data_2F8W # _entry.id 2F8W # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.377 _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 2F8W pdb_00002f8w 10.2210/pdb2f8w/pdb NDB ZD0016 ? ? RCSB RCSB035597 ? ? WWPDB D_1000035597 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2F8W _pdbx_database_status.recvd_initial_deposition_date 2005-12-04 _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 N _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Narayana, N.' 1 'Shamala, N.' 2 'Ganesh, K.N.' 3 'Viswamitra, M.A.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Interaction between the Z-Type DNA Duplex and 1,3-Propanediamine: Crystal Structure of d(CACGTG)2 at 1.2 A Resolution' Biochemistry 45 1200 1211 2006 BICHAW US 0006-2960 0033 ? 16430216 10.1021/bi051569l 1 'Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-resolution' Biochemistry 30 11388 11402 1991 BICHAW US 0006-2960 0033 ? ? ? 2 'Structure of d(TGCGCA)2 at 293 K: comparison of the effects of sequence and temperature' 'Acta Crystallogr.,Sect.D' 58 1381 1384 2002 ABCRE6 DK 0907-4449 0766 ? ? ? 3 ;Sequence-dependent microheterogeneity of Z-DNA: The crystal and molecular structures of d(CACGCG).d(CGCGTG) and d(CGCACG).d(CGTGCG) ; J.Mol.Biol. 248 918 930 1995 JMOBAK UK 0022-2836 0070 ? ? ? 4 'Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA)*d(TGCGCG) in two crystal forms' 'Nucleic Acids Res.' 32 5945 5953 2004 NARHAD UK 0305-1048 0389 ? ? ? 5 'Structure of d(TGCGCA)2 and a comparison to other DNA hexamers.' 'Acta Crystallogr.,Sect.D' 54 1273 1284 1998 ABCRE6 DK 0907-4449 0766 ? ? ? 6 'Structure of d(CACGTG), Z-DNA hexamer containing AT base pairs' 'Nucleic Acids Res.' 16 8695 8705 1988 NARHAD UK 0305-1048 0389 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Narayana, N.' 1 ? primary 'Shamala, N.' 2 ? primary 'Ganesh, K.N.' 3 ? primary 'Viswamitra, M.A.' 4 ? 1 'Egli, M.' 5 ? 1 'Williams, L.D.' 6 ? 1 'Gao, Q.' 7 ? 1 'Rich, A.' 8 ? 2 'Thiyagarajan, S.' 9 ? 2 'Satheesh Kumar, P.' 10 ? 2 'Rajan, S.S.' 11 ? 2 'Gautham, N.' 12 ? 3 'Sadasivan, C.' 13 ? 3 'Gautham, N.' 14 ? 4 'Thiyagarajan, S.' 15 ? 4 'Rajan, S.S.' 16 ? 4 'Gautham, N.' 17 ? 5 'Harper, A.' 18 ? 5 'Brannigan, J.A.' 19 ? 5 'Buck, M.' 20 ? 5 'Hewitt, L.' 21 ? 5 'Lewis, R.J.' 22 ? 5 'Moore, M.H.' 23 ? 5 'Schneider, B.' 24 ? 6 'Coll, M.' 25 ? 6 'Fita, I.' 26 ? 6 'Lloveras, J.' 27 ? 6 'Subirana, J.A.' 28 ? 6 'Bardella, F.' 29 ? 6 'Huynh-Dinh, T.' 30 ? 6 'Igolen, J.' 31 ? # _cell.entry_id 2F8W _cell.length_a 18.420 _cell.length_b 30.740 _cell.length_c 43.180 _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 2F8W _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'-D(*CP*AP*CP*GP*TP*G)-3'" 1809.217 2 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 3 non-polymer syn 1,3-DIAMINOPROPANE 74.125 1 ? ? ? ? 4 water nat water 18.015 71 ? ? ? ? # _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)(DA)(DC)(DG)(DT)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CACGTG _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 DA n 1 3 DC n 1 4 DG n 1 5 DT 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 'synthetic oligonucleotide' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2F8W _struct_ref.pdbx_db_accession 2F8W _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2F8W A 1 ? 6 ? 2F8W 1 ? 6 ? 1 6 2 1 2F8W B 1 ? 6 ? 2F8W 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 13D non-polymer . 1,3-DIAMINOPROPANE ? 'C3 H10 N2' 74.125 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 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 # _exptl.entry_id 2F8W _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.71 _exptl_crystal.density_percent_sol 28.0 _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 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details '7.5 mM sodium cacodylate, 2.5 mM SrCl2, 2.5 mM spermine, 50% Isopropanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K' _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 cacodylate' ? ? ? 