data_2ELG # _entry.id 2ELG # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 2ELG pdb_00002elg 10.2210/pdb2elg/pdb NDB ZD0024 ? ? RCSB RCSB026810 ? ? WWPDB D_1000026810 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 292d 'DEOXYRIBONUCLEIC ACID' unspecified PDB 293d 'DEOXYRIBONUCLEIC ACID' unspecified PDB 336d 'DEOXYRIBONUCLEIC ACID' unspecified PDB 1DJ6 'DEOXYRIBONUCLEIC ACID' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2ELG _pdbx_database_status.recvd_initial_deposition_date 2007-03-27 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ohishi, H.' 1 'Tozuka, Y.' 2 'Zhou, D.Y.' 3 'Ishida, T.' 4 'Nakatani, K.' 5 # _citation.id primary _citation.title ;The rare crystallographic structure of d(CGCGCG)(2): The natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)(2) at 10 degrees C ; _citation.journal_abbrev Biochem.Biophys.Res.Commun. _citation.journal_volume 358 _citation.page_first 24 _citation.page_last 28 _citation.year 2007 _citation.journal_id_ASTM BBRCA9 _citation.country US _citation.journal_id_ISSN 0006-291X _citation.journal_id_CSD 0146 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17467661 _citation.pdbx_database_id_DOI 10.1016/j.bbrc.2007.04.026 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ohishi, H.' 1 ? primary 'Tozuka, Y.' 2 ? primary 'Da-Yang, Z.' 3 ? primary 'Ishida, T.' 4 ? primary 'Nakatani, K.' 5 ? # _cell.entry_id 2ELG _cell.length_a 17.847 _cell.length_b 30.988 _cell.length_c 44.022 _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 2ELG _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 ;DNA (5'-D(*DCP*DGP*DCP*DGP*DCP*DG)-3') ; 1810.205 2 ? ? ? ? 2 non-polymer syn SPERMIDINE 145.246 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 3 ? ? ? ? 4 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 5 water nat water 18.015 67 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGCG _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 DC n 1 4 DG n 1 5 DC n 1 6 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 ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'This sequence occurs naturally in humans.' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2ELG _struct_ref.pdbx_db_accession 2ELG _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code CGCGCG _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 2ELG A 1 ? 6 ? 2ELG 1 ? 6 ? 1 6 2 1 2ELG B 1 ? 6 ? 2ELG 7 ? 12 ? 7 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 SPD non-polymer . SPERMIDINE 'N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)' 'C7 H19 N3' 145.246 # _exptl.entry_id 2ELG _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.681153 _exptl_crystal.density_percent_sol 26.835920 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 283 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;10mM Sodium cacodilate, 1M Magnesium chloride, 100mM spermidine trichloride, 8%MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 283K ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'Sodium cacodilate' ? ? ? 