data_1D41 # _entry.id 1D41 # _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 1D41 pdb_00001d41 10.2210/pdb1d41/pdb RCSB ZDFB24 ? ? WWPDB D_1000172646 ? ? # 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 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 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' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_conn_type 7 4 'Structure model' struct_site 8 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' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.value' 16 4 'Structure model' '_struct_conn.conn_type_id' 17 4 'Structure model' '_struct_conn.id' 18 4 'Structure model' '_struct_conn.pdbx_dist_value' 19 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 20 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 21 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 22 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 25 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 26 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 27 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 28 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 29 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 31 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 32 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 33 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 34 4 'Structure model' '_struct_conn_type.id' 35 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 36 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 37 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1D41 _pdbx_database_status.recvd_initial_deposition_date 1991-05-07 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zhou, G.' 1 'Ho, P.S.' 2 # _citation.id primary _citation.title 'Stabilization of Z-DNA by demethylation of thymine bases: 1.3-A single-crystal structure of d(m5CGUAm5CG).' _citation.journal_abbrev Biochemistry _citation.journal_volume 29 _citation.page_first 7229 _citation.page_last 7236 _citation.year 1990 _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 2207101 _citation.pdbx_database_id_DOI 10.1021/bi00483a010 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhou, G.W.' 1 ? primary 'Ho, P.S.' 2 ? # 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(*(5CM)P*GP*UP*AP*(5CM)P*G)-3') ; 1823.245 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 3 water nat water 18.015 60 ? ? ? ? # _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 '(5CM)(DG)(DU)(DA)(5CM)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGUACG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 5CM n 1 2 DG n 1 3 DU n 1 4 DA n 1 5 5CM 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 5CM 'DNA linking' n "5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O7 P' 321.224 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DU 'DNA linking' y "2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O8 P' 308.182 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # 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 5CM 1 1 1 5CM +C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DU 3 3 3 DU U A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 5CM 5 5 5 5CM +C A . n A 1 6 DG 6 6 6 DG G A . n B 1 1 5CM 1 7 7 5CM +C B . n B 1 2 DG 2 8 8 DG G B . n B 1 3 DU 3 9 9 DU U B . n B 1 4 DA 4 10 10 DA A B . n B 1 5 5CM 5 11 11 5CM +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 MG 1 13 13 MG MO5 B . D 2 MG 1 14 14 MG MO6 B . E 3 HOH 1 16 16 HOH HOH A . E 3 HOH 2 17 17 HOH HOH A . E 3 HOH 3 18 18 HOH HOH A . E 3 HOH 4 19 19 HOH HOH A . E 3 HOH 5 20 20 HOH HOH A . E 3 HOH 6 21 21 HOH HOH A . E 3 HOH 7 24 24 HOH HOH A . E 3 HOH 8 26 26 HOH HOH A . E 3 HOH 9 27 27 HOH HOH A . E 3 HOH 10 29 29 HOH HOH A . E 3 HOH 11 33 33 HOH HOH A . E 3 HOH 12 34 34 HOH HOH A . E 3 HOH 13 36 36 HOH HOH A . E 3 HOH 14 37 37 HOH HOH A . E 3 HOH 15 38 38 HOH HOH A . E 3 HOH 16 39 39 HOH HOH A . E 3 HOH 17 40 40 HOH HOH A . E 3 HOH 18 41 41 HOH HOH A . E 3 HOH 19 44 44 HOH HOH A . E 3 HOH 20 46 46 HOH HOH A . E 3 HOH 21 48 48 HOH HOH A . E 3 HOH 22 49 49 HOH HOH A . E 3 HOH 23 51 51 HOH HOH A . E 3 HOH 24 52 52 HOH HOH A . E 3 HOH 25 53 53 HOH HOH A . E 3 HOH 26 54 54 HOH HOH A . E 3 HOH 27 55 55 HOH HOH A . E 3 HOH 