ? ? 112.51 119.90 -7.39 0.70 N 31 1 C5 B DG 8 ? ? C6 B DG 8 ? ? O6 B DG 8 ? ? 122.98 128.60 -5.62 0.60 N 32 1 C2 B DC 9 ? ? N3 B DC 9 ? ? C4 B DC 9 ? ? 123.00 119.90 3.10 0.50 N 33 1 N3 B DC 9 ? ? C4 B DC 9 ? ? C5 B DC 9 ? ? 118.69 121.90 -3.21 0.40 N 34 1 N1 B DC 9 ? ? C2 B DC 9 ? ? O2 B DC 9 ? ? 124.70 118.90 5.80 0.60 N 35 1 "O5'" B DG 10 ? ? "C5'" B DG 10 ? ? "C4'" B DG 10 ? ? 104.00 109.40 -5.40 0.80 N 36 1 C6 B DG 10 ? ? N1 B DG 10 ? ? C2 B DG 10 ? ? 120.57 125.10 -4.53 0.60 N 37 1 C5 B DG 10 ? ? C6 B DG 10 ? ? N1 B DG 10 ? ? 117.20 111.50 5.70 0.50 N 38 1 N1 B DG 10 ? ? C2 B DG 10 ? ? N2 B DG 10 ? ? 122.02 116.20 5.82 0.90 N 39 1 N3 B DG 10 ? ? C2 B DG 10 ? ? N2 B DG 10 ? ? 111.09 119.90 -8.81 0.70 N 40 1 C5 B DG 10 ? ? C6 B DG 10 ? ? O6 B DG 10 ? ? 122.56 128.60 -6.04 0.60 N 41 1 "C3'" B DC 11 ? ? "C2'" B DC 11 ? ? "C1'" B DC 11 ? ? 97.43 102.40 -4.97 0.80 N 42 1 C2 B DC 11 ? ? N3 B DC 11 ? ? C4 B DC 11 ? ? 124.03 119.90 4.13 0.50 N 43 1 N3 B DC 11 ? ? C4 B DC 11 ? ? C5 B DC 11 ? ? 117.91 121.90 -3.99 0.40 N 44 1 N1 B DC 11 ? ? C2 B DC 11 ? ? O2 B DC 11 ? ? 123.32 118.90 4.42 0.60 N 45 1 C5 B DC 11 ? ? C4 B DC 11 ? ? N4 B DC 11 ? ? 124.90 120.20 4.70 0.70 N 46 1 C6 B DG 12 ? ? N1 B DG 12 ? ? C2 B DG 12 ? ? 120.53 125.10 -4.57 0.60 N 47 1 N1 B DG 12 ? ? C2 B DG 12 ? ? N3 B DG 12 ? ? 128.87 123.90 4.97 0.60 N 48 1 C2 B DG 12 ? ? N3 B DG 12 ? ? C4 B DG 12 ? ? 108.71 111.90 -3.19 0.50 N 49 1 C5 B DG 12 ? ? C6 B DG 12 ? ? N1 B DG 12 ? ? 115.80 111.50 4.30 0.50 N 50 1 N3 B DG 12 ? ? C2 B DG 12 ? ? N2 B DG 12 ? ? 112.93 119.90 -6.97 0.70 N 51 1 C5 B DG 12 ? ? C6 B DG 12 ? ? O6 B DG 12 ? ? 123.14 128.60 -5.46 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 SPM N1 N N N 75 SPM C2 C N N 76 SPM C3 C N N 77 SPM C4 C N N 78 SPM N5 N N N 79 SPM C6 C N N 80 SPM C7 C N N 81 SPM C8 C N N 82 SPM C9 C N N 83 SPM N10 N N N 84 SPM C11 C N N 85 SPM C12 C N N 86 SPM C13 C N N 87 SPM N14 N N N 88 SPM HN11 H N N 89 SPM HN12 H N N 90 SPM H21 H N N 91 SPM H22 H N N 92 SPM H31 H N N 93 SPM H32 H N N 94 SPM H41 H N N 95 SPM H42 H N N 96 SPM HN5 H N N 97 SPM H61 H N N 98 SPM H62 H N N 99 SPM H71 H N N 100 SPM H72 H N N 101 SPM H81 H N N 102 SPM H82 H N N 103 SPM H91 H N N 104 SPM H92 H N N 105 SPM HN0 H N N 106 SPM H111 H N N 107 SPM H112 H N N 108 SPM H121 H N N 109 SPM H122 H N N 110 SPM H131 H N N 111 SPM H132 H N N 112 SPM HN41 H N N 113 SPM HN42 H N N 114 # 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 SPM N1 C2 sing N N 77 SPM N1 HN11 sing N N 78 SPM N1 HN12 sing N N 79 SPM C2 C3 sing N N 80 SPM C2 H21 sing N N 81 SPM C2 H22 sing N N 82 SPM C3 C4 sing N N 83 SPM C3 H31 sing N