data_417D # _entry.id 417D # _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 417D pdb_0000417d 10.2210/pdb417d/pdb RCSB ZD0002 ? ? WWPDB D_1000179217 ? ? # 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 1998-09-30 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-28 5 'Structure model' 1 4 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 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' 7 5 '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' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' diffrn_source 5 4 'Structure model' software 6 4 'Structure model' struct_conn 7 5 '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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 4 4 'Structure model' '_software.name' 5 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 417D _pdbx_database_status.recvd_initial_deposition_date 1998-07-15 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Lin, P.K.T.' 1 'Schuerman, M.H.' 2 'Moore, G.S.' 3 'Van Meervelt, L.' 4 'Loakes, D.' 5 'Brown, D.M.' 6 'Moore, M.H.' 7 # _citation.id primary _citation.title 'A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex.' _citation.journal_abbrev J.Mol.Biol. _citation.journal_volume 282 _citation.page_first 1005 _citation.page_last 1011 _citation.year 1998 _citation.journal_id_ASTM JMOBAK _citation.country UK _citation.journal_id_ISSN 0022-2836 _citation.journal_id_CSD 0070 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9753550 _citation.pdbx_database_id_DOI 10.1006/jmbi.1998.2080 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Schuerman, G.S.' 1 ? primary 'Van Meervelt, L.' 2 ? primary 'Loakes, D.' 3 ? primary 'Brown, D.M.' 4 ? primary 'Kong Thoo Lin, P.' 5 ? primary 'Moore, M.H.' 6 ? primary 'Salisbury, S.A.' 7 ? # 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 man ;DNA (5'-D(*CP*AP*CP*GP*(C46)P*G)-3') ; 1836.243 2 ? ? ? ? 2 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)(DA)(DC)(DG)(C46)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CACGCG _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 DA 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 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 DA 2 2 2 DA A 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 DA 2 8 8 DA A 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 17 17 HOH HOH A . C 2 HOH 4 18 18 HOH HOH A . C 2 HOH 5 19 19 HOH HOH A . C 2 HOH 6 20 20 HOH HOH A . C 2 HOH 7 22 22 HOH HOH A . C 2 HOH 8 25 25 HOH HOH A . C 2 HOH 9 26 26 HOH HOH A . C 2 HOH 10 30 30 HOH HOH A . C 2 HOH 11 33 33 HOH HOH A . C 2 HOH 12 34 34 HOH HOH A . C 2 HOH 13 36 36 HOH HOH A . C 2 HOH 14 37 37 HOH HOH A . C 2 HOH 15 39 39 HOH HOH A . C 2 HOH 16 42 42 HOH HOH A . C 2 HOH 17 43 43 HOH HOH A . C 2 HOH 18 51 51 HOH HOH A . C 2 HOH 19 52 52 HOH HOH A . C 2 HOH 20 53 53 HOH HOH A . C 2 HOH 21 55 55 HOH HOH A . C 2 HOH 22 56 56 HOH HOH A . C 2 HOH 23 57 57 HOH HOH A . C 2 HOH 24 58 58 HOH HOH A . C 2 HOH 25 61 61 HOH HOH A . C 2 HOH 26 66 66 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 21 21 HOH HOH B . D 