data_308D # _entry.id 308D # _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 308D pdb_0000308d 10.2210/pdb308d/pdb RCSB DDFB70 ? ? WWPDB D_1000178776 ? ? # 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 1997-01-21 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2020-07-29 5 'Structure model' 1 4 2024-02-21 6 'Structure model' 1 5 2024-04-03 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 4 'Structure model' repository Remediation 'Carbohydrate remediation' ? # 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' 'Derived calculations' 5 4 'Structure model' 'Structure summary' 6 5 'Structure model' 'Data collection' 7 5 'Structure model' 'Database references' 8 5 'Structure model' 'Structure summary' 9 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp 2 4 'Structure model' entity 3 4 'Structure model' pdbx_chem_comp_identifier 4 4 'Structure model' pdbx_entity_nonpoly 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_site 8 4 'Structure model' struct_site_gen 9 5 'Structure model' chem_comp 10 5 'Structure model' chem_comp_atom 11 5 'Structure model' chem_comp_bond 12 5 'Structure model' database_2 13 6 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_chem_comp.name' 2 4 'Structure model' '_chem_comp.type' 3 4 'Structure model' '_entity.pdbx_description' 4 4 'Structure model' '_pdbx_entity_nonpoly.name' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_asym_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 18 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 19 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 20 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 21 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 22 4 'Structure model' '_pdbx_struct_conn_angle.value' 23 4 'Structure model' '_struct_conn.pdbx_dist_value' 24 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 25 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 26 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 27 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 28 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 29 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 30 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 31 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 32 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 33 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 34 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 35 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 36 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 37 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 38 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 39 5 'Structure model' '_chem_comp.pdbx_synonyms' 40 5 'Structure model' '_database_2.pdbx_DOI' 41 5 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 308D _pdbx_database_status.recvd_initial_deposition_date 1997-01-15 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Gao, Y.-G.' 1 'Robinson, H.' 2 'Wijsman, E.R.' 3 'Van Der Marel, G.A.' 4 'Van Boom, J.H.' 5 'Wang, A.H.-J.' 6 # _citation.id primary _citation.title 'Binding of Daunomycin to beta-D-Glucosylated DNA Found in Protozoa Trypanosoma brucei Studied by X-Ray Crystallography' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 119 _citation.page_first 1496 _citation.page_last 1497 _citation.year 1997 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed -1 _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Gao, Y.-G.' 1 ? primary 'Robinson, H.' 2 ? primary 'Wijsman, E.R.' 3 ? primary 'Van Der Marel, G.A.' 4 ? primary 'Van Boom, J.H.' 5 ? primary 'Wang, A.H.-J.' 6 ? # 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*TP*AP*CP*G)-3') ; 1809.217 2 ? ? ? ? 2 non-polymer man beta-D-glucopyranose 180.156 2 ? ? ? ? 3 non-polymer syn DAUNOMYCIN 527.520 2 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 3 ? ? ? ? 