1 2 1 'Magnesium chloride' ? ? ? 1 3 1 'spermidine trichloride' ? ? ? 1 4 1 MPD ? ? ? 1 5 1 HOH ? ? ? 1 6 2 'Sodium cacodilate' ? ? ? 1 7 2 'Magnesium chloride' ? ? ? 1 8 2 MPD ? ? ? 1 9 2 HOH ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 95 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.pdbx_collection_date 2005-12-15 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator GRAPHITE _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-6A' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-6A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.000 # _reflns.entry_id 2ELG _reflns.observed_criterion_sigma_F 2.0 _reflns.observed_criterion_sigma_I 2.0 _reflns.d_resolution_high 1.0 _reflns.d_resolution_low 25.0 _reflns.number_all ? _reflns.number_obs 11287 _reflns.percent_possible_obs 99.5 _reflns.pdbx_Rmerge_I_obs 0.047 _reflns.pdbx_Rsym_value 0.057 _reflns.pdbx_netI_over_sigmaI 20.7 _reflns.B_iso_Wilson_estimate 5.3 _reflns.pdbx_redundancy 4.7 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.0 _reflns_shell.d_res_low ? _reflns_shell.percent_possible_all 99.5 _reflns_shell.Rmerge_I_obs 0.047 _reflns_shell.pdbx_Rsym_value 0.057 _reflns_shell.meanI_over_sigI_obs 20.7 _reflns_shell.pdbx_redundancy 4.7 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 11287 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2ELG _refine.ls_d_res_high 1.0 _refine.ls_d_res_low 7.0 _refine.pdbx_ls_sigma_F 2.0 _refine.pdbx_ls_sigma_I 2.0 _refine.ls_number_reflns_all 11287 _refine.ls_number_reflns_obs 11232 _refine.ls_number_reflns_R_free 520 _refine.ls_percent_reflns_obs 99.5 _refine.ls_R_factor_all 0.253 _refine.ls_R_factor_obs 0.244 _refine.ls_R_factor_R_work 0.232 _refine.ls_R_factor_R_free 0.247 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'PDB ENTRY 1DJ6' _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model Isotropic _refine.B_iso_mean 5.8 _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 273 _refine_hist.pdbx_number_atoms_ligand 36 _refine_hist.number_atoms_solvent 201 _refine_hist.number_atoms_total 510 _refine_hist.d_res_high 1.0 _refine_hist.d_res_low 7.0 # _struct.entry_id 2ELG _struct.title ;The rare crystallographic structure of d(CGCGCG)2: The natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)2 at 10 degree celsius ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2ELG _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'd(CGCGCG)2, left-handed Z-DNA, spermidine, polyamine, 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 ? F N N 3 ? G N N 4 ? H N N 5 ? I N N 5 ? # _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 hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SPD 120 ? 7 'BINDING SITE FOR RESIDUE SPD A 120' AC2 Software A MG 92 ? 