2 HOH 4 23 23 HOH HOH B . D 2 HOH 5 24 24 HOH HOH B . D 2 HOH 6 27 27 HOH HOH B . D 2 HOH 7 28 28 HOH HOH B . D 2 HOH 8 29 29 HOH HOH B . D 2 HOH 9 31 31 HOH HOH B . D 2 HOH 10 32 32 HOH HOH B . D 2 HOH 11 35 35 HOH HOH B . D 2 HOH 12 38 38 HOH HOH B . D 2 HOH 13 40 40 HOH HOH B . D 2 HOH 14 41 41 HOH HOH B . D 2 HOH 15 44 44 HOH HOH B . D 2 HOH 16 45 45 HOH HOH B . D 2 HOH 17 46 46 HOH HOH B . D 2 HOH 18 47 47 HOH HOH B . D 2 HOH 19 48 48 HOH HOH B . D 2 HOH 20 49 49 HOH HOH B . D 2 HOH 21 50 50 HOH HOH B . D 2 HOH 22 54 54 HOH HOH B . D 2 HOH 23 59 59 HOH HOH B . D 2 HOH 24 60 60 HOH HOH B . D 2 HOH 25 62 62 HOH HOH B . D 2 HOH 26 63 63 HOH HOH B . D 2 HOH 27 64 64 HOH HOH B . D 2 HOH 28 65 65 HOH HOH B . D 2 HOH 29 67 67 HOH HOH B . D 2 HOH 30 68 68 HOH HOH B . D 2 HOH 31 69 69 HOH HOH B . D 2 HOH 32 70 70 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal AMoRE phasing . ? 1 SHELXL-93 refinement . ? 2 DENZO 'data reduction' . ? 3 CCP4 'data scaling' '(AGROVATA' ? 4 ROTAVATA 'data scaling' . ? 5 # _cell.entry_id 417D _cell.length_a 17.338 _cell.length_b 31.432 _cell.length_c 44.486 _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 417D _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 19 # _exptl.entry_id 417D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.65 _exptl_crystal.density_percent_sol 35.0000 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 277.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.50 _exptl_crystal_grow.pdbx_details ;CRYSTALS WERE OBTAINED FROM A SOLUTION THAT CONTAINED NA CACODYLATE, MG CHLORIDE, SPERMINE, MPD., pH 6.50, VAPOR DIFFUSION, SITTING DROP, 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 'NA CACODYLATE' ? ? ? 1 2 1 MGCL2 ? ? ? 1 3 1 SPERMINE ? ? ? 1 4 1 MPD ? ? ? 1 5 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 150.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 1995-10-19 _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 SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE BW7B' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline BW7B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 417D _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F 0.000 _reflns.d_resolution_low 10.000 _reflns.d_resolution_high 1.530 _reflns.number_obs 3920 _reflns.number_all 3920 _reflns.percent_possible_obs 97.500 _reflns.pdbx_Rmerge_I_obs 0.086 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 21.0800 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.200 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.530 _reflns_shell.d_res_low 1.560 _reflns_shell.percent_possible_all 92.50 _reflns_shell.Rmerge_I_obs 0.104 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 11.92 _reflns_shell.pdbx_redundancy ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 417D _refine.ls_number_reflns_obs 3696 _refine.ls_number_reflns_all 3920 _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 10.000 _refine.ls_d_res_high 1.500 _refine.ls_percent_reflns_obs 97.500 _refine.ls_R_factor_obs 0.15 _refine.ls_R_factor_all 0.156 _refine.ls_R_factor_R_work 0.155 _refine.ls_R_factor_R_free 0.25 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.000 _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters 2724 _refine.ls_number_restraints 5294 _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 ;BABINET'S PRINCIPLE ; _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model PDB _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values SHELXL _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details CCP4 _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 244 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 58 _refine_hist.number_atoms_total 302 _refine_hist.d_res_high 1.500 _refine_hist.d_res_low 10.000 # 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 s_bond_d 0.014 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.014 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.020 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.041 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.083 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr ? ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.004 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.020 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.058 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 417D _pdbx_refine.R_factor_all_no_cutoff 0.156 _pdbx_refine.R_factor_obs_no_cutoff 0.155 _pdbx_refine.free_R_factor_no_cutoff 0.25 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 10.000 _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff 0.15 _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 10.00 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff 3696 _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 417D _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 417D _struct.title 'A THYMINE-LIKE BASE ANALOGUE FORMS WOBBLE PAIRS WITH ADENINE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 417D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'P.A BASE-PAIRS, PYRIMIDINE ANALOGUE, Z-DNA, 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 417D _struct_ref.pdbx_db_accession 417D _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 417D A 1 ? 6 ? 417D 1 ? 6 ? 1 6 2 1 417D B 1 ? 6 ? 417D 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 ? ? ? ? ? ? ? 1.599 ? ? covale2 covale one ? A C46 5 "O3'" ? ? ? 1_555 A DG 6 P ? ? A C46 5 A DG 6 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale3 covale both ? B DG 4 "O3'" ? ? ? 1_555 B C46 5 P ? ? B DG 10 B C46 11 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale4 covale one ? B C46 5 "O3'" ? ? ? 1_555 B DG 6 P ? ? B C46 11 B DG 12 1_555 ? ? ? ? ? ? ? 1.608 ? ? 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 DA 2 N6 ? ? ? 1_555 B C46 5 N3 ? ? A DA 2 B C46 11 1_555 ? ? ? ? ? ? 'DA-C46 MISPAIR' ? ? ? 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 DA 2 N6 ? ? A C46 5 B DA 8 1_555 ? ? ? ? ? ? 'C46-DA MISPAIR' ? ? ? hydrog12 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 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 "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? 