5 water nat water 18.015 105 ? ? ? ? # _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)(DT)(DA)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGTACG _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 beta-D-glucopyranose BGC 3 DAUNOMYCIN DM1 4 'MAGNESIUM ION' MG 5 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 DT n 1 4 DA 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 BGC 'D-saccharide, beta linking' . beta-D-glucopyranose 'beta-D-glucose; D-glucose; glucose' 'C6 H12 O6' 180.156 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 DM1 non-polymer . DAUNOMYCIN DAUNORUBICIN 'C27 H29 N O10' 527.520 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier BGC 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGlcpb BGC 'COMMON NAME' GMML 1.0 b-D-glucopyranose BGC 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-Glcp BGC 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Glc # 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 DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n B 1 1 DC 1 7 7 DC DC B . n B 1 2 DG 2 8 8 DG DG B . n B 1 3 DT 3 9 9 DT DT B . n B 1 4 DA 4 10 10 DA DA B . n B 1 5 DC 5 11 11 DC DC B . n B 1 6 DG 6 12 12 DG DG 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 BGC 1 7 7 BGC BGC A . D 3 DM1 1 14 14 DM1 DM1 A . E 4 MG 1 16 16 MG MG A . F 4 MG 1 17 17 MG MG A . G 2 BGC 1 13 13 BGC BGC B . H 3 DM1 1 14 14 DM1 DM1 B . I 4 MG 1 15 15 MG MG B . J 5 HOH 1 18 18 HOH HOH A . J 5 HOH 2 19 19 HOH HOH A . J 5 HOH 3 22 22 HOH HOH A . J 5 HOH 4 23 23 HOH HOH A . J 5 HOH 5 24 24 HOH HOH A . J 5 HOH 6 25 25 HOH HOH A . J 5 HOH 7 27 27 HOH HOH A . J 5 HOH 8 29 29 HOH HOH A . J 5 HOH 9 30 30 HOH HOH A . J 5 HOH 10 31 31 HOH HOH A . J 5 HOH 11 32 32 HOH HOH A . J 5 HOH 12 34 34 HOH HOH A . J 5 HOH 13 35 35 HOH HOH A . J 5 HOH 14 36 36 HOH HOH A . J 5 HOH 15 37 37 HOH HOH A . J 5 HOH 16 38 38 HOH HOH A . J 5 HOH 17 39 39 HOH HOH A . J 5 HOH 18 41 41 HOH HOH A . J 5 HOH 19 42 42 HOH HOH A . J 5 HOH 20 44 44 HOH HOH A . J 5 HOH 21 47 47 HOH HOH A . J 5 HOH 22 48 48 HOH HOH A . J 5 HOH 23 50 50 HOH HOH A . J 5 HOH 24 51 51 HOH HOH A . J 5 HOH 25 52 52 HOH HOH A . J 5 HOH 26 56 56 HOH HOH A . J 5 HOH 27 57 57 HOH HOH A . J 5 HOH 28 58 58 HOH HOH A . J 5 HOH 29 59 59 HOH HOH A . J 5 HOH 30 60 60 HOH HOH A . J 5 HOH 31 61 61 HOH HOH A . J 5 HOH 32 62 62 HOH HOH A . J 5 HOH 33 64 64 HOH HOH A . J 5 HOH 34 65 65 HOH HOH A . J 5 HOH 35 66 66 HOH HOH A . J 5 HOH 36 68 68 HOH HOH A . J 5 HOH 37 69 69 HOH HOH A . J 5 HOH 38 70 70 HOH HOH A . J 5 HOH 39 71 71 HOH HOH A . J 5 HOH 40 72 72 HOH HOH A . J 5 HOH 41 73 73 HOH HOH A . J 5 HOH 42 74 74 HOH HOH A . J 5 HOH 43 75 75 HOH HOH A . J 5 HOH 44 76 76 HOH HOH A . J 5 HOH 45 81 81 HOH HOH A . J 5 HOH 46 83 83 HOH HOH A . J 5 HOH 47 84 84 HOH HOH A . J 5 HOH 48 87 87 HOH HOH A . J 5 HOH 49 92 92 HOH HOH A . J 5 HOH 50 93 93 HOH HOH A . J 5 HOH 51 94 94 HOH HOH A . J 5 HOH 52 95 95 HOH HOH A . J 5 HOH 53 96 96 HOH HOH A . J 5 HOH 54 97 97 HOH HOH A . J 5 HOH 55 98 98 HOH HOH A . J 5 HOH 56 99 99 HOH HOH A . J 5 HOH 57 100 100 HOH HOH A . J 5 HOH 58 103 103 HOH HOH A . J 5 HOH 59 106 106 HOH HOH A . J 5 HOH 60 107 107 HOH HOH A . J 5 HOH 61 108 108 HOH HOH A . J 5 HOH 62 113 113 HOH HOH A . J 5 HOH 63 114 114 HOH HOH A . J 5 HOH 64 115 115 HOH HOH A . J 5 HOH 65 116 116 HOH HOH A . J 5 HOH 66 117 117 HOH HOH A . J 5 HOH 67 118 118 HOH HOH A . J 5 HOH 68 119 119 HOH HOH A . J 5 HOH 69 120 120 HOH HOH A . J 5 HOH 70 121 121 HOH HOH A . J 5 HOH 71 122 122 HOH HOH A . K 5 HOH 1 20 20 HOH HOH B . K 5 HOH 2 21 21 HOH HOH B . K 5 HOH 3 26 26 HOH HOH B . K 5 HOH 4 28 28 HOH HOH B . K 5 HOH 5 33 33 HOH HOH B . K 5 HOH 6 40 40 HOH HOH B . K 5 HOH 7 43 43 HOH HOH B . K 5 HOH 8 45 45 HOH HOH B . K 5 HOH 9 46 46 HOH HOH B . K 5 HOH 10 49 49 HOH HOH B . K 5 HOH 11 53 53 HOH HOH B . K 5 HOH 12 54 54 HOH HOH B . K 5 HOH 13 55 55 HOH HOH B . K 5 HOH 14 63 63 HOH HOH B . K 5 HOH 15 67 67 HOH HOH B . K 5 HOH 16 77 77 HOH HOH B . K 5 HOH 17 78 78 HOH HOH B . K 5 HOH 18 79 79 HOH HOH B . K 5 HOH 19 80 80 HOH HOH B . K 5 HOH 20 82 82 HOH HOH B . K 5 HOH 21 85 85 HOH HOH B . K 5 HOH 22 86 86 HOH HOH B . K 5 HOH 23 88 88 HOH HOH B . K 5 HOH 24 89 89 HOH HOH B . K 5 HOH 25 90 90 HOH HOH B . K 5 HOH 26 91 91 HOH HOH B . K 5 HOH 27 101 101 HOH HOH B . K 5 HOH 28 102 102 HOH HOH B . K 5 HOH 29 104 104 HOH HOH B . K 5 HOH 30 105 105 HOH HOH B . K 5 HOH 31 109 109 HOH HOH B . K 5 HOH 32 110 110 HOH HOH B . K 5 HOH 33 111 111 HOH HOH B . K 5 HOH 34 112 112 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ULTIMA 'model building' . ? 