data_4GJU # _entry.id 4GJU # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 4GJU pdb_00004gju 10.2210/pdb4gju/pdb NDB NA1970 ? ? RCSB RCSB074273 ? ? WWPDB D_1000074273 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4GJU _pdbx_database_status.recvd_initial_deposition_date 2012-08-10 _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 'Spingler, B.' 1 'Renciuk, D.' 2 'Vorlickova, M.' 3 # _citation.id primary _citation.title 'Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 41 _citation.page_first 9891 _citation.page_last 9900 _citation.year 2013 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23963698 _citation.pdbx_database_id_DOI 10.1093/nar/gkt738 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Renciuk, D.' 1 ? primary 'Blacque, O.' 2 ? primary 'Vorlickova, M.' 3 ? primary 'Spingler, B.' 4 ? # _cell.entry_id 4GJU _cell.length_a 25.495 _cell.length_b 40.400 _cell.length_c 65.500 _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 4GJU _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 ? # 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 '5-Methylcytosine modified DNA oligomer' 3677.419 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 water nat water 18.015 127 ? ? ? ? # _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)(5CM)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # 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 5CM 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 # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'Synthetic DNA' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4GJU _struct_ref.pdbx_db_accession 4GJU _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 4GJU A 1 ? 12 ? 4GJU 1 ? 12 ? 1 12 2 1 4GJU B 1 ? 12 ? 4GJU 1 ? 12 ? 1 12 # 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 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 # _exptl.entry_id 4GJU _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.29 _exptl_crystal.density_percent_sol 46.36 _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 298.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details ;0.04M sodium cacodylate buffer, 0.08M NaCl, 0.02M MgCl2, 0.012M spermine tetra hydrochloride, 35% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K ; _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 PIXEL _diffrn_detector.type 'DECTRIS PILATUS 2M-F' _diffrn_detector.pdbx_collection_date 2012-06-09 _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 'BARTELS MONOCHROMATOR' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00067 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SLS BEAMLINE X06DA' _diffrn_source.pdbx_synchrotron_site SLS _diffrn_source.pdbx_synchrotron_beamline X06DA _diffrn_source.pdbx_wavelength 1.00067 _diffrn_source.pdbx_wavelength_list 1.00067 # _reflns.entry_id 4GJU _reflns.observed_criterion_sigma_I 2 _reflns.observed_criterion_sigma_F 4 _reflns.d_resolution_low 40.40 _reflns.d_resolution_high 1.412 _reflns.number_obs 22852 _reflns.number_all 24635 _reflns.percent_possible_obs 92.8 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 30.59 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.61 _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 # _reflns_shell.d_res_high 1.412 _reflns_shell.d_res_low 1.50 _reflns_shell.percent_possible_all 97.1 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 8.12 _reflns_shell.pdbx_redundancy 3.72 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 3958 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4GJU _refine.ls_number_reflns_obs 22852 _refine.ls_number_reflns_all 24635 _refine.pdbx_ls_sigma_I 2 _refine.pdbx_ls_sigma_F 4 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 40.4 _refine.ls_d_res_high 1.412 _refine.ls_percent_reflns_obs 92.8 _refine.ls_R_factor_obs 0.177 _refine.ls_R_factor_all 0.178 _refine.ls_R_factor_R_work 0.177 _refine.ls_R_factor_R_free 0.215 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.013 _refine.ls_number_reflns_R_free 1235 _refine.ls_number_parameters 4907 _refine.ls_number_restraints 10677 _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 ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 1DPN' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'KLOSTERMAN & SINES' _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 ? _refine.pdbx_overall_phase_error ? _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_analyze.entry_id 4GJU _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 0 _refine_analyze.occupancy_sum_hydrogen 0. _refine_analyze.occupancy_sum_non_hydrogen 611.0 _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 127 _refine_hist.number_atoms_total 616 _refine_hist.d_res_high 1.412 _refine_hist.d_res_low 40.4 # 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 s_bond_d 0.0183 ? ? ? ? 'X-RAY DIFFRACTION' s_angle_d 0.0388 ? ? ? ? 'X-RAY DIFFRACTION' s_similar_dist 0.0000 ? ? ? ? 'X-RAY DIFFRACTION' s_from_restr_planes 0.0636 ? ? ? ? 'X-RAY DIFFRACTION' s_zero_chiral_vol 0.0000 ? ? ? ? 'X-RAY DIFFRACTION' s_non_zero_chiral_vol 0.0156 ? ? ? ? 'X-RAY DIFFRACTION' s_anti_bump_dis_restr 0.0141 ? ? ? ? 'X-RAY DIFFRACTION' s_rigid_bond_adp_cmpnt 0.0120 ? ? ? ? 'X-RAY DIFFRACTION' s_similar_adp_cmpnt 0.0262 ? ? ? ? 'X-RAY DIFFRACTION' s_approx_iso_adps 0.0000 ? ? ? ? 'X-RAY DIFFRACTION' # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 4GJU _pdbx_refine.R_factor_all_no_cutoff 0.178 _pdbx_refine.R_factor_obs_no_cutoff 0.177 _pdbx_refine.free_R_factor_no_cutoff 0.215 _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 5.013 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 1235 _pdbx_refine.R_factor_all_4sig_cutoff 0.176 _pdbx_refine.R_factor_obs_4sig_cutoff 0.174 _pdbx_refine.free_R_factor_4sig_cutoff 0.210 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 5.010 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 1145 _pdbx_refine.number_reflns_obs_4sig_cutoff 22852 # _struct.entry_id 4GJU _struct.title '5-Methylcytosine modified DNA oligomer' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4GJU _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'double-stranded B-DNA, 5-Methylcytosine, epigenetics, 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_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 5CM 3 P ? ? A DG 2 A 5CM 3 1_555 ? ? ? ? ? ? ? 1.571 ? ? covale2 covale both ? A 5CM 3 "O3'" ? ? ? 1_555 A DG 4 P ? ? A 5CM 3 A DG 4 1_555 ? ? ? ? ? ? ? 1.562 ? ? covale3 covale both ? B DG 2 "O3'" ? ? ? 1_555 B 5CM 3 P ? ? B DG 2 B 5CM 3 1_555 ? ? ? ? ? ? ? 1.628 ? ? covale4 covale both ? B 5CM 3 "O3'" ? ? ? 1_555 B DG 4 P ? ? B 5CM 3 B DG 4 1_555 ? ? ? ? ? ? ? 1.577 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 201 1_555 ? ? ? ? ? ? ? 2.075 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 101 A HOH 202 1_555 ? ? ? ? ? ? ? 2.058 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 B HOH 101 1_555 ? ? ? ? ? ? ? 2.036 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 B HOH 102 1_555 ? ? ? ? ? ? ? 2.055 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 B HOH 103 1_555 ? ? ? ? ? ? ? 