N 84 SPM C3 H32 sing N N 85 SPM C4 N5 sing N N 86 SPM C4 H41 sing N N 87 SPM C4 H42 sing N N 88 SPM N5 C6 sing N N 89 SPM N5 HN5 sing N N 90 SPM C6 C7 sing N N 91 SPM C6 H61 sing N N 92 SPM C6 H62 sing N N 93 SPM C7 C8 sing N N 94 SPM C7 H71 sing N N 95 SPM C7 H72 sing N N 96 SPM C8 C9 sing N N 97 SPM C8 H81 sing N N 98 SPM C8 H82 sing N N 99 SPM C9 N10 sing N N 100 SPM C9 H91 sing N N 101 SPM C9 H92 sing N N 102 SPM N10 C11 sing N N 103 SPM N10 HN0 sing N N 104 SPM C11 C12 sing N N 105 SPM C11 H111 sing N N 106 SPM C11 H112 sing N N 107 SPM C12 C13 sing N N 108 SPM C12 H121 sing N N 109 SPM C12 H122 sing N N 110 SPM C13 N14 sing N N 111 SPM C13 H131 sing N N 112 SPM C13 H132 sing N N 113 SPM N14 HN41 sing N N 114 SPM N14 HN42 sing N N 115 # _ndb_struct_conf_na.entry_id 1D48 _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 -0.251 -0.116 0.188 4.165 -1.134 1.246 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B DC 5 1_555 0.324 -0.188 -0.017 -4.993 -0.272 1.442 2 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A DC 3 1_555 B DG 4 1_555 -0.255 -0.126 -0.044 2.909 3.257 1.732 3 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 3 1_555 0.272 -0.177 0.104 -6.176 4.605 2.665 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A DC 5 1_555 B DG 2 1_555 -0.245 -0.179 0.047 2.638 -4.592 1.782 5 A_DC5:DG8_B A 5 ? B 8 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 0.262 -0.161 0.079 -3.530 3.052 1.557 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 DC 5 1_555 0.209 5.513 3.733 2.816 -1.639 -9.376 -27.899 8.029 4.376 9.649 16.581 -9.925 1 AA_DC1DG2:DC11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B DC 5 1_555 A DC 3 1_555 B DG 4 1_555 0.546 -0.435 3.247 0.677 -6.311 -52.190 0.898 0.661 3.171 7.144 0.767 -52.548 2 AA_DG2DC3:DG10DC11_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 -0.277 5.418 3.680 -2.521 0.444 -9.131 -33.770 -7.314 3.217 -2.721 -15.438 -9.482 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 DC 5 1_555 B DG 2 1_555 -0.495 -1.032 3.364 1.259 -1.095 -50.412 1.291 -0.489 3.353 1.285 1.478 -50.438 4 AA_DG4DC5:DG8DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DC 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 0.040 5.550 3.713 1.861 2.503 -8.931 -38.390 3.764 2.032 -15.469 11.502 -9.459 5 AA_DC5DG6:DC7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ? # _atom_sites.entry_id 1D48 _atom_sites.fract_transf_matrix[1][1] 0.054333 _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] 0.032501 _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] 0.023174 _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_