1 'BINDING SITE FOR RESIDUE MG A 92' # 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 7 DC A 1 ? DC A 1 . ? 4_445 ? 2 AC1 7 DC A 5 ? DC A 5 . ? 3_545 ? 3 AC1 7 DG A 6 ? DG A 6 . ? 3_545 ? 4 AC1 7 DC B 1 ? DC B 7 . ? 3_545 ? 5 AC1 7 DG B 2 ? DG B 8 . ? 3_545 ? 6 AC1 7 DC B 3 ? DC B 9 . ? 3_545 ? 7 AC1 7 DG B 6 ? DG B 12 . ? 4_445 ? 8 AC2 1 DG A 6 ? DG A 6 . ? 1_555 ? # _database_PDB_matrix.entry_id 2ELG _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 # _atom_sites.entry_id 2ELG _atom_sites.fract_transf_matrix[1][1] 0.056032 _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] 0.032271 _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] 0.022716 _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 H MG N NA 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 CYT A . n A 1 2 DG 2 2 2 DG GUA A . n A 1 3 DC 3 3 3 DC CYT A . n A 1 4 DG 4 4 4 DG GUA A . n A 1 5 DC 5 5 5 DC CYT A . n A 1 6 DG 6 6 6 DG GUA A . n B 1 1 DC 1 7 7 DC CYT B . n B 1 2 DG 2 8 8 DG GUA B . n B 1 3 DC 3 9 9 DC CYT B . n B 1 4 DG 4 10 10 DG GUA B . n B 1 5 DC 5 11 11 DC CYT B . n B 1 6 DG 6 12 12 DG GUA 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 SPD 1 120 120 SPD PA3 A . D 3 MG 1 92 92 MG MG A . E 3 MG 1 93 93 MG MG A . F 3 MG 1 94 94 MG MG A . G 4 NA 1 116 116 NA NA A . H 5 HOH 1 13 13 HOH WAT A . H 5 HOH 2 14 14 HOH WAT A . H 5 HOH 3 15 15 HOH WAT A . H 5 HOH 4 16 16 HOH WAT A . H 5 HOH 5 20 20 HOH WAT A . H 5 HOH 6 23 23 HOH WAT A . H 5 HOH 7 28 28 HOH WAT A . H 5 HOH 8 30 30 HOH WAT A . H 5 HOH 9 33 33 HOH WAT A . H 5 HOH 10 34 34 HOH WAT A . H 5 HOH 11 36 36 HOH WAT A . H 5 HOH 12 37 37 HOH WAT A . H 5 HOH 13 39 39 HOH WAT A . H 5 HOH 14 40 40 HOH WAT A . H 5 HOH 15 41 41 HOH WAT A . H 5 HOH 16 47 47 HOH WAT A . H 5 HOH 17 50 50 HOH WAT A . H 5 HOH 18 52 52 HOH WAT A . H 5 HOH 19 54 54 HOH WAT A . H 5 HOH 20 55 55 HOH WAT A . H 5 HOH 21 62 62 HOH WAT A . H 5 HOH 22 67 67 HOH WAT A . H 5 HOH 23 79 79 HOH WAT A . H 5 HOH 24 80 80 HOH WAT A . H 5 HOH 25 81 81 HOH WAT A . H 5 HOH 26 85 85 HOH WAT A . H 5 HOH 27 87 87 HOH WAT A . H 5 HOH 28 88 88 HOH WAT A . H 5 HOH 29 95 95 HOH WAT A . H 5 HOH 30 96 96 HOH WAT A . H 5 HOH 31 100 100 HOH WAT A . H 5 HOH 32 101 101 HOH WAT A . H 5 HOH 33 102 102 HOH WAT A . H 5 HOH 34 113 113 HOH WAT A . H 5 HOH 35 114 114 HOH WAT A . H 5 HOH 36 115 115 HOH WAT A . I 5 HOH 1 18 18 HOH WAT B . I 5 HOH 2 22 22 HOH WAT B . I 5 HOH 3 24 24 HOH WAT B . I 5 HOH 4 29 29 HOH WAT B . I 5 HOH 5 35 35 HOH WAT B . I 5 HOH 6 38 38 HOH WAT B . I 5 HOH 7 43 43 HOH WAT B . I 5 HOH 8 44 44 HOH WAT B . I 5 HOH 9 46 46 HOH WAT B . I 5 HOH 10 51 51 HOH WAT B . I 5 HOH 11 53 53 HOH WAT B . I 5 HOH 12 56 56 HOH WAT B . I 5 HOH 13 57 57 HOH WAT B . I 5 HOH 14 59 59 HOH WAT B . I 5 HOH 15 60 60 HOH WAT B . I 5 HOH 16 61 61 HOH WAT B . I 5 HOH 17 64 64 HOH WAT B . I 5 HOH 18 65 65 HOH WAT B . I 5 HOH 