2.069 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 101 B HOH 104 1_555 ? ? ? ? ? ? ? 2.022 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A 5CM 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A 5CM 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A 5CM 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A 5CM 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A 5CM 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A 5CM 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B 5CM 3 N3 ? ? A DG 10 B 5CM 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B 5CM 3 O2 ? ? A DG 10 B 5CM 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B 5CM 3 N4 ? ? A DG 10 B 5CM 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # _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 202 . ? 1_555 ? 3 AC1 6 HOH E . ? HOH B 101 . ? 1_555 ? 4 AC1 6 HOH E . ? HOH B 102 . ? 1_555 ? 5 AC1 6 HOH E . ? HOH B 103 . ? 1_555 ? 6 AC1 6 HOH E . ? HOH B 104 . ? 1_555 ? # _database_PDB_matrix.entry_id 4GJU _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _atom_sites.entry_id 4GJU _atom_sites.fract_transf_matrix[1][1] 0.039223 _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] 0.024752 _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] 0.015267 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C MG N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 5CM 3 3 3 5CM 5CM A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 DG 10 10 10 DG G A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 DC 1 1 1 DC C B . n B 1 2 DG 2 2 2 DG G B . n B 1 3 5CM 3 3 3 5CM 5CM B . n B 1 4 DG 4 4 4 DG G B . n B 1 5 DA 5 5 5 DA A B . n B 1 6 DA 6 6 6 DA A B . n B 1 7 DT 7 7 7 DT T B . n B 1 8 DT 8 8 8 DT T B . n B 1 9 DC 9 9 9 DC C B . n B 1 10 DG 10 10 10 DG G B . n B 1 11 DC 11 11 11 DC C B . n B 1 12 DG 12 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 1 101 51 MG MO6 A . D 3 HOH 1 201 51 HOH MO6 A . D 3 HOH 2 202 51 HOH MO6 A . D 3 HOH 3 203 101 HOH HOH A . D 3 HOH 4 204 102 HOH HOH A . D 3 HOH 5 205 104 HOH HOH A . D 3 HOH 6 206 106 HOH HOH A . D 3 HOH 7 207 107 HOH HOH A . D 3 HOH 8 208 108 HOH HOH A . D 3 HOH 9 209 109 HOH HOH A . D 3 HOH 10 210 110 HOH HOH A . D 3 HOH 11 211 111 HOH HOH A . D 3 HOH 12 212 112 HOH HOH A . D 3 HOH 13 213 115 HOH HOH A . D 3 HOH 14 214 116 HOH HOH A . D 3 HOH 15 215 118 HOH HOH A . D 3 HOH 16 216 119 HOH HOH A . D 3 HOH 17 217 121 HOH HOH A . D 3 HOH 18 218 122 HOH HOH A . D 3 HOH 19 219 128 HOH HOH A . D 3 HOH 20 220 129 HOH HOH A . D 3 HOH 21 221 132 HOH HOH A . D 3 HOH 22 222 134 HOH HOH A . D 3 HOH 23 223 136 HOH HOH A . D 3 HOH 24 224 140 HOH HOH A . D 3 HOH 25 225 144 HOH HOH A . D 3 HOH 26 226 145 HOH HOH A . D 3 HOH 27 227 148 HOH HOH A . D 3 HOH 28 228 151 HOH HOH A . D 3 HOH 29 229 152 HOH HOH A . D 3 HOH 30 230 156 HOH HOH A . D 3 HOH 31 231 161 HOH HOH A . D 3 HOH 32 232 162 HOH HOH A . D 3 HOH 33 233 163 HOH HOH A . D 3 HOH 34 234 164 HOH HOH A . D 3 HOH 35 235 166 HOH HOH A . D 3 HOH 36 236 168 HOH HOH A . D 3 HOH 37 237 170 HOH HOH A . D 3 HOH 38 238 174 HOH HOH A . D 3 HOH 39 239 176 HOH HOH A . D 3 HOH 40 240 177 HOH HOH A . D 3 HOH 41 241 178 HOH HOH A . D 3 HOH 42 242 179 HOH HOH A . D 3 HOH 43 243 180 HOH HOH A . D 3 HOH 44 244 181 HOH HOH A . D 3 HOH 45 245 182 HOH HOH A . D 3 HOH 46 246 183 HOH HOH A . D 3 HOH 47 247 184 HOH HOH A . D 3 HOH 48 248 185 HOH HOH A . D 3 HOH 49 249 186 HOH HOH A . D 3 HOH 50 250 187 HOH HOH A . D 3 HOH 51 251 189 HOH HOH A . D 3 HOH 52 252 192 HOH HOH A . D 3 HOH 53 