28 58 58 HOH HOH A . E 3 HOH 29 63 63 HOH HOH A . E 3 HOH 30 69 14 HOH MO6 A . E 3 HOH 31 71 14 HOH MO6 A . E 3 HOH 32 72 14 HOH MO6 A . E 3 HOH 33 73 14 HOH MO6 A . E 3 HOH 34 74 14 HOH MO6 A . F 3 HOH 1 15 15 HOH HOH B . F 3 HOH 2 22 22 HOH HOH B . F 3 HOH 3 23 23 HOH HOH B . F 3 HOH 4 25 25 HOH HOH B . F 3 HOH 5 28 28 HOH HOH B . F 3 HOH 6 30 30 HOH HOH B . F 3 HOH 7 31 31 HOH HOH B . F 3 HOH 8 32 32 HOH HOH B . F 3 HOH 9 35 35 HOH HOH B . F 3 HOH 10 42 42 HOH HOH B . F 3 HOH 11 43 43 HOH HOH B . F 3 HOH 12 45 45 HOH HOH B . F 3 HOH 13 47 47 HOH HOH B . F 3 HOH 14 50 50 HOH HOH B . F 3 HOH 15 56 56 HOH HOH B . F 3 HOH 16 57 57 HOH HOH B . F 3 HOH 17 59 59 HOH HOH B . F 3 HOH 18 60 60 HOH HOH B . F 3 HOH 19 61 61 HOH HOH B . F 3 HOH 20 62 62 HOH HOH B . F 3 HOH 21 64 13 HOH MO5 B . F 3 HOH 22 65 13 HOH MO5 B . F 3 HOH 23 66 13 HOH MO5 B . F 3 HOH 24 67 13 HOH MO5 B . F 3 HOH 25 68 13 HOH MO5 B . F 3 HOH 26 70 14 HOH MO6 B . # _software.name NUCLSQ _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 1D41 _cell.length_a 17.820 _cell.length_b 30.440 _cell.length_c 44.520 _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 1D41 _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 1D41 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.66 _exptl_crystal.density_percent_sol 25.71 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _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' _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 'NA CACODYLATE' ? ? ? 1 4 1 MGCL2 ? ? ? 1 5 2 WATER ? ? ? 1 6 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 'IMAGE PLATE' _diffrn_detector.type RIGAKU _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 ? _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 1D41 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 2.000 _reflns.d_resolution_low ? _reflns.d_resolution_high 1.300 _reflns.number_obs 2870 _reflns.number_all 3869 _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 1D41 _refine.ls_number_reflns_obs 2870 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _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 1.300 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.208 _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 'ZDFB06 IN WHICH THE METHYL GROUPS OF THE THYMINE BASES WERE REMOVED FROM THE C5 POSITIONS.' _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 238 _refine_hist.pdbx_number_atoms_ligand 17 _refine_hist.number_atoms_solvent 49 _refine_hist.number_atoms_total 304 _refine_hist.d_res_high 1.300 _refine_hist.d_res_low . # _database_PDB_matrix.entry_id 1D41 _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 1D41 _struct.title 'STABILIZATION OF Z-DNA BY DEMETHYLATION OF THYMINE BASES: 1.3 ANGSTROMS SINGLE-CRYSTAL STRUCTURE OF D(M5CGUAM5CG)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1D41 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Z-DNA, DOUBLE HELIX, MODIFIED, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1D41 _struct_ref.pdbx_db_accession 1D41 _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 1D41 A 1 ? 6 ? 1D41 1 ? 6 ? 1 6 2 1 1D41 B 1 ? 6 ? 1D41 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 # _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 5CM 1 "O3'" ? ? ? 1_555 A DG 2 P ? ? A 5CM 1 A DG 2 1_555 ? ? ? ? ? ? ? 1.643 ? ? covale2 covale both ? A DA 4 "O3'" ? ? ? 1_555 A 5CM 5 P ? ? A DA 4 A 5CM 5 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale3 covale both ? A 5CM 5 "O3'" ? ? ? 1_555 A DG 6 P ? ? A 5CM 5 A DG 6 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale4 covale both ? B 5CM 1 "O3'" ? ? ? 1_555 B DG 2 P ? ? B 5CM 7 B DG 8 1_555 ? ? ? ? ? ? ? 1.523 ? ? covale5 covale both ? B DA 4 "O3'" ? ? ? 1_555 B 5CM 5 P ? ? B DA 10 B 5CM 11 1_555 ? ? ? ? ? ? ? 1.626 ? ? covale6 covale both ? B 5CM 5 "O3'" ? ? ? 1_555 B DG 6 P ? ? B 5CM 11 B DG 12 1_555 ? ? ? ? ? ? ? 1.604 ? ? metalc1 metalc ? ? E HOH . O ? ? ? 1_555 D MG . MG ? ? A HOH 69 B MG 14 1_555 ? ? ? ? ? ? ? 2.124 ? ? metalc2 metalc ? ? E HOH . O ? ? ? 1_555 D MG . MG ? ? A HOH 71 B MG 14 1_555 ? ? ? ? ? ? ? 2.076 ? ? metalc3 metalc ? ? E HOH . O ? ? ? 1_555 D MG . MG ? ? A HOH 72 B MG 14 1_555 ? ? ? ? ? ? ? 2.050 ? ? metalc4 metalc ? ? E HOH . O ? ? ? 