data_4MGW # _entry.id 4MGW # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 4MGW pdb_00004mgw 10.2210/pdb4mgw/pdb NDB NA2716 ? ? RCSB RCSB081895 ? ? WWPDB D_1000081895 ? ? # 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 2013-11-06 2 'Structure model' 1 1 2013-12-11 3 'Structure model' 1 2 2024-02-28 # _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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_struct_conn_angle 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.value' 10 3 'Structure model' '_struct_conn.conn_type_id' 11 3 'Structure model' '_struct_conn.id' 12 3 'Structure model' '_struct_conn.pdbx_dist_value' 13 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 14 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 15 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 16 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 17 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 18 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 19 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 20 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 21 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 22 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 23 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 24 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 25 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 26 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 27 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 28 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 29 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 30 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4MGW _pdbx_database_status.recvd_initial_deposition_date 2013-08-29 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Theruvathu, J.A.' 1 'Whitney, Y.' 2 'Montgomery Pettitt, B.' 3 'Sowers, L.C.' 4 # _citation.id primary _citation.title 'Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence.' _citation.journal_abbrev Biochemistry _citation.journal_volume 52 _citation.page_first 8590 _citation.page_last 8598 _citation.year 2013 _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 24147911 _citation.pdbx_database_id_DOI 10.1021/bi400980c # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Theruvathu, J.A.' 1 ? primary 'Yin, Y.W.' 2 ? primary 'Pettitt, B.M.' 3 ? primary 'Sowers, L.C.' 4 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'ClC containing Dickerson-Drew dodecamer' 3695.821 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 water nat water 18.015 38 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(2GF)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGXGAATTCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 2GF n 1 4 DG n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 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 2GF 'DNA linking' . '[(2R,5R)-5-(4-amino-5-chloro-2-oxopyrimidin-1(2H)-yl)-3-oxotetrahydrofuran-2-yl]methyl dihydrogen phosphate' ;5-CHLORO DEOXYCYTIDINE-5'-MONOPHOSPHATE ; 'C9 H11 Cl N3 O7 P' 339.626 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 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_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 2GF 3 3 3 2GF