253 193 HOH HOH A . D 3 HOH 54 254 194 HOH HOH A . D 3 HOH 55 255 195 HOH HOH A . D 3 HOH 56 256 196 HOH HOH A . D 3 HOH 57 257 197 HOH HOH A . D 3 HOH 58 258 200 HOH HOH A . D 3 HOH 59 259 201 HOH HOH A . D 3 HOH 60 260 205 HOH HOH A . D 3 HOH 61 261 206 HOH HOH A . D 3 HOH 62 262 210 HOH HOH A . D 3 HOH 63 263 212 HOH HOH A . D 3 HOH 64 264 213 HOH HOH A . D 3 HOH 65 265 214 HOH HOH A . D 3 HOH 66 266 215 HOH HOH A . D 3 HOH 67 267 216 HOH HOH A . D 3 HOH 68 268 220 HOH HOH A . D 3 HOH 69 269 221 HOH HOH A . E 3 HOH 1 101 51 HOH MO6 B . E 3 HOH 2 102 51 HOH MO6 B . E 3 HOH 3 103 51 HOH MO6 B . E 3 HOH 4 104 51 HOH MO6 B . E 3 HOH 5 105 103 HOH HOH B . E 3 HOH 6 106 105 HOH HOH B . E 3 HOH 7 107 113 HOH HOH B . E 3 HOH 8 108 114 HOH HOH B . E 3 HOH 9 109 117 HOH HOH B . E 3 HOH 10 110 120 HOH HOH B . E 3 HOH 11 111 123 HOH HOH B . E 3 HOH 12 112 124 HOH HOH B . E 3 HOH 13 113 125 HOH HOH B . E 3 HOH 14 114 126 HOH HOH B . E 3 HOH 15 115 127 HOH HOH B . E 3 HOH 16 116 130 HOH HOH B . E 3 HOH 17 117 131 HOH HOH B . E 3 HOH 18 118 133 HOH HOH B . E 3 HOH 19 119 135 HOH HOH B . E 3 HOH 20 120 137 HOH HOH B . E 3 HOH 21 121 138 HOH HOH B . E 3 HOH 22 122 139 HOH HOH B . E 3 HOH 23 123 141 HOH HOH B . E 3 HOH 24 124 142 HOH HOH B . E 3 HOH 25 125 143 HOH HOH B . E 3 HOH 26 126 146 HOH HOH B . E 3 HOH 27 127 147 HOH HOH B . E 3 HOH 28 128 149 HOH HOH B . E 3 HOH 29 129 150 HOH HOH B . E 3 HOH 30 130 153 HOH HOH B . E 3 HOH 31 131 154 HOH HOH B . E 3 HOH 32 132 155 HOH HOH B . E 3 HOH 33 133 157 HOH HOH B . E 3 HOH 34 134 158 HOH HOH B . E 3 HOH 35 135 159 HOH HOH B . E 3 HOH 36 136 160 HOH HOH B . E 3 HOH 37 137 165 HOH HOH B . E 3 HOH 38 138 167 HOH HOH B . E 3 HOH 39 139 169 HOH HOH B . E 3 HOH 40 140 171 HOH HOH B . E 3 HOH 41 141 172 HOH HOH B . E 3 HOH 42 142 173 HOH HOH B . E 3 HOH 43 143 175 HOH HOH B . E 3 HOH 44 144 188 HOH HOH B . E 3 HOH 45 145 190 HOH HOH B . E 3 HOH 46 146 191 HOH HOH B . E 3 HOH 47 147 198 HOH HOH B . E 3 HOH 48 148 199 HOH HOH B . E 3 HOH 49 149 202 HOH HOH B . E 3 HOH 50 150 203 HOH HOH B . E 3 HOH 51 151 204 HOH HOH B . E 3 HOH 52 152 207 HOH HOH B . E 3 HOH 53 153 208 HOH HOH B . E 3 HOH 54 154 209 HOH HOH B . E 3 HOH 55 155 211 HOH HOH B . E 3 HOH 56 156 217 HOH HOH B . E 3 HOH 57 157 218 HOH HOH B . E 3 HOH 58 158 219 HOH HOH B . # 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 3 A 5CM 3 ? DC ? 2 B 5CM 3 B 5CM 3 ? DC ? # _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 # _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 # 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)' 2380 ? 1 MORE 3 ? 1 'SSA (A^2)' 4330 ? # _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 # 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 202 ? 1_555 90.3 ? 2 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 101 ? 1_555 92.1 ? 3 O ? D HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 101 ? 1_555 94.4 ? 4 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 102 ? 1_555 176.4 ? 5 O ? D HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 102 ? 1_555 88.2 ? 6 O ? E HOH . ? B HOH 101 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 102 ? 1_555 84.8 ? 7 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 103 ? 1_555 91.1 ? 8 O ? D HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 103 ? 1_555 84.3 ? 9 O ? E HOH . ? B HOH 101 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 103 ? 1_555 176.5 ? 10 O ? E HOH . ? B HOH 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 103 ? 1_555 92.0 ? 