19 68 68 HOH WAT B . I 5 HOH 20 69 69 HOH WAT B . I 5 HOH 21 78 78 HOH WAT B . I 5 HOH 22 82 82 HOH WAT B . I 5 HOH 23 86 86 HOH WAT B . I 5 HOH 24 89 89 HOH WAT B . I 5 HOH 25 90 90 HOH WAT B . I 5 HOH 26 91 91 HOH WAT B . I 5 HOH 27 97 97 HOH WAT B . I 5 HOH 28 99 99 HOH WAT B . I 5 HOH 29 103 103 HOH WAT B . I 5 HOH 30 105 105 HOH WAT B . I 5 HOH 31 108 108 HOH WAT B . # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? tetrameric 4 2 software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,B,C,D,E,F,G,H,I 2 1 A,B,C,D,E,F,G,H,I # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 2 'ABSA (A^2)' 1170 ? 2 MORE -22.2 ? 2 'SSA (A^2)' 2590 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_555 -x+1/2,-y,z+1/2 -1.0000000000 0.0000000000 0.0000000000 8.9235000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 22.0110000000 # 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 2008-04-01 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-10-25 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 '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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 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' '_struct_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 MERLOT phasing . ? 2 X-PLOR refinement 3.851 ? 3 MOSFLM 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A HOH 30 ? ? H2 A HOH 100 ? ? 1.51 2 1 O A HOH 16 ? ? H2 A HOH 114 ? ? 1.53 3 1 O A HOH 34 ? ? H1 A HOH 100 ? ? 1.57 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 H1 B HOH 38 ? ? 1_555 O B HOH 64 ? ? 3_645 1.57 2 1 O A HOH 20 ? ? 1_555 H1 B HOH 64 ? ? 3_545 1.59 3 1 H1 A HOH 115 ? ? 1_555 O B HOH 68 ? ? 2_555 1.59 4 1 MG A MG 94 ? ? 1_555 O A HOH 100 ? ? 3_645 1.64 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C3'" A DC 1 ? ? "C2'" A DC 1 ? ? 1.606 1.518 0.088 0.012 N 2 1 C5 A DG 2 ? ? N7 A DG 2 ? ? 1.445 1.388 0.057 0.006 N 3 1 "O3'" A DG 2 ? ? P A DC 3 ? ? 1.695 1.607 0.088 0.012 Y 4 1 P A DC 3 ? ? OP2 A DC 3 ? ? 1.612 1.485 0.127 0.017 N 5 1 P A DC 3 ? ? "O5'" A DC 3 ? ? 1.666 1.593 0.073 0.010 N 6 1 C4 A DC 3 ? ? C5 A DC 3 ? ? 1.489 1.425 0.064 0.008 N 7 1 "O3'" A DC 3 ? ? P A DG 4 ? ? 1.682 1.607 0.075 0.012 Y 8 1 P A DG 4 ? ? "O5'" A DG 4 ? ? 1.706 1.593 0.113 0.010 N 9 1 N1 A DG 4 ? ? C2 A DG 4 ? ? 1.429 1.373 0.056 0.008 N 10 1 C2 A DG 4 ? ? N3 A DG 4 ? ? 1.375 1.323 0.052 0.008 N 11 1 N3 A DG 4 ? ? C4 A DG 4 ? ? 1.398 1.350 0.048 0.007 N 12 1 C5 A DG 4 ? ? C6 A DG 4 ? ? 1.483 1.419 0.064 0.010 N 13 1 C6 A DG 4 ? ? N1 A DG 4 ? ? 1.445 1.391 0.054 0.007 N 14 1 C5 A DG 4 ? ? N7 A DG 4 ? ? 1.458 1.388 0.070 0.006 N 15 1 N9 A DG 4 ? ? C4 A DG 4 ? ? 1.426 1.375 0.051 0.008 N 16 1 P A DC 5 ? ? "O5'" A DC 5 ? ? 1.698 1.593 0.105 0.010 N 17 1 "C4'" A DC 5 ? ? "C3'" A DC 5 ? ? 1.596 1.529 0.067 0.010 N 18 1 N1 A DC 5 ? ? C6 A DC 5 ? ? 1.414 1.367 0.047 0.006 N 19 1 C4 A DC 5 ? ? C5 A DC 5 ? ? 