CLC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 DG DG A . n B 1 1 DC 1 13 13 DC DC B . n B 1 2 DG 2 14 14 DG DG B . n B 1 3 2GF 3 15 15 2GF CLC B . n B 1 4 DG 4 16 16 DG DG B . n B 1 5 DA 5 17 17 DA DA B . n B 1 6 DA 6 18 18 DA DA B . n B 1 7 DT 7 19 19 DT DT B . n B 1 8 DT 8 20 20 DT DT B . n B 1 9 DC 9 21 21 DC DC B . n B 1 10 DG 10 22 22 DG DG B . n B 1 11 DC 11 23 23 DC DC B . n B 1 12 DG 12 24 24 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 MG 1 101 25 MG MG A . D 3 HOH 1 201 1 HOH HOH A . D 3 HOH 2 202 4 HOH HOH A . D 3 HOH 3 203 5 HOH HOH A . D 3 HOH 4 204 7 HOH HOH A . D 3 HOH 5 205 11 HOH HOH A . D 3 HOH 6 206 12 HOH HOH A . D 3 HOH 7 207 16 HOH HOH A . D 3 HOH 8 208 17 HOH HOH A . D 3 HOH 9 209 18 HOH HOH A . D 3 HOH 10 210 20 HOH HOH A . D 3 HOH 11 211 21 HOH HOH A . D 3 HOH 12 212 26 HOH HOH A . D 3 HOH 13 213 27 HOH HOH A . D 3 HOH 14 214 29 HOH HOH A . D 3 HOH 15 215 31 HOH HOH A . D 3 HOH 16 216 32 HOH HOH A . D 3 HOH 17 217 33 HOH HOH A . D 3 HOH 18 218 36 HOH HOH A . D 3 HOH 19 219 37 HOH HOH A . E 3 HOH 1 101 2 HOH HOH B . E 3 HOH 2 102 3 HOH HOH B . E 3 HOH 3 103 6 HOH HOH B . E 3 HOH 4 104 8 HOH HOH B . E 3 HOH 5 105 9 HOH HOH B . E 3 HOH 6 106 10 HOH HOH B . E 3 HOH 7 107 13 HOH HOH B . E 3 HOH 8 108 14 HOH HOH B . E 3 HOH 9 109 15 HOH HOH B . E 3 HOH 10 110 19 HOH HOH B . E 3 HOH 11 111 22 HOH HOH B . E 3 HOH 12 112 23 HOH HOH B . E 3 HOH 13 113 24 HOH HOH B . E 3 HOH 14 114 25 HOH HOH B . E 3 HOH 15 115 28 HOH HOH B . E 3 HOH 16 116 30 HOH HOH B . E 3 HOH 17 117 34 HOH HOH B . E 3 HOH 18 118 35 HOH HOH B . E 3 HOH 19 119 38 HOH HOH B . # _software.name PHENIX _software.classification refinement _software.version '(phenix.refine: 1.8.1_1168)' _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 4MGW _cell.length_a 24.629 _cell.length_b 39.918 _cell.length_c 65.364 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 4MGW _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 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4MGW _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.17 _exptl_crystal.density_percent_sol 43.41 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 290 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details '35-40% 2-methyl-2,4-pentanediol (MPD), 5-10 mM spermine and 5-10 mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-ID _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.00 # _reflns.entry_id 4MGW _reflns.observed_criterion_sigma_I 2 _reflns.observed_criterion_sigma_F 2 _reflns.d_resolution_low 10 _reflns.d_resolution_high 1.93 _reflns.number_obs 4411 _reflns.number_all 4411 _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _refine.entry_id 4MGW _refine.ls_number_reflns_obs 4395 _refine.ls_number_reflns_all 4411 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.34 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 9.995 _refine.ls_d_res_high 1.930 _refine.ls_percent_reflns_obs 85.06 _refine.ls_R_factor_obs 0.1989 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1957 _refine.ls_R_factor_R_free 0.2629 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.01 _refine.ls_number_reflns_R_free 220 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _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 