11 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 104 ? 1_555 92.0 ? 12 O ? D HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 104 ? 1_555 171.6 ? 13 O ? E HOH . ? B HOH 101 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 104 ? 1_555 93.7 ? 14 O ? E HOH . ? B HOH 102 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 104 ? 1_555 90.0 ? 15 O ? E HOH . ? B HOH 103 ? 1_555 MG ? C MG . ? A MG 101 ? 1_555 O ? E HOH . ? B HOH 104 ? 1_555 87.5 ? # 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 2013-08-28 2 'Structure model' 1 1 2013-09-04 3 'Structure model' 1 2 2013-12-04 4 'Structure model' 1 3 2023-09-13 # _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' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 '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_initial_refinement_model 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.value' 10 4 'Structure model' '_struct_conn.pdbx_dist_value' 11 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 13 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 15 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 16 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 17 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal RemDAq 'data collection' . ? 1 PHASER phasing . ? 2 SHELXL-97 refinement . ? 3 XDS 'data reduction' . ? 4 XDS 'data scaling' . ? 5 # 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 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? 1.507 1.420 0.087 0.011 N 2 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? 1.495 1.420 0.075 0.011 N 3 1 "O4'" B DT 8 ? ? "C1'" B DT 8 ? ? 1.493 1.420 0.073 0.011 N 4 1 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? 1.487 1.420 0.067 0.011 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 103.23 108.00 -4.77 0.70 N 2 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 102.60 108.00 -5.40 0.70 N 3 1 "C3'" A DG 4 ? ? "O3'" A DG 4 ? ? P A DA 5 ? ? 128.46 119.70 8.76 1.20 Y 4 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 102.14 108.00 -5.86 0.70 N 5 1 C6 A DA 5 ? ? N1 A DA 5 ? ? C2 A DA 5 ? ? 122.81 118.60 4.21 0.60 N 6 1 C5 A DA 5 ? ? C6 A DA 5 ? ? N1 A DA 5 ? ? 113.81 117.70 -3.89 0.50 N 7 1 "C3'" A DA 5 ? ? "O3'" A DA 5 ? ? P A DA 6 ? ? 127.96 119.70 8.26 1.20 Y 8 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 102.31 108.00 -5.69 0.70 N 9 1 C4 A DA 6 ? ? C5 A DA 6 ? ? C6 A DA 6 ? ? 120.32 117.00 3.32 0.50 N 10 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 103.39 108.00 -4.61 0.70 N 11 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? N1 A DT 8 ? ? 101.66 108.00 -6.34 0.70 N 12 1 N3 A DT 8 ? ? C2 A DT 8 ? ? O2 A DT 8 ? ? 118.47 122.30 -3.83 0.60 N 13 1 N1 A DC 9 ? ? "C1'" A DC 9 ? ? "C2'" A DC 9 ? ? 123.59 114.30 9.29 1.40 N 14 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 97.87 108.00 -10.13 0.70 N 15 1 N3 A DC 9 ? ? C4 A DC 9 ? ? C5 A DC 9 ? ? 118.31 121.90 -3.59 0.40 N 16 1 C4 A DC 9 ? ? C5 A DC 9 ? ? C6 A DC 9 ? ? 120.44 117.40 3.04 0.50 N 17 1 "C3'" A DG 10 ? ? "C2'" A DG 10 ? ? "C1'" A DG 10 ? ? 95.94 102.40 -6.46 0.80 N 18 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 110.51 108.30 2.21 0.30 N 19 1 C6 A DG 10 ? ? N1 A DG 10 ? ? C2 A DG 10 ? ? 121.06 125.10 -4.04 0.60 N 20 1 N1 A DC 11 ? ? "C1'" A DC 11 ? ? "C2'" A DC 11 ? ? 123.90 114.30 9.60 1.40 N 21 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? N1 A DC 11 ? ? 99.55 108.00 -8.45 0.70 N 22 1 C6 A DC 11 ? ? N1 A DC 11 ? ? C2 A DC 11 ? ? 117.87 120.30 -2.43 0.40 N 23 1 C2 A DC 11 ? ? N3 A DC 11 ? ? C4 A DC 11 ? ? 