1 X-PLOR refinement 3.1 ? 2 R-AXIS 'data reduction' . ? 3 ULTIMA phasing . ? 4 # _cell.entry_id 308D _cell.length_a 18.619 _cell.length_b 20.096 _cell.length_c 26.553 _cell.angle_alpha 69.09 _cell.angle_beta 90.40 _cell.angle_gamma 108.03 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 308D _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? # _exptl.entry_id 308D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 49.22 _exptl_crystal.density_Matthews 2.42 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 293.00 _exptl_crystal_grow.temp_details 'ROOM TEMPERATURE' _exptl_crystal_grow.pH 6.00 _exptl_crystal_grow.pdbx_details 'pH 6.00, VAPOR DIFFUSION, temperature 293.00K' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 MGCL2 ? ? ? 1 4 1 'NA CACODYLATE' ? ? ? 1 5 1 SPERMINE ? ? ? 1 6 1 DIOXANE ? ? ? 1 7 2 WATER ? ? ? 1 8 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 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IIC' _diffrn_detector.pdbx_collection_date 1996-08-26 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 308D _reflns.observed_criterion_sigma_I 2.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 15.000 _reflns.d_resolution_high 1.500 _reflns.number_obs 4688 _reflns.number_all ? _reflns.percent_possible_obs 86.000 _reflns.pdbx_Rmerge_I_obs 0.0960000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 308D _refine.ls_number_reflns_obs 4678 _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 10.000 _refine.ls_d_res_high 1.500 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1750000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1750000 _refine.ls_R_factor_R_free 0.2210000 _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 13.40 _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 DDF001 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 240 _refine_hist.pdbx_number_atoms_ligand 103 _refine_hist.number_atoms_solvent 105 _refine_hist.number_atoms_total 448 _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 x_bond_d 0.019 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 3.10 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 308D _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 308D _struct.title 'BINDING OF DAUNOMYCIN TO B-D-GLUCOSYLATED DNA FOUND IN PROTOZOA TRYPANOSOMA BRUCEI STUDIED BY X-RAY CRYSTALLOGRAPH' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 308D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 4 ? F N N 4 ? G N N 2 ? H N N 3 ? I N N 4 ? J N N 5 ? K N N 5 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 308D _struct_ref.pdbx_db_accession 308D _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 308D A 1 ? 6 ? 308D 1 ? 6 ? 1 6 2 1 308D B 1 ? 6 ? 308D 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,F,G,H,I,J,K # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale one ? A DT 3 C7 ? ? ? 1_555 C BGC . O1 ? ? A DT 3 A BGC 7 1_555 ? ? ? ? ? ? ? 1.409 ? ? covale2 covale one ? B DT 3 C7 ? ? ? 1_555 G BGC . O1 ? ? B DT 9 B BGC 13 1_555 ? ? ? ? ? ? ? 1.400 ? ? metalc1 metalc ? ? A DT 3 OP1 ? ? ? 1_555 E MG . MG ? ? A DT 3 A MG 16 1_555 ? ? ? ? ? ? ? 2.204 ? ? metalc2 metalc ? ? A DA 4 OP2 ? ? ? 1_555 F MG . MG ? ? A DA 4 A MG 17 1_555 ? ? ? ? ? ? ? 2.237 ? ? metalc3 metalc ? ? E MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 16 A HOH 113 1_555 ? ? ? ? ? ? ? 1.953 ? ? metalc4 metalc ? ? E MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 16 A HOH 114 1_555 ? ? ? ? ? ? ? 1.954 ? ? metalc5 metalc ? ? E MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 16 A HOH 115 1_555 ? ? ? ? ? ? ? 1.944 ? ? metalc6 metalc ? ? E MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 16 A HOH 116 1_555 ? ? ? ? ? ? ? 