1_555 D MG . MG ? ? A HOH 73 B MG 14 1_555 ? ? ? ? ? ? ? 2.189 ? ? metalc5 metalc ? ? E HOH . O ? ? ? 1_555 D MG . MG ? ? A HOH 74 B MG 14 1_555 ? ? ? ? ? ? ? 2.079 ? ? metalc6 metalc ? ? B DU 3 OP2 ? ? ? 1_555 C MG . MG ? ? B DU 9 B MG 13 1_555 ? ? ? ? ? ? ? 1.968 ? ? metalc7 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 13 B HOH 64 1_555 ? ? ? ? ? ? ? 2.051 ? ? metalc8 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 13 B HOH 65 1_555 ? ? ? ? ? ? ? 2.090 ? ? metalc9 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 13 B HOH 66 1_555 ? ? ? ? ? ? ? 2.240 ? ? metalc10 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 13 B HOH 67 1_555 ? ? ? ? ? ? ? 2.024 ? ? metalc11 metalc ? ? C MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 13 B HOH 68 1_555 ? ? ? ? ? ? ? 2.180 ? ? metalc12 metalc ? ? D MG . MG ? ? ? 1_555 F HOH . O ? ? B MG 14 B HOH 70 1_555 ? ? ? ? ? ? ? 2.171 ? ? hydrog1 hydrog ? ? A 5CM 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A 5CM 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A 5CM 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A 5CM 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A 5CM 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A 5CM 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B 5CM 5 N3 ? ? A DG 2 B 5CM 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B 5CM 5 O2 ? ? A DG 2 B 5CM 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B 5CM 5 N4 ? ? A DG 2 B 5CM 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DU 3 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DU 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DU 3 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DU 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DU 3 N3 ? ? A DA 4 B DU 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DU 3 O4 ? ? A DA 4 B DU 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A 5CM 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A 5CM 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A 5CM 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A 5CM 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A 5CM 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A 5CM 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B 5CM 1 N3 ? ? A DG 6 B 5CM 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B 5CM 1 O2 ? ? A DG 6 B 5CM 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B 5CM 1 N4 ? ? A DG 6 B 5CM 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? E HOH . ? A HOH 69 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? E HOH . ? A HOH 71 ? 1_555 94.3 ? 2 O ? E HOH . ? A HOH 69 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? E HOH . ? A HOH 72 ? 1_555 85.9 ? 3 O ? E HOH . ? A HOH 71 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? E HOH . ? A HOH 72 ? 1_555 177.3 ? 4 O ? E HOH . ? A HOH 69 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? E HOH . ? A HOH 73 ? 1_555 85.9 ? 5 O ? E HOH . ? A HOH 71 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? E HOH . ? A HOH 73 ? 1_555 82.6 ? 6 O ? E HOH . ? A HOH 72 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? E HOH . ? A HOH 73 ? 1_555 94.7 ? 7 O ? E HOH . ? A HOH 69 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? E HOH . ? A HOH 74 ? 1_555 92.3 ? 8 O ? E HOH . ? A HOH 71 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? E HOH . ? A HOH 74 ? 1_555 83.9 ? 9 O ? E HOH . ? A HOH 72 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? E HOH . ? A HOH 74 ? 1_555 98.8 ? 10 O ? E HOH . ? A HOH 73 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? E HOH . ? A HOH 74 ? 1_555 166.2 ? 11 O ? E HOH . ? A HOH 69 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? F HOH . ? B HOH 70 ? 1_555 175.0 ? 12 O ? E HOH . ? A HOH 71 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? F HOH . ? B HOH 70 ? 1_555 89.5 ? 13 O ? E HOH . ? A HOH 72 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? F HOH . ? B HOH 70 ? 1_555 90.2 ? 14 O ? E HOH . ? A HOH 73 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? F HOH . ? B HOH 70 ? 1_555 91.3 ? 15 O ? E HOH . ? A HOH 74 ? 1_555 MG ? D MG . ? B MG 14 ? 1_555 O ? F HOH . ? B HOH 70 ? 1_555 91.3 ? 