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details Random _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.22 _refine.pdbx_overall_phase_error 32.45 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 488 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 38 _refine_hist.number_atoms_total 527 _refine_hist.d_res_high 1.930 _refine_hist.d_res_low 9.995 # 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_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.010 ? ? 546 ? 'X-RAY DIFFRACTION' f_angle_d 1.985 ? ? 840 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 32.361 ? ? 228 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.060 ? ? 90 ? 'X-RAY DIFFRACTION' f_plane_restr 0.009 ? ? 26 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id . 1.9302 2.4261 2006 0.2662 83.00 0.3770 . . 104 . . . . 'X-RAY DIFFRACTION' . 2.4261 9.9950 2169 0.1791 87.00 0.2360 . . 116 . . . . 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 4MGW _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 4MGW _struct.title 'Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4MGW _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA dodecamer, Structural study of DNA, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4MGW _struct_ref.pdbx_db_accession 4MGW _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 4MGW A 1 ? 12 ? 4MGW 1 ? 12 ? 1 12 2 1 4MGW B 1 ? 12 ? 4MGW 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1200 ? 1 MORE -9 ? 1 'SSA (A^2)' 4600 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DG 2 "O3'" ? ? ? 1_555 A 2GF 3 P ? ? A DG 2 A 2GF 3 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale2 covale one ? A 2GF 3 "O3'" ? ? ? 1_555 A DG 4 P ? ? A 2GF 3 A DG 4 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale3 covale both ? B DG 2 "O3'" ? ? ? 1_555 B 2GF 3 P ? ? B DG 14 B 2GF 15 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale4 covale one ? B 2GF 3 "O3'" ? ? ? 1_555 B DG 4 P ? ? B 2GF 15 B DG 16 1_555 ? ? ? ? ? ? ? 1.594 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 201 1_555 ? ? ? ? ? ? ? 1.819 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 212 1_555 ? ? ? ? ? ? ? 1.987 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 213 1_555 ? ? ? ? ? ? ? 2.126 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 B HOH 101 1_555 ? ? ? ? ? ? ? 1.840 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 B HOH 102 1_555 ? ? ? ? ? ? ? 1.823 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 B HOH 115 1_555 ? ? ? ? ? ? ? 2.086 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 212 ? 1_555 88.5 ? 2 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 213 ? 1_555 96.1 ? 3 O ? D HOH . ? A HOH 212 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? D HOH . ? A HOH 213 ? 1_555 84.8 ? 4 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 101 ? 1_555 85.1 ? 5 O ? D HOH . ? A HOH 212 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 101 ? 1_555 91.0 ? 6 O ? D HOH . ? A HOH 213 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 101 ? 1_555 175.6 ? 7 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 102 ? 1_555 170.9 ? 8 O ? D HOH . ? A HOH 212 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 102 ? 