1.892 ? ? metalc7 metalc ? ? E MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 16 A HOH 117 1_555 ? ? ? ? ? ? ? 1.934 ? ? metalc8 metalc ? ? F MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 17 A HOH 118 1_555 ? ? ? ? ? ? ? 1.945 ? ? metalc9 metalc ? ? F MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 17 A HOH 119 1_555 ? ? ? ? ? ? ? 1.943 ? ? metalc10 metalc ? ? F MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 17 A HOH 120 1_555 ? ? ? ? ? ? ? 1.930 ? ? metalc11 metalc ? ? F MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 17 A HOH 121 1_555 ? ? ? ? ? ? ? 1.938 ? ? metalc12 metalc ? ? F MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 17 A HOH 122 1_555 ? ? ? ? ? ? ? 1.951 ? ? metalc13 metalc ? ? J HOH . O ? ? ? 1_555 I MG . MG ? ? A HOH 107 B MG 15 1_555 ? ? ? ? ? ? ? 1.924 ? ? metalc14 metalc ? ? J HOH . O ? ? ? 1_555 I MG . MG ? ? A HOH 108 B MG 15 1_555 ? ? ? ? ? ? ? 1.954 ? ? metalc15 metalc ? ? I MG . MG ? ? ? 1_555 K HOH . O ? ? B MG 15 B HOH 109 1_555 ? ? ? ? ? ? ? 1.926 ? ? metalc16 metalc ? ? I MG . MG ? ? ? 1_555 K HOH . O ? ? B MG 15 B HOH 110 1_555 ? ? ? ? ? ? ? 1.907 ? ? metalc17 metalc ? ? I MG . MG ? ? ? 1_555 K HOH . O ? ? B MG 15 B HOH 111 1_555 ? ? ? ? ? ? ? 1.892 ? ? metalc18 metalc ? ? I MG . MG ? ? ? 1_555 K HOH . O ? ? B MG 15 B HOH 112 1_555 ? ? ? ? ? ? ? 1.950 ? ? 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 DT 3 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? 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 OP1 ? A DT 3 ? A DT 3 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 113 ? 1_555 91.8 ? 2 OP1 ? A DT 3 ? A DT 3 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 114 ? 1_555 98.3 ? 3 O ? J HOH . ? A HOH 113 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 114 ? 1_555 169.8 ? 4 OP1 ? A DT 3 ? A DT 3 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 115 ? 1_555 89.8 ? 5 O ? J HOH . ? A HOH 113 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 115 ? 1_555 88.3 ? 6 O ? J HOH . ? A HOH 114 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 115 ? 1_555 90.1 ? 7 OP1 ? A DT 3 ? A DT 3 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 116 ? 1_555 175.2 ? 8 O ? J HOH . ? A HOH 113 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 116 ? 1_555 83.5 ? 9 O ? J HOH . ? A HOH 114 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 116 ? 1_555 86.4 ? 10 O ? J HOH . ? A HOH 115 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 116 ? 1_555 89.0 ? 11 OP1 ? A DT 3 ? A DT 3 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 117 ? 1_555 95.1 ? 12 O ? J HOH . ? A HOH 113 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 117 ? 1_555 92.3 ? 13 O ? J HOH . ? A HOH 114 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 117 ? 1_555 88.4 ? 14 O ? J HOH . ? A HOH 115 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 117 ? 1_555 175.1 ? 15 O ? J HOH . ? A HOH 116 ? 1_555 MG ? E MG . ? A MG 16 ? 1_555 O ? J HOH . ? A HOH 117 ? 1_555 86.2 ? 16 OP2 ? A DA 4 ? A DA 4 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 118 ? 1_555 98.4 ? 17 OP2 ? A DA 4 ? A DA 4 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 119 ? 1_555 90.9 ? 18 O ? J HOH . ? A HOH 118 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 119 ? 1_555 170.1 ? 19 OP2 ? A DA 4 ? A DA 4 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 120 ? 1_555 96.8 ? 20 O ? J HOH . ? A HOH 118 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 120 ? 1_555 86.6 ? 21 O ? J HOH . ? A HOH 119 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 120 ? 1_555 89.0 ? 22 OP2 ? A DA 4 ? A DA 4 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 121 ? 1_555 174.8 ? 23 O ? J HOH . ? A HOH 118 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 121 ? 1_555 85.9 ? 24 O ? J HOH . ? A HOH 119 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 121 ? 1_555 85.0 ? 25 O ? J HOH . ? A HOH 120 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 121 ? 1_555 86.3 ? 