16 OP2 ? B DU 3 ? B DU 9 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 64 ? 1_555 91.5 ? 17 OP2 ? B DU 3 ? B DU 9 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 65 ? 1_555 89.0 ? 18 O ? F HOH . ? B HOH 64 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 65 ? 1_555 172.7 ? 19 OP2 ? B DU 3 ? B DU 9 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 66 ? 1_555 91.3 ? 20 O ? F HOH . ? B HOH 64 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 66 ? 1_555 89.9 ? 21 O ? F HOH . ? B HOH 65 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 66 ? 1_555 82.9 ? 22 OP2 ? B DU 3 ? B DU 9 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 67 ? 1_555 96.8 ? 23 O ? F HOH . ? B HOH 64 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 67 ? 1_555 105.1 ? 24 O ? F HOH . ? B HOH 65 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 67 ? 1_555 82.0 ? 25 O ? F HOH . ? B HOH 66 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 67 ? 1_555 162.6 ? 26 OP2 ? B DU 3 ? B DU 9 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 68 ? 1_555 172.0 ? 27 O ? F HOH . ? B HOH 64 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 68 ? 1_555 96.0 ? 28 O ? F HOH . ? B HOH 65 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 68 ? 1_555 83.2 ? 29 O ? F HOH . ? B HOH 66 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 68 ? 1_555 86.0 ? 30 O ? F HOH . ? B HOH 67 ? 1_555 MG ? C MG . ? B MG 13 ? 1_555 O ? F HOH . ? B HOH 68 ? 1_555 83.9 ? # loop_ _struct_site.id _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 AC1 Software B MG 13 ? 6 'BINDING SITE FOR RESIDUE MG B 13' AC2 Software B MG 14 ? 6 'BINDING SITE FOR RESIDUE MG B 14' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 DU B 3 ? DU B 9 . ? 1_555 ? 2 AC1 6 HOH F . ? HOH B 64 . ? 1_555 ? 3 AC1 6 HOH F . ? HOH B 65 . ? 1_555 ? 4 AC1 6 HOH F . ? HOH B 66 . ? 1_555 ? 5 AC1 6 HOH F . ? HOH B 67 . ? 1_555 ? 6 AC1 6 HOH F . ? HOH B 68 . ? 1_555 ? 7 AC2 6 HOH E . ? HOH A 69 . ? 1_555 ? 8 AC2 6 HOH E . ? HOH A 71 . ? 1_555 ? 9 AC2 6 HOH E . ? HOH A 72 . ? 1_555 ? 10 AC2 6 HOH E . ? HOH A 73 . ? 1_555 ? 11 AC2 6 HOH E . ? HOH A 74 . ? 1_555 ? 12 AC2 6 HOH F . ? HOH B 70 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A HOH 19 ? ? O A HOH 39 ? ? 1.69 2 1 "O3'" A DG 2 ? ? O A HOH 20 ? ? 1.92 3 1 "C5'" B 5CM 7 ? ? O B HOH 30 ? ? 2.16 # 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 "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? 1.636 1.529 0.107 0.010 N 2 1 "C3'" A DG 2 ? ? "C2'" A DG 2 ? ? 1.454 1.516 -0.062 0.008 N 3 1 "C2'" A DG 2 ? ? "C1'" A DG 2 ? ? 1.646 1.519 0.127 0.010 N 4 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? 1.502 1.420 0.082 0.011 N 5 1 "C1'" A DG 2 ? ? N9 A DG 2 ? ? 1.326 1.468 -0.142 0.014 N 6 1 N1 A DG 2 ? ? C2 A DG 2 ? ? 1.307 1.373 -0.066 0.008 N 7 1 C2 A DG 2 ? ? N3 A DG 2 ? ? 1.275 1.323 -0.048 0.008 N 8 1 N7 A DG 2 ? ? C8 A DG 2 ? ? 1.356 1.305 0.051 0.006 N 9 1 C2 A DG 2 ? ? N2 A DG 2 ? ? 1.251 1.341 -0.090 0.010 N 10 1 "O3'" A DG 2 ? ? P A DU 3 ? ? 1.696 1.607 0.089 0.012 Y 11 1 "C2'" A DU 3 ? ? "C1'" A DU 3 ? ? 1.663 1.519 0.144 0.010 N 12 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? 1.556 1.420 0.136 0.011 N 13 1 C4 A DA 4 ? ? C5 A DA 4 ? ? 1.318 1.383 -0.065 0.007 N 14 1 N7 A DA 4 ? ? C8 A DA 4 ? ? 1.354 1.311 0.043 0.007 N 15 1 C8 A DA 4 ? ? N9 A DA 4 ? ? 1.302 1.373 -0.071 0.008 N 16 1 C6 A DA 4 ? ? N6 A DA 4 ? ? 1.412 1.335 0.077 0.008 N 17 1 P A DG 6 ? ? "O5'" A DG 6 ? ? 1.676 1.593 0.083 0.010 N 18 1 "C5'" A DG 6 ? ? "C4'" A DG 6 ? ? 1.594 1.512 0.082 0.007 N 19 1 "C4'" A DG 6 ? ? "C3'" A DG 6 ? ? 1.413 1.521 -0.108 0.010 N 20 1 "C3'" A DG 6 ? ? "C2'" A DG 6 ? ? 1.439 1.516 -0.077 0.008 N 21 1 N1 A DG 6 ? ? C2 A DG 6 ? ? 1.301 1.373 -0.072 0.008 N 22 1 C2 A DG 6 ? ? N3 A DG 6 ? ? 1.376 1.323 0.053 0.008 N 23 1 C4 A DG 6 ? ? C5 A DG 6 ? ? 1.316 1.379 -0.063 0.007 N 24 1 C5 A DG 6 ? ? N7 A DG 6 ? ? 1.444 1.388 0.056 0.006 N 25 1 C8 A DG 6 ? ? N9 A DG 6 ? ? 1.306 1.374 -0.068 0.007 N 26 1 "O3'" B 5CM 7 ? ? P B DG 8 ? ? 1.523 1.607 -0.084 0.012 Y 27 1 "C4'" B DG 8 ? ? "C3'" B DG 8 ? ? 1.663 1.529 0.134 0.010 N 28 1 "C3'" B DG 8 ? ? "C2'" B DG 8 ? ? 1.447 1.516 -0.069 0.008 N 29 1 "C2'" B DG 8 ? ? "C1'" B DG 8 ? ? 1.409 1.518 -0.109 0.010 N 30 1 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? 