1_555 87.0 ? 9 O ? D HOH . ? A HOH 213 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 102 ? 1_555 91.3 ? 10 O ? E HOH . ? B HOH 101 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 102 ? 1_555 87.2 ? 11 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 115 ? 1_555 94.4 ? 12 O ? D HOH . ? A HOH 212 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 115 ? 1_555 175.5 ? 13 O ? D HOH . ? A HOH 213 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 115 ? 1_555 91.5 ? 14 O ? E HOH . ? B HOH 101 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 115 ? 1_555 92.6 ? 15 O ? E HOH . ? B HOH 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 115 ? 1_555 90.6 ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id MG _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE MG A 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 HOH D . ? HOH A 201 . ? 1_555 ? 2 AC1 6 HOH D . ? HOH A 212 . ? 1_555 ? 3 AC1 6 HOH D . ? HOH A 213 . ? 1_555 ? 4 AC1 6 HOH E . ? HOH B 101 . ? 1_555 ? 5 AC1 6 HOH E . ? HOH B 102 . ? 1_555 ? 6 AC1 6 HOH E . ? HOH B 115 . ? 1_555 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OP1 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 DA _pdbx_validate_close_contact.auth_seq_id_1 5 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 208 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.15 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "O3'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DC _pdbx_validate_rmsd_bond.auth_seq_id_1 13 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C3'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DC _pdbx_validate_rmsd_bond.auth_seq_id_2 13 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.381 _pdbx_validate_rmsd_bond.bond_target_value 1.419 _pdbx_validate_rmsd_bond.bond_deviation -0.038 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.006 _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 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 100.57 108.00 -7.43 0.70 N 2 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 111.22 108.30 2.92 0.30 N 3 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? N1 A DC 11 ? ? 103.38 108.00 -4.62 0.70 N 4 1 "O4'" B DT 19 ? ? "C1'" B DT 19 ? ? N1 B DT 19 ? ? 103.76 108.00 -4.24 0.70 N 5 1 "O4'" B DC 21 ? ? "C1'" B DC 21 ? ? N1 B DC 21 ? ? 102.42 108.00 -5.58 0.70 N # 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 2GF P P N N 1 2GF OP1 O N N 2 2GF OP2 O N N 3 2GF "O5'" O N N 4 2GF "C5'" C N N 5 2GF "C4'" C N R 6 2GF "O4'" O N N 7 2GF "C3'" C N N 8 2GF "O3'" O N N 9 2GF "C2'" C N N 10 2GF "C1'" C N R 11 2GF N1 N N N 12 2GF C2 C N N 13 2GF O2 O N N 14 2GF N3 N N N 15 2GF C4 C N N 16 2GF N4 N N N 17 2GF C5 C N N 18 2GF C6 C N N 19 2GF CL CL N N 20 2GF H1 H N N 21 2GF "H5'1" H N N 22 2GF "H5'2" H N N 23 2GF "H4'" H N N 24 2GF "H2'2" H N N 25 2GF "H2'" H N N 26 2GF "H1'" H N N 27 2GF H42 H N N 28 2GF H41 H N N 29 2GF H6 H N N 30 2GF OP3 O N N 31 2GF H4 H N N 32 DA OP3 O N N 33 DA P P N N 34 DA OP1 O N N 35 DA OP2 O N N 36 DA "O5'" O N N 37 DA "C5'" C N N 38 DA "C4'" C N R 39 DA "O4'" O N N 40 DA "C3'" C N S 41 DA "O3'" O N N 42 DA "C2'" C N N 43 DA "C1'" C N R 44 DA N9 N Y N 45 DA C8 C Y N 46 DA N7 N Y N 47 DA C5 C Y N 48 DA