1.451 1.516 -0.065 0.008 N 2 1 "C3'" A DA 2 ? ? "C2'" A DA 2 ? ? 1.411 1.516 -0.105 0.008 N 3 1 "C3'" A DC 3 ? ? "C2'" A DC 3 ? ? 1.441 1.516 -0.075 0.008 N 4 1 "C3'" A DG 4 ? ? "C2'" A DG 4 ? ? 1.429 1.516 -0.087 0.008 N 5 1 "C3'" A DG 6 ? ? "C2'" A DG 6 ? ? 1.435 1.516 -0.081 0.008 N 6 1 "C3'" B DC 7 ? ? "C2'" B DC 7 ? ? 1.448 1.516 -0.068 0.008 N 7 1 "O4'" B DC 7 ? ? "C4'" B DC 7 ? ? 1.385 1.446 -0.061 0.010 N 8 1 "C3'" B DA 8 ? ? "C2'" B DA 8 ? ? 1.434 1.516 -0.082 0.008 N 9 1 "C3'" B DC 9 ? ? "C2'" B DC 9 ? ? 1.431 1.516 -0.085 0.008 N 10 1 "C3'" B DG 10 ? ? "C2'" B DG 10 ? ? 1.423 1.516 -0.093 0.008 N 11 1 "C3'" B DG 12 ? ? "C2'" B DG 12 ? ? 1.426 1.516 -0.090 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 C2 A DC 1 ? ? N3 A DC 1 ? ? C4 A DC 1 ? ? 123.13 119.90 3.23 0.50 N 2 1 "O4'" A DA 2 ? ? "C4'" A DA 2 ? ? "C3'" A DA 2 ? ? 101.86 104.50 -2.64 0.40 N 3 1 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 101.51 108.00 -6.49 0.70 N 4 1 C6 A DA 2 ? ? N1 A DA 2 ? ? C2 A DA 2 ? ? 122.61 118.60 4.01 0.60 N 5 1 N1 A DA 2 ? ? C2 A DA 2 ? ? N3 A DA 2 ? ? 124.85 129.30 -4.45 0.50 N 6 1 C2 A DA 2 ? ? N3 A DA 2 ? ? C4 A DA 2 ? ? 113.75 110.60 3.15 0.50 N 7 1 C5 A DA 2 ? ? C6 A DA 2 ? ? N1 A DA 2 ? ? 113.73 117.70 -3.97 0.50 N 8 1 OP1 A DC 3 ? ? P A DC 3 ? ? OP2 A DC 3 ? ? 109.34 119.60 -10.26 1.50 N 9 1 "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? "C3'" A DG 4 ? ? 101.53 104.50 -2.97 0.40 N 10 1 "O4'" A DG 6 ? ? "C4'" A DG 6 ? ? "C3'" A DG 6 ? ? 102.09 104.50 -2.41 0.40 N 11 1 C5 A DG 6 ? ? C6 A DG 6 ? ? N1 A DG 6 ? ? 114.78 111.50 3.28 0.50 N 12 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.03 108.30 2.73 0.30 N 13 1 "O4'" B DA 8 ? ? "C1'" B DA 8 ? ? N9 B DA 8 ? ? 103.70 108.00 -4.30 0.70 N 14 1 C5 B DA 8 ? ? C6 B DA 8 ? ? N1 B DA 8 ? ? 114.29 117.70 -3.41 0.50 N 15 1 "C3'" B DA 8 ? ? "O3'" B DA 8 ? ? P B DC 9 ? ? 131.72 119.70 12.02 1.20 Y 16 1 OP1 B DC 9 ? ? P B DC 9 ? ? OP2 B DC 9 ? ? 109.06 119.60 -10.54 1.50 N 17 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 101.09 105.90 -4.81 0.80 N 18 1 C6 B DC 9 ? ? N1 B DC 9 ? ? C2 B DC 9 ? ? 123.96 120.30 3.66 0.40 N 19 1 "C3'" B DC 9 ? ? "O3'" B DC 9 ? ? P B DG 10 ? ? 128.06 119.70 8.36 1.20 Y 20 1 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 101.82 108.00 -6.18 0.70 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 DA OP3 O N N 40 DA P P N N 41 DA OP1 O N N 42 DA OP2 O N N 43 DA "O5'" O N N 44 DA "C5'" C N N 45 DA "C4'" C N R 46 DA "O4'" O N N 47 DA "C3'" C N S 48 DA "O3'" O N N 49 DA "C2'" C N N 50 DA "C1'" C N R 51 DA N9 N Y N 52 DA C8 C Y N 53 DA N7 N Y N 54 DA C5 C Y N 55 DA C6 C Y N 56 DA N6 N N N 57 DA N1 N Y N 58 DA C2 C Y N 59 DA N3 N Y N 60 DA C4 C Y N 61 DA HOP3 H N N 62 DA HOP2 H N N 63 DA "H5'" H N N 64 DA "H5''" H N N 65 DA "H4'" H N N 66 DA "H3'" H N N 67 DA "HO3'" H N N 68 DA "H2'" H N N 69 DA "H2''" H N N 70 DA "H1'" H N N 71 DA H8 H N N 72 DA H61 H N N 73 DA H62 H N N 74 DA H2 H N N 75 DC OP3 O N N 76 DC P P N N 77 DC OP1 O N N 78 DC OP2 O N N 79 DC "O5'" O N N 80 DC "C5'" C N N 81 DC "C4'" C N R 82 DC "O4'" O N N 83 DC "C3'" C N S 84 DC "O3'" O N N 85 DC "C2'" C N N 86 DC "C1'" C N R 87 DC N1 N N N 88 DC C2 C N N 89 DC O2 O N N 90 DC N3 N N N 91 DC C4 C N N 92 DC N4 N N N 93 DC C5 C N N 94 DC C6 C N N 95 DC HOP3 H N N 96 DC HOP2 H N N 97 DC "H5'" H N N 98 DC "H5''" H N N 99 DC "H4'" H N N 100 DC "H3'" H N N 101 DC "HO3'" H N N 102 DC "H2'" H N N 103 DC "H2''" H N N 104 DC "H1'" H N N 105 DC H41 H N N 106 DC H42 H N N 107 DC H5 H N N 108 DC H6 H N N 109 DG OP3 O N N 110 DG P P N N 111 DG OP1 O N N 112 DG OP2 O N N 113 DG "O5'" O N N 114 DG "C5'" C N N 115 DG "C4'" C N R 116 DG "O4'" O N N 117 DG "C3'" C N S 118 DG "O3'" O N N 119 DG "C2'" C N N 120 DG "C1'" C N R 121 DG N9 N Y N 122 DG C8 C Y N 123 DG N7 N Y N 124 DG C5 C Y N 125 DG C6 C N N 126 DG O6 O N N 127 DG N1 N N N 128 DG C2 C N N 129 DG N2 N N N 130 DG N3 N N N 131 DG C4 C Y N 132 DG HOP3 H N N 133 DG HOP2 H N N 134 DG "H5'" H N N 135 DG "H5''" H N N 136 DG "H4'" H N N 137 DG "H3'" H N N 138 DG "HO3'" H N N 139 DG "H2'" H N N 140 DG "H2''" H N N 141 DG "H1'" H N N 142 DG H8 H N N 143 DG H1 H N N 144 DG H21 H N N 145 DG H22 H N N 146 HOH O O N N 147 HOH H1 H N N 148 HOH H2 H N N 149 # 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 DA OP3 P sing N N 42 DA OP3 HOP3 sing N N 43 DA P OP1 doub N N 44 DA P OP2 sing N N 45 DA P "O5'" sing N N 46 DA OP2 HOP2 sing N N 47 DA "O5'" "C5'" sing N N 48 DA "C5'" "C4'" sing N N 49 DA "C5'" "H5'" sing N N 50 DA "C5'" "H5''" sing N N 51 DA "C4'" "O4'" sing N N 52 DA "C4'" "C3'" sing N N 53 DA "C4'" "H4'" sing N N 54 DA "O4'" "C1'" sing N N 55 DA "C3'" "O3'" sing N N 56 DA "C3'" "C2'" sing N N 57 DA "C3'" "H3'" sing N N 58 DA "O3'" "HO3'" sing N N 59 DA "C2'" "C1'" sing N N 60 DA "C2'" "H2'" sing N N 61 DA "C2'" "H2''" sing N N 62 DA "C1'" N9 sing N N 63 DA "C1'" "H1'" sing N N 64 DA N9 C8 sing Y N 65 DA N9 C4 sing Y N 66 DA C8 N7 doub Y N 67 DA C8 H8 sing N N 68 DA N7 C5 sing Y N 69 DA C5 C6 sing Y N 70 DA C5 C4 doub Y N 71 DA C6 N6 sing N N 72 DA C6 N1 doub Y N 73 DA N6 H61 sing N N 74 DA N6 H62 sing N N 75 DA N1 C2 sing Y N 76 DA C2 N3 doub Y N 77 DA C2 H2 sing N N 78 DA N3 C4 sing Y N 79 DC OP3 P sing N N 80 DC OP3 HOP3 sing N N 81 DC P OP1 doub N N 82 DC P OP2 sing N N 83 DC P "O5'" sing N N 84 DC OP2 HOP2 sing N N 85 DC "O5'" "C5'" sing N N 86 DC "C5'" "C4'" sing N N 87 DC "C5'" "H5'" sing N N 88 DC "C5'" "H5''" sing N N 89 DC "C4'" "O4'" sing N N 90 DC "C4'" "C3'" sing N N 91 DC "C4'" "H4'" sing N N 92 DC "O4'" "C1'" sing N N 93 DC "C3'" "O3'" sing N N 94 DC "C3'" "C2'" sing N N 95 DC "C3'" "H3'" sing N N 96 DC "O3'" "HO3'" sing N N 97 DC "C2'" "C1'" sing N N 98 DC "C2'" "H2'" sing N N 99 DC "C2'" "H2''" sing N N 100 DC "C1'" N1 sing N N 101 DC "C1'" "H1'" sing N N 102 DC N1 C2 sing N N 103 DC N1 C6 sing N N 104 DC C2 O2 doub N N 105 DC C2 N3 sing N N 106 DC N3 C4 doub N N 107 DC C4 N4 sing N N 108 DC C4 C5 sing N N 109 DC N4 H41 sing N N 110 DC N4 H42 sing N N 111 DC C5 C6 doub N N 112 DC C5 H5 sing N N 113 DC C6 H6 sing N N 114 DG OP3 P sing N N 115 DG OP3 HOP3 sing N N 