1.503 1.420 0.083 0.011 N 31 1 N7 B DG 8 ? ? C8 B DG 8 ? ? 1.385 1.305 0.080 0.006 N 32 1 C8 B DG 8 ? ? N9 B DG 8 ? ? 1.329 1.374 -0.045 0.007 N 33 1 N9 B DG 8 ? ? C4 B DG 8 ? ? 1.456 1.375 0.081 0.008 N 34 1 C2 B DG 8 ? ? N2 B DG 8 ? ? 1.265 1.341 -0.076 0.010 N 35 1 "C5'" B DU 9 ? ? "C4'" B DU 9 ? ? 1.560 1.512 0.048 0.007 N 36 1 "C2'" B DU 9 ? ? "C1'" B DU 9 ? ? 1.605 1.519 0.086 0.010 N 37 1 "O3'" B DU 9 ? ? "C3'" B DU 9 ? ? 1.358 1.419 -0.061 0.006 N 38 1 "C1'" B DU 9 ? ? N1 B DU 9 ? ? 1.607 1.488 0.119 0.013 N 39 1 N1 B DU 9 ? ? C2 B DU 9 ? ? 1.318 1.381 -0.063 0.009 N 40 1 P B DA 10 ? ? OP2 B DA 10 ? ? 1.372 1.485 -0.113 0.017 N 41 1 P B DA 10 ? ? "O5'" B DA 10 ? ? 1.681 1.593 0.088 0.010 N 42 1 "C5'" B DA 10 ? ? "C4'" B DA 10 ? ? 1.429 1.509 -0.080 0.011 N 43 1 "C1'" B DA 10 ? ? N9 B DA 10 ? ? 1.379 1.468 -0.089 0.014 N 44 1 C2 B DA 10 ? ? N3 B DA 10 ? ? 1.389 1.331 0.058 0.009 N 45 1 C6 B DA 10 ? ? N6 B DA 10 ? ? 1.384 1.335 0.049 0.008 N 46 1 P B DG 12 ? ? "O5'" B DG 12 ? ? 1.675 1.593 0.082 0.010 N 47 1 "C3'" B DG 12 ? ? "C2'" B DG 12 ? ? 1.466 1.516 -0.050 0.008 N 48 1 "O4'" B DG 12 ? ? "C4'" B DG 12 ? ? 1.344 1.446 -0.102 0.010 N 49 1 "O3'" B DG 12 ? ? "C3'" B DG 12 ? ? 1.320 1.419 -0.099 0.006 N 50 1 N1 B DG 12 ? ? C2 B DG 12 ? ? 1.309 1.373 -0.064 0.008 N 51 1 N7 B DG 12 ? ? C8 B DG 12 ? ? 1.355 1.305 0.050 0.006 N 52 1 C8 B DG 12 ? ? N9 B DG 12 ? ? 1.327 1.374 -0.047 0.007 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 OP1 A DG 2 ? ? P A DG 2 ? ? OP2 A DG 2 ? ? 136.88 119.60 17.28 1.50 N 2 1 "O5'" A DG 2 ? ? P A DG 2 ? ? OP1 A DG 2 ? ? 90.48 105.70 -15.22 0.90 N 3 1 "O5'" A DG 2 ? ? P A DG 2 ? ? OP2 A DG 2 ? ? 119.28 110.70 8.58 1.20 N 4 1 "C4'" A DG 2 ? ? "C3'" A DG 2 ? ? "C2'" A DG 2 ? ? 109.24 103.10 6.14 0.90 N 5 1 N1 A DG 2 ? ? C2 A DG 2 ? ? N3 A DG 2 ? ? 130.67 123.90 6.77 0.60 N 6 1 C4 A DG 2 ? ? C5 A DG 2 ? ? N7 A DG 2 ? ? 114.70 110.80 3.90 0.40 N 7 1 C5 A DG 2 ? ? N7 A DG 2 ? ? C8 A DG 2 ? ? 100.53 104.30 -3.77 0.50 N 8 1 N3 A DG 2 ? ? C2 A DG 2 ? ? N2 A DG 2 ? ? 111.79 119.90 -8.11 0.70 N 9 1 C5 A DG 2 ? ? C6 A DG 2 ? ? O6 A DG 2 ? ? 123.97 128.60 -4.63 0.60 N 10 1 "O3'" A DG 2 ? ? P A DU 3 ? ? OP1 A DU 3 ? ? 91.46 105.20 -13.74 2.20 Y 11 1 "O5'" A DU 3 ? ? "C5'" A DU 3 ? ? "C4'" A DU 3 ? ? 91.88 109.40 -17.52 0.80 N 12 1 "O4'" A DU 3 ? ? "C4'" A DU 3 ? ? "C3'" A DU 3 ? ? 101.72 104.50 -2.78 0.40 N 13 1 "C4'" A DU 3 ? ? "C3'" A DU 3 ? ? "C2'" A DU 3 ? ? 110.35 103.10 7.25 0.90 N 14 1 "C3'" A DU 3 ? ? "C2'" A DU 3 ? ? "C1'" A DU 3 ? ? 91.79 102.40 -10.61 0.80 N 15 1 "O4'" A DU 3 ? ? "C1'" A DU 3 ? ? N1 A DU 3 ? ? 102.55 108.00 -5.45 0.70 N 16 1 "O5'" A DA 4 ? ? "C5'" A DA 4 ? ? "C4'" A DA 4 ? ? 102.94 109.40 -6.46 0.80 N 17 1 "C4'" A DA 4 ? ? "C3'" A DA 4 ? ? "O3'" A DA 4 ? ? 94.23 109.70 -15.47 2.50 N 18 1 "C3'" A DA 4 ? ? "C2'" A DA 4 ? ? "C1'" A DA 4 ? ? 109.90 102.50 7.40 1.20 N 19 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? "C2'" A DA 4 ? ? 100.77 105.90 -5.13 0.80 N 20 1 C5 A DA 4 ? ? N7 A DA 4 ? ? C8 A DA 4 ? ? 100.48 103.90 -3.42 0.50 N 21 1 "O5'" A DG 6 ? ? P A DG 6 ? ? OP1 A DG 6 ? ? 98.14 105.70 -7.56 0.90 N 22 1 "O5'" A DG 6 ? ? P A DG 6 ? ? OP2 A DG 6 ? ? 119.25 110.70 8.55 1.20 N 23 1 "O5'" A DG 6 ? ? "C5'" A DG 6 ? ? "C4'" A DG 6 ? ? 96.17 109.40 -13.23 0.80 N 24 1 P A DG 6 ? ? "O5'" A DG 6 ? ? "C5'" A DG 6 ? ? 108.03 120.90 -12.87 1.60 N 25 1 "O4'" A DG 6 ? ? "C4'" A DG 6 ? ? "C3'" A DG 6 ? ? 115.35 106.00 9.35 0.60 N 26 1 "C4'" A DG 6 ? ? "C3'" A DG 6 ? ? "C2'" A DG 6 ? ? 97.70 102.20 -4.50 0.70 N 27 1 "C3'" A DG 6 ? ? "C2'" A DG 6 ? ? "C1'" A DG 6 ? ? 110.98 102.50 8.48 1.20 N 28 1 C6 A DG 6 ? ? N1 A DG 6 ? ? C2 A DG 6 ? ? 116.03 125.10 -9.07 0.60 N 29 1 N1 A DG 6 ? ? C2 A DG 6 ? ? N3 A DG 6 ? ? 130.87 123.90 6.97 0.60 N 30 1 C2 A DG 6 ? ? N3 A DG 6 ? ? C4 A DG 6 ? ? 106.83 111.90 -5.07 0.50 N 31 1 C5 A DG 6 ? ? C6 A DG 6 ? ? N1 A DG 6 ? ? 116.46 111.50 4.96 0.50 N 32 1 C8 A DG 6 ? ? N9 A DG 6 ? ? C4 A DG 6 ? ? 109.82 106.40 3.42 0.40 N 33 1 N3 A DG 6 ? ? C2 A DG 6 ? ? N2 A DG 6 ? ? 111.08 119.90 -8.82 0.70 N 34 1 N1 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 114.98 119.90 -4.92 0.60 N 35 1 "O5'" B DG 8 ? ? "C5'" B DG 8 ? ? "C4'" B DG 8 ? ? 