115.93 119.90 -3.97 0.50 N 24 1 "C1'" A DG 12 ? ? "O4'" A DG 12 ? ? "C4'" A DG 12 ? ? 115.09 110.30 4.79 0.70 N 25 1 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 102.32 108.00 -5.68 0.70 N 26 1 N3 B DC 1 ? ? C4 B DC 1 ? ? C5 B DC 1 ? ? 125.42 121.90 3.52 0.40 N 27 1 C4 B DC 1 ? ? C5 B DC 1 ? ? C6 B DC 1 ? ? 114.30 117.40 -3.10 0.50 N 28 1 OP1 B DG 2 ? ? P B DG 2 ? ? OP2 B DG 2 ? ? 130.93 119.60 11.33 1.50 N 29 1 P B DG 2 ? ? "O5'" B DG 2 ? ? "C5'" B DG 2 ? ? 109.91 120.90 -10.99 1.60 N 30 1 "O4'" B DG 4 ? ? "C1'" B DG 4 ? ? N9 B DG 4 ? ? 111.22 108.30 2.92 0.30 N 31 1 "C3'" B DG 4 ? ? "O3'" B DG 4 ? ? P B DA 5 ? ? 130.33 119.70 10.63 1.20 Y 32 1 "O4'" B DA 5 ? ? "C1'" B DA 5 ? ? N9 B DA 5 ? ? 98.34 108.00 -9.66 0.70 N 33 1 "O4'" B DA 6 ? ? "C1'" B DA 6 ? ? N9 B DA 6 ? ? 101.65 108.00 -6.35 0.70 N 34 1 "C3'" B DA 6 ? ? "O3'" B DA 6 ? ? P B DT 7 ? ? 127.15 119.70 7.45 1.20 Y 35 1 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? N1 B DT 7 ? ? 102.07 108.00 -5.93 0.70 N 36 1 "O4'" B DT 8 ? ? "C1'" B DT 8 ? ? "C2'" B DT 8 ? ? 100.68 105.90 -5.22 0.80 N 37 1 N1 B DT 8 ? ? "C1'" B DT 8 ? ? "C2'" B DT 8 ? ? 125.57 114.30 11.27 1.40 N 38 1 "O4'" B DT 8 ? ? "C1'" B DT 8 ? ? N1 B DT 8 ? ? 97.14 108.00 -10.86 0.70 N 39 1 P B DC 9 ? ? "O5'" B DC 9 ? ? "C5'" B DC 9 ? ? 111.30 120.90 -9.60 1.60 N 40 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 101.41 108.00 -6.59 0.70 N 41 1 C6 B DC 9 ? ? N1 B DC 9 ? ? C2 B DC 9 ? ? 116.72 120.30 -3.58 0.40 N 42 1 C2 B DC 9 ? ? N3 B DC 9 ? ? C4 B DC 9 ? ? 124.02 119.90 4.12 0.50 N 43 1 N3 B DC 9 ? ? C4 B DC 9 ? ? C5 B DC 9 ? ? 117.28 121.90 -4.62 0.40 N 44 1 C5 B DC 9 ? ? C6 B DC 9 ? ? N1 B DC 9 ? ? 124.27 121.00 3.27 0.50 N 45 1 "C3'" B DG 10 ? ? "C2'" B DG 10 ? ? "C1'" B DG 10 ? ? 95.80 102.40 -6.60 0.80 N 46 1 N9 B DG 10 ? ? C4 B DG 10 ? ? C5 B DG 10 ? ? 102.52 105.40 -2.88 0.40 N 47 1 "O4'" B DC 11 ? ? "C4'" B DC 11 ? ? "C3'" B DC 11 ? ? 100.96 104.50 -3.54 0.40 N 48 1 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 99.44 108.00 -8.56 0.70 N 49 1 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 101.06 108.00 -6.94 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 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 DC OP3 O N N 74 DC P P N N 75 DC OP1 O N N 76 DC OP2 O N N 77 DC "O5'" O N N 78 DC "C5'" C N N 79 DC "C4'" C N R 80 DC "O4'" O N N 81 DC "C3'" C N S 82 DC "O3'" O N N 83 DC "C2'" C N N 84 DC "C1'" C N R 85 DC N1 N N N 86 DC C2 C N N 87 DC O2 O N N 88 DC N3 N N N 89 DC C4 C N N 90 DC N4 N N N 91 DC C5 C N N 92 DC C6 C N N 93 DC HOP3 H N N 94 DC HOP2 H N N 95 DC "H5'" H N N 96 DC "H5''" H N N 97 DC "H4'" H N N 98 DC "H3'" H N N 99 DC "HO3'" H N N 100 DC "H2'" H N N 101 DC "H2''" H N N 102 DC "H1'" H N N 103 DC H41 H N N 104 DC H42 H N N 105 DC H5 H N N 106 DC H6 H N N 107 DG OP3 O N N 108 DG P P N N 109 DG OP1 O N N 110 DG OP2 O N N 111 DG "O5'" O N N 112 DG "C5'" C N N 113 DG "C4'" C N R 114 DG "O4'" O N N 115 DG "C3'" C N S 116 DG "O3'" O N N 117 DG "C2'" C N N 118 DG "C1'" C N R 119 DG N9 N Y N 120 DG C8 C Y N 121 DG N7 N Y N 122 DG C5 C Y N 123 DG C6 C N N 124 DG O6 O N N 125 DG N1 N N N 126 DG C2 C N N 127 DG N2 N N N 128 DG N3 N N N 129 DG C4 C Y N 130 DG HOP3 H N N 131 DG HOP2 H N N 132 DG "H5'" H N N 133 DG "H5''" H N N 134 DG "H4'" H N N 135 DG "H3'" H N N 136 DG "HO3'" H N N 137 DG "H2'" H N N 138 DG "H2''" H N N 139 DG "H1'" H N N 140 DG H8 H N N 141 DG H1 H N N 142 DG H21 H N N 143 DG H22 H N N 144 DT OP3 O N N 145 DT P P N N 146 DT OP1 O N N 147 DT OP2 O N N 148 DT "O5'" O N N 149 DT "C5'" C N N 150 