1.497 1.425 0.072 0.008 N 20 1 "O3'" A DC 5 ? ? P A DG 6 ? ? 1.704 1.607 0.097 0.012 Y 21 1 P A DG 6 ? ? "O5'" A DG 6 ? ? 1.660 1.593 0.067 0.010 N 22 1 N3 A DG 6 ? ? C4 A DG 6 ? ? 1.397 1.350 0.047 0.007 N 23 1 C5 A DG 6 ? ? N7 A DG 6 ? ? 1.456 1.388 0.068 0.006 N 24 1 C8 A DG 6 ? ? N9 A DG 6 ? ? 1.427 1.374 0.053 0.007 N 25 1 "C5'" B DC 7 ? ? "C4'" B DC 7 ? ? 1.569 1.512 0.057 0.007 N 26 1 N1 B DC 7 ? ? C6 B DC 7 ? ? 1.414 1.367 0.047 0.006 N 27 1 C2 B DC 7 ? ? N3 B DC 7 ? ? 1.415 1.353 0.062 0.008 N 28 1 C5 B DG 8 ? ? N7 B DG 8 ? ? 1.429 1.388 0.041 0.006 N 29 1 C8 B DG 8 ? ? N9 B DG 8 ? ? 1.426 1.374 0.052 0.007 N 30 1 N9 B DG 8 ? ? C4 B DG 8 ? ? 1.426 1.375 0.051 0.008 N 31 1 P B DC 9 ? ? "O5'" B DC 9 ? ? 1.666 1.593 0.073 0.010 N 32 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? 1.504 1.420 0.084 0.011 N 33 1 P B DG 10 ? ? "O5'" B DG 10 ? ? 1.705 1.593 0.112 0.010 N 34 1 N1 B DG 10 ? ? C2 B DG 10 ? ? 1.428 1.373 0.055 0.008 N 35 1 C2 B DG 10 ? ? N3 B DG 10 ? ? 1.371 1.323 0.048 0.008 N 36 1 C5 B DG 10 ? ? N7 B DG 10 ? ? 1.437 1.388 0.049 0.006 N 37 1 N7 B DG 10 ? ? C8 B DG 10 ? ? 1.347 1.305 0.042 0.006 N 38 1 N9 B DG 10 ? ? C4 B DG 10 ? ? 1.438 1.375 0.063 0.008 N 39 1 P B DC 11 ? ? "O5'" B DC 11 ? ? 1.680 1.593 0.087 0.010 N 40 1 "C4'" B DC 11 ? ? "C3'" B DC 11 ? ? 1.615 1.529 0.086 0.010 N 41 1 "C3'" B DC 11 ? ? "C2'" B DC 11 ? ? 1.595 1.518 0.077 0.012 N 42 1 "C2'" B DC 11 ? ? "C1'" B DC 11 ? ? 1.623 1.519 0.104 0.010 N 43 1 N1 B DC 11 ? ? C6 B DC 11 ? ? 1.420 1.367 0.053 0.006 N 44 1 P B DG 12 ? ? "O5'" B DG 12 ? ? 1.686 1.593 0.093 0.010 N 45 1 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? 1.503 1.420 0.083 0.011 N 46 1 C2 B DG 12 ? ? N3 B DG 12 ? ? 1.385 1.323 0.062 0.008 N 47 1 C5 B DG 12 ? ? N7 B DG 12 ? ? 1.447 1.388 0.059 0.006 N 48 1 C8 B DG 12 ? ? N9 B DG 12 ? ? 1.420 1.374 0.046 0.007 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O5'" A DG 2 ? ? "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 101.51 109.40 -7.89 0.80 N 2 1 "C1'" A DG 2 ? ? "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? 102.61 110.10 -7.49 1.00 N 3 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? "C2'" A DG 2 ? ? 111.31 106.80 4.51 0.50 N 4 1 "C3'" A DC 3 ? ? "C2'" A DC 3 ? ? "C1'" A DC 3 ? ? 97.16 102.40 -5.24 0.80 N 5 1 "O5'" A DG 4 ? ? "C5'" A DG 4 ? ? "C4'" A DG 4 ? ? 103.61 109.40 -5.79 0.80 N 6 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 102.86 108.00 -5.14 0.70 N 7 1 "C3'" A DC 5 ? ? "O3'" A DC 5 ? ? P A DG 6 ? ? 111.26 119.70 -8.44 1.20 Y 8 1 "O5'" A DG 6 ? ? "C5'" A DG 6 ? ? "C4'" A DG 6 ? ? 104.40 109.40 -5.00 0.80 N 9 1 C2 A DG 6 ? ? N3 A DG 6 ? ? C4 A DG 6 ? ? 108.62 111.90 -3.28 0.50 N 10 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.04 108.30 2.74 0.30 N 11 1 "O5'" B DG 8 ? ? "C5'" B DG 8 ? ? "C4'" B DG 8 ? ? 