98.77 109.40 -10.63 0.80 N 36 1 "C5'" B DG 8 ? ? "C4'" B DG 8 ? ? "C3'" B DG 8 ? ? 101.16 114.10 -12.94 1.80 N 37 1 "C5'" B DG 8 ? ? "C4'" B DG 8 ? ? "O4'" B DG 8 ? ? 117.14 109.80 7.34 1.10 N 38 1 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? "C2'" B DG 8 ? ? 114.40 106.80 7.60 0.50 N 39 1 C6 B DG 8 ? ? N1 B DG 8 ? ? C2 B DG 8 ? ? 117.93 125.10 -7.17 0.60 N 40 1 N1 B DG 8 ? ? C2 B DG 8 ? ? N3 B DG 8 ? ? 128.53 123.90 4.63 0.60 N 41 1 C5 B DG 8 ? ? C6 B DG 8 ? ? N1 B DG 8 ? ? 117.71 111.50 6.21 0.50 N 42 1 C4 B DG 8 ? ? C5 B DG 8 ? ? N7 B DG 8 ? ? 115.01 110.80 4.21 0.40 N 43 1 N9 B DG 8 ? ? C4 B DG 8 ? ? C5 B DG 8 ? ? 101.70 105.40 -3.70 0.40 N 44 1 N3 B DG 8 ? ? C4 B DG 8 ? ? N9 B DG 8 ? ? 130.94 126.00 4.94 0.60 N 45 1 N3 B DG 8 ? ? C2 B DG 8 ? ? N2 B DG 8 ? ? 111.78 119.90 -8.12 0.70 N 46 1 C5 B DG 8 ? ? C6 B DG 8 ? ? O6 B DG 8 ? ? 123.41 128.60 -5.19 0.60 N 47 1 "C3'" B DG 8 ? ? "O3'" B DG 8 ? ? P B DU 9 ? ? 129.67 119.70 9.97 1.20 Y 48 1 OP1 B DU 9 ? ? P B DU 9 ? ? OP2 B DU 9 ? ? 105.24 119.60 -14.36 1.50 N 49 1 "O5'" B DU 9 ? ? P B DU 9 ? ? OP1 B DU 9 ? ? 117.97 110.70 7.27 1.20 N 50 1 "O5'" B DU 9 ? ? "C5'" B DU 9 ? ? "C4'" B DU 9 ? ? 104.36 109.40 -5.04 0.80 N 51 1 "O4'" B DU 9 ? ? "C4'" B DU 9 ? ? "C3'" B DU 9 ? ? 101.12 104.50 -3.38 0.40 N 52 1 "C5'" B DU 9 ? ? "C4'" B DU 9 ? ? "C3'" B DU 9 ? ? 124.46 115.70 8.76 1.20 N 53 1 "C3'" B DU 9 ? ? "C2'" B DU 9 ? ? "C1'" B DU 9 ? ? 93.73 102.40 -8.67 0.80 N 54 1 "O4'" B DU 9 ? ? "C1'" B DU 9 ? ? N1 B DU 9 ? ? 102.26 108.00 -5.74 0.70 N 55 1 C6 B DU 9 ? ? N1 B DU 9 ? ? C2 B DU 9 ? ? 125.84 121.00 4.84 0.60 N 56 1 C5 B DU 9 ? ? C6 B DU 9 ? ? N1 B DU 9 ? ? 116.26 122.70 -6.44 0.50 N 57 1 N3 B DU 9 ? ? C4 B DU 9 ? ? O4 B DU 9 ? ? 114.22 119.40 -5.18 0.70 N 58 1 "C3'" B DU 9 ? ? "O3'" B DU 9 ? ? P B DA 10 ? ? 128.11 119.70 8.41 1.20 Y 59 1 "O5'" B DA 10 ? ? P B DA 10 ? ? OP2 B DA 10 ? ? 98.50 105.70 -7.20 0.90 N 60 1 "O5'" B DA 10 ? ? "C5'" B DA 10 ? ? "C4'" B DA 10 ? ? 104.37 109.40 -5.03 0.80 N 61 1 "O4'" B DA 10 ? ? "C4'" B DA 10 ? ? "C3'" B DA 10 ? ? 100.51 104.50 -3.99 0.40 N 62 1 "C1'" B DA 10 ? ? "O4'" B DA 10 ? ? "C4'" B DA 10 ? ? 119.45 110.30 9.15 0.70 N 63 1 "C4'" B DA 10 ? ? "C3'" B DA 10 ? ? "C2'" B DA 10 ? ? 111.42 103.10 8.32 0.90 N 64 1 "O4'" B DA 10 ? ? "C1'" B DA 10 ? ? "C2'" B DA 10 ? ? 101.05 105.90 -4.85 0.80 N 65 1 "O4'" B DA 10 ? ? "C1'" B DA 10 ? ? N9 B DA 10 ? ? 114.74 108.30 6.44 0.30 N 66 1 N1 B DA 10 ? ? C2 B DA 10 ? ? N3 B DA 10 ? ? 125.62 129.30 -3.68 0.50 N 67 1 N9 B DA 10 ? ? C4 B DA 10 ? ? C5 B DA 10 ? ? 102.66 105.80 -3.14 0.40 N 68 1 N1 B DA 10 ? ? C6 B DA 10 ? ? N6 B DA 10 ? ? 123.38 118.60 4.78 0.60 N 69 1 C5 B DA 10 ? ? C6 B DA 10 ? ? N6 B DA 10 ? ? 118.60 123.70 -5.10 0.80 N 70 1 "C3'" B DA 10 ? ? "O3'" B DA 10 ? ? P B 5CM 11 ? ? 128.41 119.70 8.71 1.20 Y 71 1 "O5'" B DG 12 ? ? P B DG 12 ? ? OP1 B DG 12 ? ? 122.08 110.70 11.38 1.20 N 72 1 "O5'" B DG 12 ? ? P B DG 12 ? ? OP2 B DG 12 ? ? 89.11 105.70 -16.59 0.90 N 73 1 "O4'" B DG 12 ? ? "C4'" B DG 12 ? ? "C3'" B DG 12 ? ? 94.67 104.50 -9.83 0.40 N 74 1 "C5'" B DG 12 ? ? "C4'" B DG 12 ? ? "C3'" B DG 12 ? ? 123.40 115.70 7.70 1.20 N 75 1 "C4'" B DG 12 ? ? "C3'" B DG 12 ? ? "C2'" B DG 12 ? ? 112.64 103.10 9.54 0.90 N 76 1 "C3'" B DG 12 ? ? "C2'" B DG 12 ? ? "C1'" B DG 12 ? ? 96.80 102.40 -5.60 0.80 N 77 1 C6 B DG 12 ? ? N1 B DG 12 ? ? C2 B DG 12 ? ? 112.63 125.10 -12.47 0.60 N 78 1 N1 B DG 12 ? ? C2 B DG 12 ? ? N3 B DG 12 ? ? 136.92 123.90 13.02 0.60 N 79 1 N3 B DG 12 ? ? C4 B DG 12 ? ? C5 B DG 12 ? ? 124.38 128.60 -4.22 0.50 N 80 1 C5 B DG 12 ? ? C6 B DG 12 ? ? N1 B DG 12 ? ? 117.23 111.50 5.73 0.50 N 81 1 C8 B DG 12 ? ? N9 B DG 12 ? ? C4 B DG 12 ? ? 109.25 106.40 2.85 0.40 N 82 1 N3 B DG 12 ? ? C4 B DG 12 ? ? N9 B DG 12 ? ? 132.16 126.00 6.16 0.60 N 83 1 N3 B DG 12 ? ? C2 B DG 12 ? ? N2 B DG 12 ? ? 103.37 119.90 -16.53 0.70 N 84 1 C5 B DG 12 ? ? C6 B DG 12 ? ? O6 B DG 12 ? ? 121.29 128.60 -7.31 0.60 N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 5CM 1 A 5CM 1 ? DC ? 2 A 5CM 5 A 5CM 5 ? DC ? 3 B 5CM 1 B 5CM 7 ? DC ? 