116 DG P OP1 doub N N 117 DG P OP2 sing N N 118 DG P "O5'" sing N N 119 DG OP2 HOP2 sing N N 120 DG "O5'" "C5'" sing N N 121 DG "C5'" "C4'" sing N N 122 DG "C5'" "H5'" sing N N 123 DG "C5'" "H5''" sing N N 124 DG "C4'" "O4'" sing N N 125 DG "C4'" "C3'" sing N N 126 DG "C4'" "H4'" sing N N 127 DG "O4'" "C1'" sing N N 128 DG "C3'" "O3'" sing N N 129 DG "C3'" "C2'" sing N N 130 DG "C3'" "H3'" sing N N 131 DG "O3'" "HO3'" sing N N 132 DG "C2'" "C1'" sing N N 133 DG "C2'" "H2'" sing N N 134 DG "C2'" "H2''" sing N N 135 DG "C1'" N9 sing N N 136 DG "C1'" "H1'" sing N N 137 DG N9 C8 sing Y N 138 DG N9 C4 sing Y N 139 DG C8 N7 doub Y N 140 DG C8 H8 sing N N 141 DG N7 C5 sing Y N 142 DG C5 C6 sing N N 143 DG C5 C4 doub Y N 144 DG C6 O6 doub N N 145 DG C6 N1 sing N N 146 DG N1 C2 sing N N 147 DG N1 H1 sing N N 148 DG C2 N2 sing N N 149 DG C2 N3 doub N N 150 DG N2 H21 sing N N 151 DG N2 H22 sing N N 152 DG N3 C4 sing N N 153 HOH O H1 sing N N 154 HOH O H2 sing N N 155 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 417D 'z-form double helix' 417D 'mismatched base pair' # 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 -0.345 -0.119 0.020 6.314 0.330 -0.229 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DA 2 1_555 B C46 5 1_555 2.659 -0.464 0.098 -6.673 2.624 -6.604 2 A_DA2:C4611_B A 2 ? B 11 ? ? ? 1 A DC 3 1_555 B DG 4 1_555 -0.302 -0.041 -0.013 4.267 3.148 0.859 3 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 3 1_555 0.234 -0.102 0.014 -5.902 4.069 0.985 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A C46 5 1_555 B DA 2 1_555 -2.420 -0.415 -0.034 8.157 2.034 -5.506 5 A_C465:DA8_B A 5 ? B 8 ? ? ? 1 A DG 6 1_555 B DC 1 1_555 0.254 -0.081 0.225 -2.914 -1.983 0.750 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 DA 2 1_555 B C46 5 1_555 -0.022 5.036 3.767 1.642 -1.687 2.014 114.270 20.971 -0.303 -35.436 -34.493 3.098 1 AA_DC1DA2:C4611DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DA 2 1_555 B C46 5 1_555 A DC 3 1_555 B DG 4 1_555 0.238 -0.241 3.179 -1.796 -5.585 -60.050 0.505 0.151 3.152 5.567 -1.790 -60.309 2 AA_DA2DC3: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 0.018 5.404 3.715 0.273 -4.454 -9.336 -18.212 0.824 5.674 25.536 1.568 -10.345 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 DA 2 1_555 -0.291 -0.383 3.176 2.426 -1.901 -62.123 0.456 -0.174 3.173 1.841 2.349 -62.191 4 AA_DG4C465:DA8DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A C46 5 1_555 B DA 2 1_555 A DG 6 1_555 B DC 1 1_555 -0.049 5.095 3.693 -3.110 -2.839 1.531 75.805 -11.028 -1.933 -47.219 51.723 4.481 5 AA_C465DG6:DC7DA8_BB A 5 ? B 8 ? A 6 ? B 7 ? # _pdbx_initial_refinement_model.accession_code ? _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 Other _pdbx_initial_refinement_model.details 'Z-DNA hexamer d(CGCGPG)' # _atom_sites.entry_id 417D _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.057677 _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] 0.031815 _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] 0.022479 _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_