26 OP2 ? A DA 4 ? A DA 4 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 122 ? 1_555 90.3 ? 27 O ? J HOH . ? A HOH 118 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 122 ? 1_555 90.5 ? 28 O ? J HOH . ? A HOH 119 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 122 ? 1_555 92.9 ? 29 O ? J HOH . ? A HOH 120 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 122 ? 1_555 172.7 ? 30 O ? J HOH . ? A HOH 121 ? 1_555 MG ? F MG . ? A MG 17 ? 1_555 O ? J HOH . ? A HOH 122 ? 1_555 86.8 ? 31 O ? J HOH . ? A HOH 107 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? J HOH . ? A HOH 108 ? 1_555 176.6 ? 32 O ? J HOH . ? A HOH 107 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 109 ? 1_555 89.9 ? 33 O ? J HOH . ? A HOH 108 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 109 ? 1_555 90.5 ? 34 O ? J HOH . ? A HOH 107 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 110 ? 1_555 87.3 ? 35 O ? J HOH . ? A HOH 108 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 110 ? 1_555 89.4 ? 36 O ? K HOH . ? B HOH 109 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 110 ? 1_555 91.4 ? 37 O ? J HOH . ? A HOH 107 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 111 ? 1_555 91.4 ? 38 O ? J HOH . ? A HOH 108 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 111 ? 1_555 88.4 ? 39 O ? K HOH . ? B HOH 109 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 111 ? 1_555 176.9 ? 40 O ? K HOH . ? B HOH 110 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 111 ? 1_555 91.5 ? 41 O ? J HOH . ? A HOH 107 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 112 ? 1_555 88.6 ? 42 O ? J HOH . ? A HOH 108 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 112 ? 1_555 94.8 ? 43 O ? K HOH . ? B HOH 109 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 112 ? 1_555 89.7 ? 44 O ? K HOH . ? B HOH 110 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 112 ? 1_555 175.7 ? 45 O ? K HOH . ? B HOH 111 ? 1_555 MG ? I MG . ? B MG 15 ? 1_555 O ? K HOH . ? B HOH 112 ? 1_555 87.5 ? # _struct_site.id 'DRUG BINDING SITE' _struct_site.pdbx_evidence_code ? _struct_site.pdbx_auth_asym_id ? _struct_site.pdbx_auth_comp_id ? _struct_site.pdbx_auth_seq_id ? _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues ? _struct_site.details ? # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "C5'" _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 DC _pdbx_validate_rmsd_bond.auth_seq_id_1 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 "C4'" _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 DC _pdbx_validate_rmsd_bond.auth_seq_id_2 1 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.569 _pdbx_validate_rmsd_bond.bond_target_value 1.512 _pdbx_validate_rmsd_bond.bond_deviation 0.057 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.007 _pdbx_validate_rmsd_bond.linker_flag 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 ? ? 110.15 108.30 1.85 0.30 N 2 1 "C3'" A DG 2 ? ? "O3'" A DG 2 ? ? P A DT 3 ? ? 127.28 119.70 7.58 1.20 Y 3 1 "O4'" A DC 5 ? ? "C4'" A DC 5 ? ? "C3'" A DC 5 ? ? 109.64 106.00 3.64 0.60 N 4 1 "C1'" A DC 5 ? ? "O4'" A DC 5 ? ? "C4'" A DC 5 ? ? 102.81 110.10 -7.29 1.00 N 5 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 111.02 108.30 2.72 0.30 N 6 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.84 108.30 3.54 0.30 N 7 1 "C1'" B DG 8 ? ? "O4'" B DG 8 ? ? "C4'" B DG 8 ? ? 102.87 110.10 -7.23 1.00 N 8 1 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 110.52 108.30 2.22 0.30 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DC A 5 ? ? 0.065 'SIDE CHAIN' 2 1 DC B 11 ? ? 