4 B 5CM 5 B 5CM 11 ? DC ? # 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 IONS' 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 IONS' 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 5CM N1 N N N 1 5CM C2 C N N 2 5CM N3 N N N 3 5CM C4 C N N 4 5CM C5 C N N 5 5CM C5A C N N 6 5CM C6 C N N 7 5CM O2 O N N 8 5CM N4 N N N 9 5CM "C1'" C N R 10 5CM "C2'" C N N 11 5CM "C3'" C N S 12 5CM "C4'" C N R 13 5CM "O4'" O N N 14 5CM "O3'" O N N 15 5CM "C5'" C N N 16 5CM "O5'" O N N 17 5CM P P N N 18 5CM OP1 O N N 19 5CM OP2 O N N 20 5CM OP3 O N N 21 5CM H5A1 H N N 22 5CM H5A2 H N N 23 5CM H5A3 H N N 24 5CM H6 H N N 25 5CM HN41 H N N 26 5CM HN42 H N N 27 5CM "H1'" H N N 28 5CM "H2'" H N N 29 5CM "H2''" H N N 30 5CM "H3'" H N N 31 5CM "H4'" H N N 32 5CM "HO3'" H N N 33 5CM "H5'" H N N 34 5CM "H5''" H N N 35 5CM HOP2 H N N 36 5CM HOP3 H N N 37 DA OP3 O N N 38 DA P P N N 39 DA OP1 O N N 40 DA OP2 O N N 41 DA "O5'" O N N 42 DA "C5'" C N N 43 DA "C4'" C N R 44 DA "O4'" O N N 45 DA "C3'" C N S 46 DA "O3'" O N N 47 DA "C2'" C N N 48 DA "C1'" C N R 49 DA N9 N Y N 50 DA C8 C Y N 51 DA N7 N Y N 52 DA C5 C Y N 53 DA C6 C Y N 54 DA N6 N N N 55 DA N1 N Y N 56 DA C2 C Y N 57 DA N3 N Y N 58 DA C4 C Y N 59 DA HOP3 H N N 60 DA HOP2 H N N 61 DA "H5'" H N N 62 DA "H5''" H N N 63 DA "H4'" H N N 64 DA "H3'" H N N 65 DA "HO3'" H N N 66 DA "H2'" H N N 67 DA "H2''" H N N 68 DA "H1'" H N N 69 DA H8 H N N 70 DA H61 H N N 71 DA H62 H N N 72 DA H2 H N N 73 DG OP3 O N N 74 DG P P N N 75 DG OP1 O N N 76 DG OP2 O N N 77 DG "O5'" O N N 78 DG "C5'" C N N 79 DG "C4'" C N R 80 DG "O4'" O N N 81 DG "C3'" C N S 82 DG "O3'" O N N 83 DG "C2'" C N N 84 DG "C1'" C N R 85 DG N9 N Y N 86 DG C8 C Y N 87 DG N7 N Y N 88 DG C5 C Y N 89 DG C6 C N N 90 DG O6 O N N 91 DG N1 N N N 92 DG C2 C N N 93 DG N2 N N N 94 DG N3 N N N 95 DG C4 C Y N 96 DG HOP3 H N N 97 DG HOP2 H N N 98 DG "H5'" H N N 99 DG "H5''" H N N 100 DG "H4'" H N N 101 DG "H3'" H N N 102 DG "HO3'" H N N 103 DG "H2'" H N N 104 DG "H2''" H N N 105 DG "H1'" H N N 106 DG H8 H N N 107 DG H1 H N N 108 DG H21 H N N 109 DG H22 H N N 110 DU OP3 O N N 111 DU P P N N 112 DU OP1 O N N 113 DU OP2 O N N 114 DU "O5'" O N N 115 DU "C5'" C N N 116 DU "C4'" C N R 117 DU "O4'" O N N 118 DU "C3'" C N S 119 DU "O3'" O N N 120 DU "C2'" C N N 121 DU "C1'" C N R 122 DU N1 N N N 123 DU C2 C N N 124 DU O2 O N N 125 DU N3 N N N 126 DU C4 C N N 127 DU O4 O N N 128 DU C5 C N N 129 DU C6 C N N 130 DU HOP3 H N N 131 DU HOP2 H N N 132 DU "H5'" H N N 133 DU "H5''" H N N 134 DU "H4'" H N N 135 DU "H3'" H N N 136 DU "HO3'" H N N 137 DU "H2'" H N N 138 DU "H2''" H N N 139 DU "H1'" H N N 140 DU H3 H N N 141 DU H5 H N N 142 DU H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 MG MG MG N N 147 # 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 5CM N1 C2 sing N N 1 5CM N1 C6 sing N N 2 5CM N1 "C1'" sing N N 3 5CM C2 N3 sing N N 4 5CM C2 O2 doub N N 5 5CM N3 C4 doub N N 6 5CM C4 C5 sing N N 7 5CM C4 N4 sing N N 8 5CM C5 C5A sing N N 9 5CM C5 C6 doub N N 10 5CM C5A H5A1 sing N N 11 5CM C5A H5A2 sing N N 12 5CM C5A H5A3 sing N N 13 5CM C6 H6 sing N N 14 5CM N4 HN41 sing N N 15 5CM N4 HN42 sing N N 16 5CM "C1'" "C2'" sing N N 17 5CM "C1'" "O4'" sing N N 18 5CM "C1'" "H1'" sing N N 19 5CM "C2'" "C3'" sing N N 20 5CM "C2'" "H2'" sing N N 21 5CM "C2'" "H2''" sing N N 22 5CM "C3'" "C4'" sing N N 23 5CM "C3'" "O3'" sing N N 24 5CM "C3'" "H3'" sing N N 25 5CM "C4'" "O4'" sing N N 26 5CM "C4'" "C5'" sing N N 27 5CM "C4'" "H4'" sing N N 28 5CM "O3'" "HO3'" sing N N 29 5CM "C5'" "O5'" sing N N 30 5CM "C5'" "H5'" sing N N 31 5CM "C5'" "H5''" sing N N 32 5CM "O5'" P sing N N 33 5CM P OP1 doub N N 34 5CM P OP2 sing N N 35 5CM P OP3 sing N N 36 5CM OP2 HOP2 sing N N 37 5CM OP3 HOP3 sing N N 38 DA OP3 P sing N N 39 DA OP3 HOP3 sing N N 40 DA P OP1 doub N N 41 DA P OP2 sing N N 42 DA P "O5'" sing N N 43 DA OP2 HOP2 sing N N 44 DA "O5'" "C5'" sing N N 45 DA "C5'" "C4'" sing N N 46 DA "C5'" "H5'" sing N N 47 DA "C5'" "H5''" sing N N 48 DA "C4'" "O4'" sing N N 49 DA "C4'" "C3'" sing N N 50 DA "C4'" "H4'" sing N N 51 DA "O4'" "C1'" sing N N 52 DA "C3'" "O3'" sing N N 53 DA "C3'" "C2'" sing N N 54 DA "C3'" "H3'" sing N N 55 DA "O3'" "HO3'" sing N N 56 DA "C2'" "C1'" sing N N 57 DA "C2'" "H2'" sing N N 58 DA "C2'" "H2''" sing N N 59 DA "C1'" N9 sing N N 60 DA "C1'" "H1'" sing N N 61 DA N9 C8 sing Y N 62 DA N9 C4 sing Y N 63 DA C8 N7 doub Y N 64 DA C8 H8 sing N N 65 DA N7 C5 sing Y N 66 DA C5 C6 sing Y N 67 DA C5 