C6 C Y N 49 DA N6 N N N 50 DA N1 N Y N 51 DA C2 C Y N 52 DA N3 N Y N 53 DA C4 C Y N 54 DA HOP3 H N N 55 DA HOP2 H N N 56 DA "H5'" H N N 57 DA "H5''" H N N 58 DA "H4'" H N N 59 DA "H3'" H N N 60 DA "HO3'" H N N 61 DA "H2'" H N N 62 DA "H2''" H N N 63 DA "H1'" H N N 64 DA H8 H N N 65 DA H61 H N N 66 DA H62 H N N 67 DA H2 H N N 68 DC OP3 O N N 69 DC P P N N 70 DC OP1 O N N 71 DC OP2 O N N 72 DC "O5'" O N N 73 DC "C5'" C N N 74 DC "C4'" C N R 75 DC "O4'" O N N 76 DC "C3'" C N S 77 DC "O3'" O N N 78 DC "C2'" C N N 79 DC "C1'" C N R 80 DC N1 N N N 81 DC C2 C N N 82 DC O2 O N N 83 DC N3 N N N 84 DC C4 C N N 85 DC N4 N N N 86 DC C5 C N N 87 DC C6 C N N 88 DC HOP3 H N N 89 DC HOP2 H N N 90 DC "H5'" H N N 91 DC "H5''" H N N 92 DC "H4'" H N N 93 DC "H3'" H N N 94 DC "HO3'" H N N 95 DC "H2'" H N N 96 DC "H2''" H N N 97 DC "H1'" H N N 98 DC H41 H N N 99 DC H42 H N N 100 DC H5 H N N 101 DC H6 H N N 102 DG OP3 O N N 103 DG P P N N 104 DG OP1 O N N 105 DG OP2 O N N 106 DG "O5'" O N N 107 DG "C5'" C N N 108 DG "C4'" C N R 109 DG "O4'" O N N 110 DG "C3'" C N S 111 DG "O3'" O N N 112 DG "C2'" C N N 113 DG "C1'" C N R 114 DG N9 N Y N 115 DG C8 C Y N 116 DG N7 N Y N 117 DG C5 C Y N 118 DG C6 C N N 119 DG O6 O N N 120 DG N1 N N N 121 DG C2 C N N 122 DG N2 N N N 123 DG N3 N N N 124 DG C4 C Y N 125 DG HOP3 H N N 126 DG HOP2 H N N 127 DG "H5'" H N N 128 DG "H5''" H N N 129 DG "H4'" H N N 130 DG "H3'" H N N 131 DG "HO3'" H N N 132 DG "H2'" H N N 133 DG "H2''" H N N 134 DG "H1'" H N N 135 DG H8 H N N 136 DG H1 H N N 137 DG H21 H N N 138 DG H22 H N N 139 DT OP3 O N N 140 DT P P N N 141 DT OP1 O N N 142 DT OP2 O N N 143 DT "O5'" O N N 144 DT "C5'" C N N 145 DT "C4'" C N R 146 DT "O4'" O N N 147 DT "C3'" C N S 148 DT "O3'" O N N 149 DT "C2'" C N N 150 DT "C1'" C N R 151 DT N1 N N N 152 DT C2 C N N 153 DT O2 O N N 154 DT N3 N N N 155 DT C4 C N N 156 DT O4 O N N 157 DT C5 C N N 158 DT C7 C N N 159 DT C6 C N N 160 DT HOP3 H N N 161 DT HOP2 H N N 162 DT "H5'" H N N 163 DT "H5''" H N N 164 DT "H4'" H N N 165 DT "H3'" H N N 166 DT "HO3'" H N N 167 DT "H2'" H N N 168 DT "H2''" H N N 169 DT "H1'" H N N 170 DT H3 H N N 171 DT H71 H N N 172 DT H72 H N N 173 DT H73 H N N 174 DT H6 H N N 175 HOH O O N N 176 HOH H1 H N N 177 HOH H2 H N N 178 MG MG MG N N 179 # 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 2GF O2 C2 doub N N 1 2GF "O4'" "C4'" sing N N 2 2GF "O4'" "C1'" sing N N 3 2GF "C4'" "C5'" sing N N 4 2GF "C4'" "C3'" sing N N 5 2GF "C5'" "O5'" sing N N 6 2GF C2 N3 sing N N 7 2GF C2 N1 sing N N 8 2GF "C1'" N1 sing N N 9 2GF "C1'" "C2'" sing N N 10 2GF N3 C4 doub N N 11 2GF OP1 P sing N N 12 2GF N1 C6 sing N N 13 2GF P "O5'" sing N N 14 2GF P OP2 doub N N 15 2GF "C3'" "O3'" doub N N 16 2GF "C3'" "C2'" sing N N 17 2GF C4 N4 sing N N 18 2GF C4 C5 sing N N 19 2GF C6 C5 doub N N 20 2GF C5 CL sing N N 21 2GF OP1 H1 sing N N 22 2GF "C5'" "H5'1" sing N N 23 2GF "C5'" "H5'2" sing N N 24 2GF "C4'" "H4'" sing N N 25 2GF "C2'" "H2'2" sing N N 26 2GF "C2'" "H2'" sing N N 27 2GF "C1'" "H1'" sing N N 28 2GF N4 H42 sing N N 29 2GF N4 H41 sing N N 30 2GF C6 H6 sing N N 31 2GF P OP3 sing N N 32 2GF OP3 H4 sing N N 33 DA OP3 P sing N N 34 DA OP3 HOP3 sing N N 35 DA P OP1 doub N N 36 DA P OP2 sing N N 37 DA P "O5'" sing N N 38 DA OP2 