0.085 'SIDE CHAIN' # _struct_site_keywords.site_id 'DRUG BINDING SITE' _struct_site_keywords.text INTERCALATION # 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 BGC C2 C N R 1 BGC C3 C N S 2 BGC C4 C N S 3 BGC C5 C N R 4 BGC C6 C N N 5 BGC C1 C N R 6 BGC O1 O N N 7 BGC O2 O N N 8 BGC O3 O N N 9 BGC O4 O N N 10 BGC O5 O N N 11 BGC O6 O N N 12 BGC H2 H N N 13 BGC H3 H N N 14 BGC H4 H N N 15 BGC H5 H N N 16 BGC H61 H N N 17 BGC H62 H N N 18 BGC H1 H N N 19 BGC HO1 H N N 20 BGC HO2 H N N 21 BGC HO3 H N N 22 BGC HO4 H N N 23 BGC HO6 H N N 24 DA OP3 O N N 25 DA P P N N 26 DA OP1 O N N 27 DA OP2 O N N 28 DA "O5'" O N N 29 DA "C5'" C N N 30 DA "C4'" C N R 31 DA "O4'" O N N 32 DA "C3'" C N S 33 DA "O3'" O N N 34 DA "C2'" C N N 35 DA "C1'" C N R 36 DA N9 N Y N 37 DA C8 C Y N 38 DA N7 N Y N 39 DA C5 C Y N 40 DA C6 C Y N 41 DA N6 N N N 42 DA N1 N Y N 43 DA C2 C Y N 44 DA N3 N Y N 45 DA C4 C Y N 46 DA HOP3 H N N 47 DA HOP2 H N N 48 DA "H5'" H N N 49 DA "H5''" H N N 50 DA "H4'" H N N 51 DA "H3'" H N N 52 DA "HO3'" H N N 53 DA "H2'" H N N 54 DA "H2''" H N N 55 DA "H1'" H N N 56 DA H8 H N N 57 DA H61 H N N 58 DA H62 H N N 59 DA H2 H N N 60 DC OP3 O N N 61 DC P P N N 62 DC OP1 O N N 63 DC OP2 O N N 64 DC "O5'" O N N 65 DC "C5'" C N N 66 DC "C4'" C N R 67 DC "O4'" O N N 68 DC "C3'" C N S 69 DC "O3'" O N N 70 DC "C2'" C N N 71 DC "C1'" C N R 72 DC N1 N N N 73 DC C2 C N N 74 DC O2 O N N 75 DC N3 N N N 76 DC C4 C N N 77 DC N4 N N N 78 DC C5 C N N 79 DC C6 C N N 80 DC HOP3 H N N 81 DC HOP2 H N N 82 DC "H5'" H N N 83 DC "H5''" H N N 84 DC "H4'" H N N 85 DC "H3'" H N N 86 DC "HO3'" H N N 87 DC "H2'" H N N 88 DC "H2''" H N N 89 DC "H1'" H N N 90 DC H41 H N N 91 DC H42 H N N 92 DC H5 H N N 93 DC H6 H N N 94 DG OP3 O N N 95 DG P P N N 96 DG OP1 O N N 97 DG OP2 O N N 98 DG "O5'" O N N 99 DG "C5'" C N N 100 DG "C4'" C N R 101 DG "O4'" O N N 102 DG "C3'" C N S 103 DG "O3'" O N N 104 DG "C2'" C N N 105 DG "C1'" C N R 106 DG N9 N Y N 107 DG C8 C Y N 108 DG N7 N Y N 109 DG C5 C Y N 110 DG C6 C N N 111 DG O6 O N N 112 DG N1 N N N 113 DG C2 C N N 114 DG N2 N N N 115 DG N3 N N N 116 DG C4 C Y N 117 DG HOP3 H N N 118 DG HOP2 H N N 119 DG "H5'" H N N 120 DG "H5''" H N N 121 DG "H4'" H N N 122 DG "H3'" H N N 123 DG "HO3'" H N N 124 DG "H2'" H N N 125 DG "H2''" H N N 126 DG "H1'" H N N 127 DG H8 H N N 128 DG H1 H N N 129 DG H21 H N N 130 DG H22 H N N 131 DM1 C1 C Y N 132 DM1 C2 C Y N 133 DM1 C3 C Y N 134 DM1 C4 C Y N 135 DM1 O4 O N N 136 DM1 C5 C Y N 137 DM1 C6 C N N 138 DM1 O6 O N N 139 DM1 C7 C Y N 140 DM1 C8 C Y N 141 DM1 O8 O N N 142 DM1 C9 C Y N 143 DM1 C10 C N S 144 DM1 O10 O N N 145 DM1 C11 C N N 146 DM1 C12 C N S 147 DM1 O12 O N N 148 DM1 C13 C N N 149 DM1 O13 O N N 150 DM1 C14 C N N 151 DM1 C15 C N N 152 DM1 C16 C Y N 153 DM1 C17 C Y N 154 DM1 O17 O N N 155 DM1 C18 C Y N 156 DM1 C19 C N N 157 DM1 O19 O N N 158 DM1 C20 C Y N 159 DM1 C21 C N N 160 DM1 "C1'" C N R 161 DM1 "C2'" C N N 162 DM1 "C3'" C N S 163 DM1 "N3'" N N N 164 DM1 "C4'" C N S 165 DM1 "O4'" O N N 166 DM1 "C5'" C N S 167 DM1 "O5'" O N N 168 DM1 "C6'" C N N 169 DM1 H1 H N N 170 DM1 H2 H N N 171 DM1 H3 H N N 172 DM1 HO8 H N N 173 DM1 H10 H N N 174 DM1 H111 H N N 175 DM1 H112 H N N 176 DM1 HO12 H N N 177 DM1 H141 H N N 178 DM1 H142 H N N 179 DM1 H143 H N N 180 DM1 H151 H N N 181 DM1 H152 H N N 182 DM1 HO17 H N N 183 DM1 H211 H N N 184 DM1 H212 H N N 185 DM1 H213 H N N 186 DM1 "H1'" H N N 187 DM1 "H2'1" H N N 188 DM1 "H2'2" H N N 189 DM1 "H3'" H N N 190 DM1 "HN'1" H N N 191 DM1 "HN'2" H N N 192 DM1 "H4'" H N N 193 DM1 "HO4'" H N N 194 DM1 "H5'" H N N 195 DM1 "H6'1" H N N 196 DM1 "H6'2" H N N 197 DM1 "H6'3" H N N 198 DT OP3 O N N 199 DT P P N N 200 DT OP1 O N N 201 DT OP2 O N N 202 DT "O5'" O N N 203 DT "C5'" C N N 204 DT "C4'" C N R 205 DT "O4'" O N N 206 DT "C3'" C N S 207 DT "O3'" O N N 208 DT "C2'" C N N 209 DT "C1'" C N R 210 DT N1 N N N 211 DT C2 C N N 212 DT O2 O N N 213 DT N3 N N N 214 DT C4 C N N 215 DT O4 O N N 216 DT C5 C N N 217 DT C7 C N N 218 DT C6 C N N 219 DT HOP3 H N N 220 DT HOP2 H N N 221 DT "H5'" H N N 222 DT "H5''" H N N 223 DT "H4'" H N N 224 DT "H3'" H N N 225 DT "HO3'" H N N 226 DT "H2'" H N N 227 DT "H2''" H N N 228 DT "H1'" H N N 229 DT H3 H N N 230 DT H71 H N N 231 DT H72 H N N 232 DT H73 H N N 233 DT H6 H N N 234 HOH O O N N 235 HOH H1 H N N 236 HOH H2 H N N 237 MG MG MG N N 238 # 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 BGC C2 C3 sing N N 1 BGC C2 C1 sing N N 2 BGC C2 O2 sing N N 3 BGC C2 H2 sing N N 4 BGC C3 C4 sing N N 5 BGC C3 O3 sing N N 6 BGC C3 H3 sing