C4 doub Y N 68 DA C6 N6 sing N N 69 DA C6 N1 doub Y N 70 DA N6 H61 sing N N 71 DA N6 H62 sing N N 72 DA N1 C2 sing Y N 73 DA C2 N3 doub Y N 74 DA C2 H2 sing N N 75 DA N3 C4 sing Y N 76 DG OP3 P sing N N 77 DG OP3 HOP3 sing N N 78 DG P OP1 doub N N 79 DG P OP2 sing N N 80 DG P "O5'" sing N N 81 DG OP2 HOP2 sing N N 82 DG "O5'" "C5'" sing N N 83 DG "C5'" "C4'" sing N N 84 DG "C5'" "H5'" sing N N 85 DG "C5'" "H5''" sing N N 86 DG "C4'" "O4'" sing N N 87 DG "C4'" "C3'" sing N N 88 DG "C4'" "H4'" sing N N 89 DG "O4'" "C1'" sing N N 90 DG "C3'" "O3'" sing N N 91 DG "C3'" "C2'" sing N N 92 DG "C3'" "H3'" sing N N 93 DG "O3'" "HO3'" sing N N 94 DG "C2'" "C1'" sing N N 95 DG "C2'" "H2'" sing N N 96 DG "C2'" "H2''" sing N N 97 DG "C1'" N9 sing N N 98 DG "C1'" "H1'" sing N N 99 DG N9 C8 sing Y N 100 DG N9 C4 sing Y N 101 DG C8 N7 doub Y N 102 DG C8 H8 sing N N 103 DG N7 C5 sing Y N 104 DG C5 C6 sing N N 105 DG C5 C4 doub Y N 106 DG C6 O6 doub N N 107 DG C6 N1 sing N N 108 DG N1 C2 sing N N 109 DG N1 H1 sing N N 110 DG C2 N2 sing N N 111 DG C2 N3 doub N N 112 DG N2 H21 sing N N 113 DG N2 H22 sing N N 114 DG N3 C4 sing N N 115 DU OP3 P sing N N 116 DU OP3 HOP3 sing N N 117 DU P OP1 doub N N 118 DU P OP2 sing N N 119 DU P "O5'" sing N N 120 DU OP2 HOP2 sing N N 121 DU "O5'" "C5'" sing N N 122 DU "C5'" "C4'" sing N N 123 DU "C5'" "H5'" sing N N 124 DU "C5'" "H5''" sing N N 125 DU "C4'" "O4'" sing N N 126 DU "C4'" "C3'" sing N N 127 DU "C4'" "H4'" sing N N 128 DU "O4'" "C1'" sing N N 129 DU "C3'" "O3'" sing N N 130 DU "C3'" "C2'" sing N N 131 DU "C3'" "H3'" sing N N 132 DU "O3'" "HO3'" sing N N 133 DU "C2'" "C1'" sing N N 134 DU "C2'" "H2'" sing N N 135 DU "C2'" "H2''" sing N N 136 DU "C1'" N1 sing N N 137 DU "C1'" "H1'" sing N N 138 DU N1 C2 sing N N 139 DU N1 C6 sing N N 140 DU C2 O2 doub N N 141 DU C2 N3 sing N N 142 DU N3 C4 sing N N 143 DU N3 H3 sing N N 144 DU C4 O4 doub N N 145 DU C4 C5 sing N N 146 DU C5 C6 doub N N 147 DU C5 H5 sing N N 148 DU C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 # _ndb_struct_conf_na.entry_id 1D41 _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 5CM 1 1_555 B DG 6 1_555 -0.373 -0.194 -0.057 9.603 0.654 1.140 1 A_5CM1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B 5CM 5 1_555 0.233 -0.182 0.148 -8.635 5.542 3.792 2 A_DG2:5CM11_B A 2 ? B 11 ? 19 1 1 A DU 3 1_555 B DA 4 1_555 -0.220 -0.180 0.303 6.575 -7.867 -1.049 3 A_DU3:DA10_B A 3 ? B 10 ? 20 1 1 A DA 4 1_555 B DU 3 1_555 0.142 -0.057 -0.014 -6.124 -3.211 2.754 4 A_DA4:DU9_B A 4 ? B 9 ? 20 1 1 A 5CM 5 1_555 B DG 2 1_555 -0.350 -0.173 0.026 -0.009 -0.801 -0.128 5 A_5CM5:DG8_B A 5 ? B 8 ? 19 1 1 A DG 6 1_555 B 5CM 1 1_555 0.226 -0.127 0.056 -3.364 -2.506 -0.735 6 A_DG6:5CM7_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 5CM 1 1_555 B DG 6 1_555 A DG 2 1_555 B 5CM 5 1_555 0.188 5.702 4.068 1.678 0.085 -11.575 -28.124 3.752 3.958 -0.418 8.261 -11.696 1 AA_5CM1DG2:5CM11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B 5CM 5 1_555 A DU 3 1_555 B DA 4 1_555 -0.174 -0.627 3.227 -1.901 0.256 -46.887 0.767 -0.373 3.221 -0.322 -2.389 -46.924 2 AA_DG2DU3:DA105CM11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DU 3 1_555 B DA 4 1_555 A DA 4 1_555 B DU 3 1_555 0.309 5.254 3.873 2.250 -9.946 -12.025 -6.039 4.097 6.221 39.429 8.919 -15.754 3 AA_DU3DA4:DU9DA10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DA 4 1_555 B DU 3 1_555 A 5CM 5 1_555 B DG 2 1_555 -0.279 -1.142 3.409 0.258 -1.165 -48.444 1.484 -0.320 3.384 1.419 0.314 -48.458 4 AA_DA45CM5:DG8DU9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A 5CM 5 1_555 B DG 2 1_555 A DG 6 1_555 B 5CM 1 1_555 0.000 5.551 3.558 -2.702 -0.295 -14.031 -22.017 -2.735 3.608 1.192 -10.928 -14.290 5 AA_5CM5DG6:5CM7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ? # _pdbx_initial_refinement_model.accession_code 1VTW _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 'ZDFB06 IN WHICH THE METHYL GROUPS OF THE THYMINE BASES WERE REMOVED FROM THE C5 POSITIONS.' # _atom_sites.entry_id 1D41 _atom_sites.fract_transf_matrix[1][1] 0.056117 _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] 0.032852 _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] 0.022462 _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_