HOP2 sing N N 39 DA "O5'" "C5'" sing N N 40 DA "C5'" "C4'" sing N N 41 DA "C5'" "H5'" sing N N 42 DA "C5'" "H5''" sing N N 43 DA "C4'" "O4'" sing N N 44 DA "C4'" "C3'" sing N N 45 DA "C4'" "H4'" sing N N 46 DA "O4'" "C1'" sing N N 47 DA "C3'" "O3'" sing N N 48 DA "C3'" "C2'" sing N N 49 DA "C3'" "H3'" sing N N 50 DA "O3'" "HO3'" sing N N 51 DA "C2'" "C1'" sing N N 52 DA "C2'" "H2'" sing N N 53 DA "C2'" "H2''" sing N N 54 DA "C1'" N9 sing N N 55 DA "C1'" "H1'" sing N N 56 DA N9 C8 sing Y N 57 DA N9 C4 sing Y N 58 DA C8 N7 doub Y N 59 DA C8 H8 sing N N 60 DA N7 C5 sing Y N 61 DA C5 C6 sing Y N 62 DA C5 C4 doub Y N 63 DA C6 N6 sing N N 64 DA C6 N1 doub Y N 65 DA N6 H61 sing N N 66 DA N6 H62 sing N N 67 DA N1 C2 sing Y N 68 DA C2 N3 doub Y N 69 DA C2 H2 sing N N 70 DA N3 C4 sing Y N 71 DC OP3 P sing N N 72 DC OP3 HOP3 sing N N 73 DC P OP1 doub N N 74 DC P OP2 sing N N 75 DC P "O5'" sing N N 76 DC OP2 HOP2 sing N N 77 DC "O5'" "C5'" sing N N 78 DC "C5'" "C4'" sing N N 79 DC "C5'" "H5'" sing N N 80 DC "C5'" "H5''" sing N N 81 DC "C4'" "O4'" sing N N 82 DC "C4'" "C3'" sing N N 83 DC "C4'" "H4'" sing N N 84 DC "O4'" "C1'" sing N N 85 DC "C3'" "O3'" sing N N 86 DC "C3'" "C2'" sing N N 87 DC "C3'" "H3'" sing N N 88 DC "O3'" "HO3'" sing N N 89 DC "C2'" "C1'" sing N N 90 DC "C2'" "H2'" sing N N 91 DC "C2'" "H2''" sing N N 92 DC "C1'" N1 sing N N 93 DC "C1'" "H1'" sing N N 94 DC N1 C2 sing N N 95 DC N1 C6 sing N N 96 DC C2 O2 doub N N 97 DC C2 N3 sing N N 98 DC N3 C4 doub N N 99 DC C4 N4 sing N N 100 DC C4 C5 sing N N 101 DC N4 H41 sing N N 102 DC N4 H42 sing N N 103 DC C5 C6 doub N N 104 DC C5 H5 sing N N 105 DC C6 H6 sing N N 106 DG OP3 P sing N N 107 DG OP3 HOP3 sing N N 108 DG P OP1 doub N N 109 DG P OP2 sing N N 110 DG P "O5'" sing N N 111 DG OP2 HOP2 sing N N 112 DG "O5'" "C5'" sing N N 113 DG "C5'" "C4'" sing N N 114 DG "C5'" "H5'" sing N N 115 DG "C5'" "H5''" sing N N 116 DG "C4'" "O4'" sing N N 117 DG "C4'" "C3'" sing N N 118 DG "C4'" "H4'" sing N N 119 DG "O4'" "C1'" sing N N 120 DG "C3'" "O3'" sing N N 121 DG "C3'" "C2'" sing N N 122 DG "C3'" "H3'" sing N N 123 DG "O3'" "HO3'" sing N N 124 DG "C2'" "C1'" sing N N 125 DG "C2'" "H2'" sing N N 126 DG "C2'" "H2''" sing N N 127 DG "C1'" N9 sing N N 128 DG "C1'" "H1'" sing N N 129 DG N9 C8 sing Y N 130 DG N9 C4 sing Y N 131 DG C8 N7 doub Y N 132 DG C8 H8 sing N N 133 DG N7 C5 sing Y N 134 DG C5 C6 sing N N 135 DG C5 C4 doub Y N 136 DG C6 O6 doub N N 137 DG C6 N1 sing N N 138 DG N1 C2 sing N N 139 DG N1 H1 sing N N 140 DG C2 N2 sing N N 141 DG C2 N3 doub N N 142 DG N2 H21 sing N N 143 DG N2 H22 sing N N 144 DG N3 C4 sing N N 145 DT OP3 P sing N N 146 DT OP3 HOP3 sing N N 147 DT P OP1 doub N N 148 DT P OP2 sing N N 149 DT P "O5'" sing N N 150 DT OP2 HOP2 sing N N 151 DT "O5'" "C5'" sing N N 152 DT "C5'" "C4'" sing N N 153 DT "C5'" "H5'" sing N N 154 DT "C5'" "H5''" sing N N 155 DT "C4'" "O4'" sing N N 156 DT "C4'" "C3'" sing N N 157 DT "C4'" "H4'" sing N N 158 DT "O4'" "C1'" sing N N 159 DT "C3'" "O3'" sing N N 160 DT "C3'" "C2'" sing N N 161 DT "C3'" "H3'" sing N N 162 DT "O3'" "HO3'" sing N N 163 DT "C2'" "C1'" sing N N 164 DT "C2'" "H2'" sing N N 165 DT "C2'" "H2''" sing N N 166 DT "C1'" N1 sing N N 167 DT "C1'" "H1'" sing N N 168 DT N1 C2 