104.38 109.40 -5.02 0.80 N 12 1 "O4'" B DG 8 ? ? "C4'" B DG 8 ? ? "C3'" B DG 8 ? ? 109.62 106.00 3.62 0.60 N 13 1 "C1'" B DG 8 ? ? "O4'" B DG 8 ? ? "C4'" B DG 8 ? ? 103.45 110.10 -6.65 1.00 N 14 1 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? "C2'" B DG 8 ? ? 113.83 106.80 7.03 0.50 N 15 1 P B DC 9 ? ? "O5'" B DC 9 ? ? "C5'" B DC 9 ? ? 110.29 120.90 -10.61 1.60 N 16 1 "O5'" B DG 10 ? ? "C5'" B DG 10 ? ? "C4'" B DG 10 ? ? 103.56 109.40 -5.84 0.80 N 17 1 "O4'" B DG 10 ? ? "C1'" B DG 10 ? ? "C2'" B DG 10 ? ? 112.75 106.80 5.95 0.50 N 18 1 "O5'" B DG 12 ? ? "C5'" B DG 12 ? ? "C4'" B DG 12 ? ? 102.64 109.40 -6.76 0.80 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DG A 2 ? ? 0.073 'SIDE CHAIN' 2 1 DG A 4 ? ? 0.058 'SIDE CHAIN' 3 1 DG A 6 ? ? 0.066 'SIDE CHAIN' 4 1 DG B 8 ? ? 0.077 'SIDE CHAIN' 5 1 DC B 11 ? ? 0.079 'SIDE CHAIN' # 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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DG OP3 O N N 35 DG P P N N 36 DG OP1 O N N 37 DG OP2 O N N 38 DG "O5'" O N N 39 DG "C5'" C N N 40 DG "C4'" C N R 41 DG "O4'" O N N 42 DG "C3'" C N S 43 DG "O3'" O N N 44 DG "C2'" C N N 45 DG "C1'" C N R 46 DG N9 N Y N 47 DG C8 C Y N 48 DG N7 N Y N 49 DG C5 C Y N 50 DG C6 C N N 51 DG O6 O N N 52 DG N1 N N N 53 DG C2 C N N 54 DG N2 N N N 55 DG N3 N N N 56 DG C4 C Y N 57 DG HOP3 H N N 58 DG HOP2 H N N 59 DG "H5'" H N N 60 DG "H5''" H N N 61 DG "H4'" H N N 62 DG "H3'" H N N 63 DG "HO3'" H N N 64 DG "H2'" H N N 65 DG "H2''" H N N 66 DG "H1'" H N N 67 DG H8 H N N 68 DG H1 H N N 69 DG H21 H N N 70 DG H22 H N N 71 HOH O O N N 72 HOH H1 H N N 73 HOH H2 H N N 74 MG MG MG N N 75 NA NA NA N N 76 SPD N1 N N N 77 SPD C2 C N N 78 SPD C3 C N N 79 SPD C4 C N N 80 SPD C5 C N N 81 SPD N6 N N N 82 SPD C7 C N N 83 SPD C8 C N N 84 SPD C9 C N N 85 SPD N10 N N N 86 SPD HN11 H N N 87 SPD HN12 H N N 88 SPD H21 H N N 89 SPD H22 H N N 90 SPD H31 H N N 91 SPD H32 H N N 92 SPD H41 H N N 93 SPD H42 H N N 94 SPD H51 H N N 95 SPD H52 H N N 96 SPD HN6 H N N 97 SPD H71 H N N 98 SPD H72 H N N 99 SPD H81 H N N 100 SPD H82 H N N 101 SPD H91 H N N 102 SPD H92 H N N 103 SPD H101 H N N 104 SPD H102 H N N 105 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DG OP3 P sing N N 36 DG OP3 HOP3 sing N N 37 DG P OP1 doub N N 38 DG P OP2 sing N N 39 DG P "O5'" sing N N 40 DG OP2 HOP2 sing N N 41 DG "O5'" "C5'" sing N N 42 DG "C5'" "C4'" sing N N 43 DG "C5'" "H5'" sing N N 44 DG "C5'" "H5''" sing N N 45 DG "C4'" "O4'" sing N N 46 DG "C4'" "C3'" sing N N 47 DG "C4'" "H4'" sing N N 48 DG "O4'" "C1'" sing N N 49 DG "C3'" "O3'" sing N N 50 DG "C3'" "C2'" sing N N 51 DG "C3'" "H3'" sing N N 52 DG "O3'" "HO3'" sing N N 53 DG "C2'" "C1'" sing N N 54 DG "C2'" "H2'" sing N N 55 DG "C2'" "H2''" sing N N 56 DG "C1'" N9 sing N N 57 DG "C1'" "H1'" sing N N 58 DG N9 C8 sing Y N 59 DG N9 C4 sing Y N 60 DG C8 N7 doub Y N 61 DG C8 H8 sing N N 62 DG N7 C5 sing Y N 63 DG C5 C6 