DT "C4'" C N R 151 DT "O4'" O N N 152 DT "C3'" C N S 153 DT "O3'" O N N 154 DT "C2'" C N N 155 DT "C1'" C N R 156 DT N1 N N N 157 DT C2 C N N 158 DT O2 O N N 159 DT N3 N N N 160 DT C4 C N N 161 DT O4 O N N 162 DT C5 C N N 163 DT C7 C N N 164 DT C6 C N N 165 DT HOP3 H N N 166 DT HOP2 H N N 167 DT "H5'" H N N 168 DT "H5''" H N N 169 DT "H4'" H N N 170 DT "H3'" H N N 171 DT "HO3'" H N N 172 DT "H2'" H N N 173 DT "H2''" H N N 174 DT "H1'" H N N 175 DT H3 H N N 176 DT H71 H N N 177 DT H72 H N N 178 DT H73 H N N 179 DT H6 H N N 180 HOH O O N N 181 HOH H1 H N N 182 HOH H2 H N N 183 MG MG MG N N 184 # 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 DC OP3 P sing N N 77 DC OP3 HOP3 sing N N 78 DC P OP1 doub N N 79 DC P OP2 sing N N 80 DC P "O5'" sing N N 81 DC OP2 HOP2 sing N N 82 DC "O5'" "C5'" sing N N 83 DC "C5'" "C4'" sing N N 84 DC "C5'" "H5'" sing N N 85 DC "C5'" "H5''" sing N N 86 DC "C4'" "O4'" sing N N 87 DC "C4'" "C3'" sing N N 88 DC "C4'" "H4'" sing N N 89 DC "O4'" "C1'" sing N N 90 DC "C3'" "O3'" sing N N 91 DC "C3'" "C2'" sing N N 92 DC "C3'" "H3'" sing N N 93 DC "O3'" "HO3'" sing N N 94 DC "C2'" "C1'" sing N N 95 DC "C2'" "H2'" sing N N 96 DC "C2'" "H2''" sing N N 97 DC "C1'" N1 sing N N 98 DC "C1'" "H1'" sing N N 99 DC N1 C2 sing N N 100 DC N1 C6 sing N N 101 DC C2 O2 doub N N 102 DC C2 N3 sing N N 103 DC N3 C4 doub N N 104 DC C4 N4 sing N N 105 DC C4 C5 sing N N 106 DC N4 H41 sing N N 107 DC N4 H42 sing N N 108 DC C5 C6 doub N N 109 DC C5 H5 sing N N 110 DC C6 H6 sing N N 111 DG OP3 P sing N N 112 DG OP3 HOP3 sing N N 113 DG P OP1 doub N N 114 DG P OP2 sing N N 115 DG P "O5'" sing N N 116 DG OP2 HOP2 sing N N 117 DG "O5'" "C5'" sing N N 118 DG "C5'" "C4'" sing N N 119 DG "C5'" "H5'" sing N N 120 DG "C5'" "H5''" sing N N 121 DG "C4'" "O4'" sing N N 122 DG "C4'" "C3'" sing N N 123 DG "C4'" "H4'" sing N N 124 DG "O4'" "C1'" sing N N 125 DG "C3'" "O3'" sing N N 126 DG "C3'" "C2'" sing N N 127 DG "C3'" "H3'" sing N N 128 DG "O3'" "HO3'" sing N N 129 DG "C2'" "C1'" sing N N 130 DG "C2'" "H2'" sing N N 131 DG "C2'" "H2''" sing N N 132 DG "C1'" N9 sing N N 133 DG "C1'" "H1'" sing N N 134 DG N9 C8 sing Y N 135 DG N9 C4 sing Y N 136 DG C8 N7 doub Y N 137 DG C8 H8 sing N N 138 DG N7 C5 sing Y N 139 DG C5 C6 sing N N 140 DG C5 C4 doub Y N 141 DG C6 O6 doub N N 142 DG C6 N1 sing N N 143 DG N1 C2 sing N N 144 DG N1 H1 sing N N 145 DG C2 N2 sing N N 146 DG C2 N3 doub N N 147 DG N2 H21 sing N N 148 DG N2 H22 sing N N 149 DG N3 C4 sing N N 150 DT OP3 P sing N N 151 DT OP3 HOP3 sing N N 152 DT P OP1 doub N N 153 DT P OP2 sing N N 154 DT P "O5'" sing N N 155 DT OP2 HOP2 sing N N 156 DT "O5'" "C5'" sing N N 157 DT "C5'" "C4'" sing N N 158 DT "C5'" "H5'" sing N N 159 DT "C5'" "H5''" sing N N 160 DT "C4'" "O4'" sing N N 161 DT "C4'" "C3'" sing N N 162 DT "C4'" "H4'" sing N N 163 DT "O4'" "C1'" sing N N 164 DT "C3'" "O3'" sing N N 165 DT "C3'" "C2'" sing N N 166 DT "C3'" "H3'" sing N N 167 DT "O3'" "HO3'" sing N N 168 DT "C2'" "C1'" sing N N 169 DT "C2'" "H2'" sing N N 170 DT "C2'" "H2''" sing N N 171 DT "C1'" N1 sing N N 172 DT "C1'" "H1'" sing N N 173 DT N1 C2 sing N N 174 DT N1 C6 sing N N 175 DT C2 O2 doub N N 176 DT C2 N3 sing N N 177 DT N3 C4 sing N N 178 DT N3 H3 sing N N 179 DT C4 O4 doub N N 180 DT C4 C5 sing N N 181 DT C5 C7 sing N N 182 DT C5 C6 doub N N 183 DT C7 H71 sing N N 184 DT C7 H72 sing N N 185 DT C7 H73 sing N N 186 DT C6 H6 sing N N 187 HOH O H1 sing N N 188 HOH O H2 sing N N 189 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4GJU 'double helix' 4GJU 