sing N N 169 DT N1 C6 sing N N 170 DT C2 O2 doub N N 171 DT C2 N3 sing N N 172 DT N3 C4 sing N N 173 DT N3 H3 sing N N 174 DT C4 O4 doub N N 175 DT C4 C5 sing N N 176 DT C5 C7 sing N N 177 DT C5 C6 doub N N 178 DT C7 H71 sing N N 179 DT C7 H72 sing N N 180 DT C7 H73 sing N N 181 DT C6 H6 sing N N 182 HOH O H1 sing N N 183 HOH O H2 sing N N 184 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4MGW 'double helix' 4MGW 'b-form double helix' 4MGW 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 12 1_555 0.358 -0.128 0.196 5.256 -16.147 -0.707 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.283 -0.193 0.504 6.053 -11.747 -3.634 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.262 -0.001 -0.051 9.386 -9.299 0.128 3 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 -0.039 -0.023 -0.070 8.738 -19.341 2.895 4 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.081 -0.019 0.122 1.730 -15.356 2.564 5 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 0.205 -0.135 0.191 -1.983 -16.424 1.444 6 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.242 -0.047 -0.085 1.063 -14.791 -1.249 7 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.334 -0.049 0.014 -12.307 -9.021 -0.035 8 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.039 -0.262 0.462 5.519 -20.145 -3.154 9 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.688 -0.243 -0.170 11.697 27.239 -2.334 10 A_DG12:DC13_B A 12 ? B 13 ? 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 12 1_555 A DG 2 1_555 B DC 11 1_555 -0.363 -0.036 3.271 -2.896 3.053 32.831 -0.580 0.146 3.273 5.374 5.098 33.092 1 AA_DC1DG2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DG 4 1_555 B DC 9 1_555 -0.198 0.637 6.723 1.302 5.495 67.658 0.140 0.279 6.747 4.926 -1.167 67.865 2 AA_DG2DG4:DC21DC23_BB A 2 ? B 23 ? A 4 ? B 21 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 5 1_555 B DT 8 1_555 -0.077 0.111 3.250 -0.263 2.592 38.521 -0.150 0.084 3.251 3.924 0.399 38.606 3 AA_DG4DA5:DT20DC21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 0.066 -0.418 3.332 -2.220 1.783 36.431 -0.917 -0.416 3.299 2.847 3.545 36.538 4 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 -0.098 -0.639 3.253 -0.033 -1.012 33.841 -0.936 0.163 3.271 -1.738 0.056 33.855 5 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.132 -0.387 3.139 2.941 -3.711 32.580 -0.073 0.718 3.139 -6.571 -5.208 32.913 6 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DC 9 1_555 B DG 4 1_555 0.068 -0.183 3.538 1.676 0.011 45.055 -0.240 0.074 3.538 0.014 -2.187 45.085 7 AA_DT8DC9:DG16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DC 9 1_555 B DG 4 1_555 A DC 11 1_555 B DG 2 1_555 -0.133 0.693 6.434 -5.012 -6.523 68.564 1.081 -0.243 6.349 -5.769 4.433 68.996 8 AA_DC9DC11:DG14DG16_BB A 9 ? B 16 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 1.273 0.315 3.513 5.245 -15.586 30.973 3.084 -1.256 3.171 -26.937 -9.064 34.973 9 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _atom_sites.entry_id 4MGW _atom_sites.fract_transf_matrix[1][1] 0.040603 _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] 0.025051 _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] 0.015299 _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 CL H MG N O P # loop_