N N 7 BGC C4 C5 sing N N 8 BGC C4 O4 sing N N 9 BGC C4 H4 sing N N 10 BGC C5 C6 sing N N 11 BGC C5 O5 sing N N 12 BGC C5 H5 sing N N 13 BGC C6 O6 sing N N 14 BGC C6 H61 sing N N 15 BGC C6 H62 sing N N 16 BGC C1 O1 sing N N 17 BGC C1 O5 sing N N 18 BGC C1 H1 sing N N 19 BGC O1 HO1 sing N N 20 BGC O2 HO2 sing N N 21 BGC O3 HO3 sing N N 22 BGC O4 HO4 sing N N 23 BGC O6 HO6 sing N N 24 DA OP3 P sing N N 25 DA OP3 HOP3 sing N N 26 DA P OP1 doub N N 27 DA P OP2 sing N N 28 DA P "O5'" sing N N 29 DA OP2 HOP2 sing N N 30 DA "O5'" "C5'" sing N N 31 DA "C5'" "C4'" sing N N 32 DA "C5'" "H5'" sing N N 33 DA "C5'" "H5''" sing N N 34 DA "C4'" "O4'" sing N N 35 DA "C4'" "C3'" sing N N 36 DA "C4'" "H4'" sing N N 37 DA "O4'" "C1'" sing N N 38 DA "C3'" "O3'" sing N N 39 DA "C3'" "C2'" sing N N 40 DA "C3'" "H3'" sing N N 41 DA "O3'" "HO3'" sing N N 42 DA "C2'" "C1'" sing N N 43 DA "C2'" "H2'" sing N N 44 DA "C2'" "H2''" sing N N 45 DA "C1'" N9 sing N N 46 DA "C1'" "H1'" sing N N 47 DA N9 C8 sing Y N 48 DA N9 C4 sing Y N 49 DA C8 N7 doub Y N 50 DA C8 H8 sing N N 51 DA N7 C5 sing Y N 52 DA C5 C6 sing Y N 53 DA C5 C4 doub Y N 54 DA C6 N6 sing N N 55 DA C6 N1 doub Y N 56 DA N6 H61 sing N N 57 DA N6 H62 sing N N 58 DA N1 C2 sing Y N 59 DA C2 N3 doub Y N 60 DA C2 H2 sing N N 61 DA N3 C4 sing Y N 62 DC OP3 P sing N N 63 DC OP3 HOP3 sing N N 64 DC P OP1 doub N N 65 DC P OP2 sing N N 66 DC P "O5'" sing N N 67 DC OP2 HOP2 sing N N 68 DC "O5'" "C5'" sing N N 69 DC "C5'" "C4'" sing N N 70 DC "C5'" "H5'" sing N N 71 DC "C5'" "H5''" sing N N 72 DC "C4'" "O4'" sing N N 73 DC "C4'" "C3'" sing N N 74 DC "C4'" "H4'" sing N N 75 DC "O4'" "C1'" sing N N 76 DC "C3'" "O3'" sing N N 77 DC "C3'" "C2'" sing N N 78 DC "C3'" "H3'" sing N N 79 DC "O3'" "HO3'" sing N N 80 DC "C2'" "C1'" sing N N 81 DC "C2'" "H2'" sing N N 82 DC "C2'" "H2''" sing N N 83 DC "C1'" N1 sing N N 84 DC "C1'" "H1'" sing N N 85 DC N1 C2 sing N N 86 DC N1 C6 sing N N 87 DC C2 O2 doub N N 88 DC C2 N3 sing N N 89 DC N3 C4 doub N N 90 DC C4 N4 sing N N 91 DC C4 C5 sing N N 92 DC N4 H41 sing N N 93 DC N4 H42 sing N N 94 DC C5 C6 doub N N 95 DC C5 H5 sing N N 96 DC C6 H6 sing N N 97 DG OP3 P sing N N 98 DG OP3 HOP3 sing N N 99 DG P OP1 doub N N 100 DG P OP2 sing N N 101 DG P "O5'" sing N N 102 DG OP2 HOP2 sing N N 103 DG "O5'" "C5'" sing N N 104 DG "C5'" "C4'" sing N N 105 DG "C5'" "H5'" sing N N 106 DG "C5'" "H5''" sing N N 107 DG "C4'" "O4'" sing N N 108 DG "C4'" "C3'" sing N N 109 DG "C4'" "H4'" sing N N 110 DG "O4'" "C1'" sing N N 111 DG "C3'" "O3'" sing N N 112 DG "C3'" "C2'" sing N N 113 DG "C3'" "H3'" sing N N 114 DG "O3'" "HO3'" sing N N 115 DG "C2'" "C1'" sing N N 116 DG "C2'" "H2'" sing N N 117 DG "C2'" "H2''" sing N N 118 DG "C1'" N9 sing N N 119 DG "C1'" "H1'" sing N N 120 DG N9 C8 sing Y N 121 DG N9 C4 sing Y N 122 DG C8 N7 doub Y N 123 DG C8 H8 sing N N 124 DG N7 C5 sing Y N 125 DG C5 C6 sing N N 126 DG C5 C4 doub Y N 127 DG C6 O6 doub N N 128 DG C6 N1 sing N N 129 DG N1 C2 sing N N 130 DG N1 H1 sing N N 131 DG C2 N2 sing N N 132 DG C2 N3 doub N N 133 DG N2 H21 sing N N 134 DG N2 H22 sing N N 135 DG N3 C4 sing N N 136 DM1 C1 C2 doub Y N 137 DM1 C1 C20 sing Y N 138 DM1 C1 H1 sing N N 139 DM1 C2 C3 sing Y N 140 DM1 C2 H2 sing N N 141 DM1 C3 C4 doub Y N 142 DM1 C3 H3 sing N N 143 DM1 C4 O4 sing N N 144 DM1 C4 C5 sing Y N 145 DM1 O4 C21 sing N N 146 DM1 C5 C6 sing N N 147 DM1 C5 C20 doub Y N 148 DM1 C6 O6 doub N N 149 DM1 C6 C7 sing N N 150 DM1 C7 C8 doub Y N 151 DM1 C7 C18 sing Y N 152 DM1 C8 O8 sing N N 153 DM1 C8 C9 sing Y N 154 DM1 O8 HO8 sing N N 155 DM1 C9 C10 sing N N 156 DM1 C9 C16 doub Y N 157 DM1 C10 O10 sing N N 158 DM1 C10 C11 sing N N 159 DM1 C10 H10 sing N N 160 DM1 O10 "C1'" sing N N 161 DM1 C11 C12 sing N N 162 DM1 C11 H111 sing N N 163 DM1 C11 H112 sing N N 164 DM1 C12 O12 sing N N 165 DM1 C12 C13 sing N N 166 DM1 C12 C15 sing N N 167 DM1 O12 HO12 sing N N 168 DM1 C13 O13 doub N N 169 DM1 C13 C14 sing N N 170 DM1 C14 H141 sing N N 171 DM1 C14 H142 sing N N 172 DM1 C14 H143 sing N N 173 DM1 C15 C16 sing N N 174 DM1 C15 