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 12 1_555 0.228 -0.167 0.245 1.824 -13.698 -1.765 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -0.199 -0.219 0.564 8.159 -11.627 -2.717 2 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A 5CM 3 1_555 B DG 10 1_555 0.214 -0.200 0.159 -4.155 -5.561 -1.925 3 A_5CM3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 -0.249 -0.149 0.083 13.808 -5.754 -0.559 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.014 -0.090 -0.090 5.846 -14.928 3.232 5 A_DA5:DT8_B A 5 ? B 8 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.056 -0.125 0.066 1.037 -17.577 4.986 6 A_DA6:DT7_B A 6 ? B 7 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.107 -0.072 0.132 -2.397 -14.622 4.151 7 A_DT7:DA6_B A 7 ? B 6 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.067 -0.107 -0.081 -0.801 -12.259 3.387 8 A_DT8:DA5_B A 8 ? B 5 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 0.239 -0.085 0.077 -13.053 -7.174 -1.703 9 A_DC9:DG4_B A 9 ? B 4 ? 19 1 1 A DG 10 1_555 B 5CM 3 1_555 -0.159 -0.074 0.272 6.158 -7.471 2.941 10 A_DG10:5CM3_B A 10 ? B 3 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 0.144 -0.268 0.180 4.620 -16.929 -2.512 11 A_DC11:DG2_B A 11 ? B 2 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -0.230 -0.132 0.265 6.854 -4.308 -1.895 12 A_DG12:DC1_B A 12 ? B 1 ? 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 -0.106 -0.004 3.118 -3.227 5.214 35.099 -0.731 -0.275 3.083 8.565 5.301 35.614 1 AA_DC1DG2:DC11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B DC 11 1_555 A 5CM 3 1_555 B DG 10 1_555 0.567 0.520 3.624 4.201 -7.812 42.637 1.534 -0.317 3.518 -10.607 -5.704 43.508 2 AA_DG25CM3:DG10DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A 5CM 3 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 -0.231 0.503 2.964 -0.071 9.589 24.390 -1.324 0.493 2.946 21.656 0.160 26.181 3 AA_5CM3DG4:DC9DG10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 5 1_555 B DT 8 1_555 -0.280 -0.080 3.434 0.846 2.480 38.119 -0.449 0.539 3.416 3.791 -1.294 38.206 4 AA_DG4DA5:DT8DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 0.093 -0.329 3.267 -1.211 1.984 37.196 -0.777 -0.305 3.241 3.107 1.896 37.266 5 AA_DA5DA6:DT7DT8_BB A 5 ? B 8 ? A 6 ? B 7 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.021 -0.591 3.291 -0.323 -2.258 31.490 -0.661 -0.099 3.324 -4.154 0.594 31.571 6 AA_DA6DT7:DA6DT7_BB A 6 ? B 7 ? A 7 ? B 6 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.081 -0.435 3.143 2.042 -1.508 34.815 -0.505 0.432 3.149 -2.516 -3.406 34.904 7 AA_DT7DT8:DA5DA6_BB A 7 ? B 6 ? A 8 ? B 5 ? 1 A DT 8 1_555 B DA 5 1_555 A DC 9 1_555 B DG 4 1_555 -0.177 -0.223 3.499 -0.326 -2.235 43.217 -0.069 0.206 3.507 -3.032 0.442 43.274 8 AA_DT8DC9:DG4DA5_BB A 8 ? B 5 ? A 9 ? B 4 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B 5CM 3 1_555 0.680 0.552 2.970 -3.186 4.270 24.683 0.130 -2.402 2.913 9.842 7.344 25.243 9 AA_DC9DG10:5CM3DG4_BB A 9 ? B 4 ? A 10 ? B 3 ? 1 A DG 10 1_555 B 5CM 3 1_555 A DC 11 1_555 B DG 2 1_555 -1.283 0.441 3.352 -2.949 -8.974 42.163 1.503 1.447 3.274 -12.290 4.039 43.161 10 AA_DG10DC11:DG25CM3_BB A 10 ? B 3 ? A 11 ? B 2 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 -0.028 0.362 3.228 -0.292 4.072 34.368 -0.015 0.002 3.248 6.862 0.493 34.603 11 AA_DC11DG12:DC1DG2_BB A 11 ? B 2 ? A 12 ? B 1 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 water HOH # _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.accession_code 1DPN _pdbx_initial_refinement_model.details 'PDB ENTRY 1DPN' #