sing N N 64 DG C5 C4 doub Y N 65 DG C6 O6 doub N N 66 DG C6 N1 sing N N 67 DG N1 C2 sing N N 68 DG N1 H1 sing N N 69 DG C2 N2 sing N N 70 DG C2 N3 doub N N 71 DG N2 H21 sing N N 72 DG N2 H22 sing N N 73 DG N3 C4 sing N N 74 HOH O H1 sing N N 75 HOH O H2 sing N N 76 SPD N1 C2 sing N N 77 SPD N1 HN11 sing N N 78 SPD N1 HN12 sing N N 79 SPD C2 C3 sing N N 80 SPD C2 H21 sing N N 81 SPD C2 H22 sing N N 82 SPD C3 C4 sing N N 83 SPD C3 H31 sing N N 84 SPD C3 H32 sing N N 85 SPD C4 C5 sing N N 86 SPD C4 H41 sing N N 87 SPD C4 H42 sing N N 88 SPD C5 N6 sing N N 89 SPD C5 H51 sing N N 90 SPD C5 H52 sing N N 91 SPD N6 C7 sing N N 92 SPD N6 HN6 sing N N 93 SPD C7 C8 sing N N 94 SPD C7 H71 sing N N 95 SPD C7 H72 sing N N 96 SPD C8 C9 sing N N 97 SPD C8 H81 sing N N 98 SPD C8 H82 sing N N 99 SPD C9 N10 sing N N 100 SPD C9 H91 sing N N 101 SPD C9 H92 sing N N 102 SPD N10 H101 sing N N 103 SPD N10 H102 sing N N 104 # _ndb_struct_conf_na.entry_id 2ELG _ndb_struct_conf_na.feature 'z-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 6 1_555 -0.287 -0.178 0.063 3.445 -6.301 2.355 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B DC 5 1_555 0.316 -0.146 0.088 -2.663 -8.590 1.419 2 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A DC 3 1_555 B DG 4 1_555 -0.309 -0.202 -0.072 8.443 -2.669 3.594 3 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 3 1_555 0.195 -0.154 0.011 -5.235 -1.489 3.746 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A DC 5 1_555 B DG 2 1_555 -0.116 -0.192 -0.063 8.018 -1.242 2.732 5 A_DC5:DG8_B A 5 ? B 8 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 0.328 -0.062 0.258 -0.412 3.262 2.256 6 A_DG6:DC7_B A 6 ? B 7 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 6 1_555 A DG 2 1_555 B DC 5 1_555 -0.085 5.207 3.702 -0.016 -3.712 -4.618 -16.850 -0.971 6.147 38.807 -0.167 -5.924 1 AA_DC1DG2:DC11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B DC 5 1_555 A DC 3 1_555 B DG 4 1_555 -0.010 -0.923 3.254 1.977 -3.079 -53.039 1.225 0.113 3.198 3.444 2.211 -53.156 2 AA_DG2DC3:DG10DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DC 3 1_555 B DG 4 1_555 A DG 4 1_555 B DC 3 1_555 -0.043 5.320 3.730 0.931 -4.875 -6.496 -14.338 4.087 6.140 36.749 7.017 -8.174 3 AA_DC3DG4:DC9DG10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DG 4 1_555 B DC 3 1_555 A DC 5 1_555 B DG 2 1_555 0.013 -0.823 3.126 0.557 -2.932 -52.775 1.104 0.049 3.079 3.296 0.626 -52.853 4 AA_DG4DC5:DG8DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DC 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 -0.025 5.348 3.722 -1.732 0.235 -8.687 -35.239 -4.770 3.503 -1.529 -11.285 -8.861 5 AA_DC5DG6:DC7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 SPERMIDINE SPD 3 'MAGNESIUM ION' MG 4 'SODIUM ION' NA 5 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 1DJ6 _pdbx_initial_refinement_model.details 'PDB ENTRY 1DJ6' #