H151 sing N N 175 DM1 C15 H152 sing N N 176 DM1 C16 C17 sing Y N 177 DM1 C17 O17 sing N N 178 DM1 C17 C18 doub Y N 179 DM1 O17 HO17 sing N N 180 DM1 C18 C19 sing N N 181 DM1 C19 O19 doub N N 182 DM1 C19 C20 sing N N 183 DM1 C21 H211 sing N N 184 DM1 C21 H212 sing N N 185 DM1 C21 H213 sing N N 186 DM1 "C1'" "C2'" sing N N 187 DM1 "C1'" "O5'" sing N N 188 DM1 "C1'" "H1'" sing N N 189 DM1 "C2'" "C3'" sing N N 190 DM1 "C2'" "H2'1" sing N N 191 DM1 "C2'" "H2'2" sing N N 192 DM1 "C3'" "N3'" sing N N 193 DM1 "C3'" "C4'" sing N N 194 DM1 "C3'" "H3'" sing N N 195 DM1 "N3'" "HN'1" sing N N 196 DM1 "N3'" "HN'2" sing N N 197 DM1 "C4'" "O4'" sing N N 198 DM1 "C4'" "C5'" sing N N 199 DM1 "C4'" "H4'" sing N N 200 DM1 "O4'" "HO4'" sing N N 201 DM1 "C5'" "O5'" sing N N 202 DM1 "C5'" "C6'" sing N N 203 DM1 "C5'" "H5'" sing N N 204 DM1 "C6'" "H6'1" sing N N 205 DM1 "C6'" "H6'2" sing N N 206 DM1 "C6'" "H6'3" sing N N 207 DT OP3 P sing N N 208 DT OP3 HOP3 sing N N 209 DT P OP1 doub N N 210 DT P OP2 sing N N 211 DT P "O5'" sing N N 212 DT OP2 HOP2 sing N N 213 DT "O5'" "C5'" sing N N 214 DT "C5'" "C4'" sing N N 215 DT "C5'" "H5'" sing N N 216 DT "C5'" "H5''" sing N N 217 DT "C4'" "O4'" sing N N 218 DT "C4'" "C3'" sing N N 219 DT "C4'" "H4'" sing N N 220 DT "O4'" "C1'" sing N N 221 DT "C3'" "O3'" sing N N 222 DT "C3'" "C2'" sing N N 223 DT "C3'" "H3'" sing N N 224 DT "O3'" "HO3'" sing N N 225 DT "C2'" "C1'" sing N N 226 DT "C2'" "H2'" sing N N 227 DT "C2'" "H2''" sing N N 228 DT "C1'" N1 sing N N 229 DT "C1'" "H1'" sing N N 230 DT N1 C2 sing N N 231 DT N1 C6 sing N N 232 DT C2 O2 doub N N 233 DT C2 N3 sing N N 234 DT N3 C4 sing N N 235 DT N3 H3 sing N N 236 DT C4 O4 doub N N 237 DT C4 C5 sing N N 238 DT C5 C7 sing N N 239 DT C5 C6 doub N N 240 DT C7 H71 sing N N 241 DT C7 H72 sing N N 242 DT C7 H73 sing N N 243 DT C6 H6 sing N N 244 HOH O H1 sing N N 245 HOH O H2 sing N N 246 # _ndb_struct_conf_na.entry_id 308D _ndb_struct_conf_na.feature 'b-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 0.198 -0.178 -0.177 9.295 3.748 -0.855 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B DC 5 1_555 -0.118 -0.080 -0.277 -11.780 5.586 2.212 2 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A DT 3 1_555 B DA 4 1_555 -0.283 -0.049 -0.180 3.030 -14.429 2.223 3 A_DT3:DA10_B A 3 ? B 10 ? 20 1 1 A DA 4 1_555 B DT 3 1_555 0.348 -0.118 -0.029 -4.480 -4.662 4.861 4 A_DA4:DT9_B A 4 ? B 9 ? 20 1 1 A DC 5 1_555 B DG 2 1_555 0.028 -0.140 -0.276 10.657 9.688 1.078 5 A_DC5:DG8_B A 5 ? B 8 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 -0.209 -0.130 -0.128 -7.979 2.307 -0.430 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 1.169 1.529 6.991 -1.116 -2.179 34.026 3.338 -2.367 6.842 -3.718 1.904 34.112 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 DT 3 1_555 B DA 4 1_555 -1.328 0.311 3.030 -0.117 -3.188 31.034 1.137 2.449 2.989 -5.938 0.218 31.194 2 AA_DG2DT3:DA10DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DT 3 1_555 B DA 4 1_555 A DA 4 1_555 B DT 3 1_555 0.376 0.155 3.613 -0.130 9.037 40.923 -0.832 -0.541 3.566 12.738 0.183 41.867 3 AA_DT3DA4:DT9DA10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DA 4 1_555 B DT 3 1_555 A DC 5 1_555 B DG 2 1_555 1.081 -0.077 3.126 0.208 -6.354 27.649 1.251 -2.161 3.074 -13.076 -0.428 28.357 4 AA_DA4DC5:DG8DT9_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 -1.248 1.035 6.954 -0.280 -3.053 31.865 3.042 2.156 6.838 -5.545 0.509 32.008 5 AA_DC5DG6:DC7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ? # _pdbx_initial_refinement_model.accession_code 1D11 _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.details DDF001 # _atom_sites.entry_id 308D _atom_sites.fract_transf_matrix[1][1] 0.053709 _atom_sites.fract_transf_matrix[1][2] 0.017482 _atom_sites.fract_transf_matrix[1][3] -0.006625 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.052331 _atom_sites.fract_transf_matrix[2][3] -0.021042 _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] 0.040592 _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 MG N O P # loop_