1 2 1 SrCl2 ? ? ? 1 3 1 spermine ? ? ? 1 4 1 Isopropanol ? ? ? 1 5 1 H2O ? ? ? 1 6 2 'sodium cacodylate' ? ? ? 1 7 2 SrCl2 ? ? ? 1 8 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 291 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type 'ENRAF-NONIUS CAD4' _diffrn_detector.pdbx_collection_date 1987-02-04 _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 GRAPHITE _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'SEALED TUBE' _diffrn_source.type ENRAF-NONIUS _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 2F8W _reflns.observed_criterion_sigma_I 4.0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 50.0 _reflns.d_resolution_high 1.2 _reflns.number_obs 5687 _reflns.number_all 8124 _reflns.percent_possible_obs 70 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.042 _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 2F8W _refine.ls_number_reflns_obs 5687 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I 4.0 _refine.pdbx_ls_sigma_F 2.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 6.0 _refine.ls_d_res_high 1.2 _refine.ls_percent_reflns_obs 70.0 _refine.ls_R_factor_obs 0.183 _refine.ls_R_factor_all 0.183 _refine.ls_R_factor_R_work 0.18 _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 1.5 _refine.ls_number_reflns_R_free 93 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 14.8 _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 THROUGHOUT _refine.details X-PLOR _refine.pdbx_starting_model 'PDB entry 1D48' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values ? _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.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 240 _refine_hist.pdbx_number_atoms_ligand 19 _refine_hist.number_atoms_solvent 71 _refine_hist.number_atoms_total 330 _refine_hist.d_res_high 1.2 _refine_hist.d_res_low 6.0 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function x_bond_d 0.013 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 3.18 ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_deg 32.14 ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_deg 1.32 ? ? ? 'X-RAY DIFFRACTION' ? # _struct.entry_id 2F8W _struct.title 'Crystal structure of d(CACGTG)2' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2F8W _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'd(CACGTG), Polyamine, Z-DNA, 1, 3-propanediamine, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 4 ? F N N 4 ? # _struct_biol.id 1 _struct_biol.details ;The biological assembly is a duplex. The coordinates deposited will generate the biological assembly. There is no need for symmetry operations to generate the biological assembly. ; _struct_biol.pdbx_parent_biol_id ? # 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 DA 2 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 2 B DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 2 B DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 3 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 2 N1 ? ? A DT 5 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 2 N6 ? ? A DT 5 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _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 SPM 13 ? 17 'BINDING SITE FOR RESIDUE SPM A 13' AC2 Software B 13D 85 ? 11 'BINDING SITE FOR RESIDUE 13D B 85' # 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 17 DA A 2 ? DA A 2 . ? 1_555 ? 2 AC1 17 DC A 3 ? DC A 3 . ? 1_555 ? 3 AC1 17 DG A 4 ? DG A 4 . ? 1_555 ? 4 AC1 17 HOH E . ? HOH A 17 . ? 4_566 ? 5 AC1 17 HOH E . ? HOH A 19 . ? 1_555 ? 6 AC1 17 HOH E . ? HOH A 36 . ? 1_555 ? 7 AC1 17 HOH E . ? HOH A 73 . ? 4_556 ? 8 AC1 17 HOH E . ? HOH A 80 . ? 4_566 ? 9 AC1 17 DA B 2 ? DA B 8 . ? 1_555 ? 10 AC1 17 DC B 3 ? DC B 9 . ? 4_556 ? 11 AC1 17 DG B 4 ? DG B 10 . ? 1_655 ? 12 AC1 17 DG B 4 ? DG B 10 . ? 4_556 ? 13 AC1 17 DT B 5 ? DT B 11 . ? 1_655 ? 14 AC1 17 DG B 6 ? DG B 12 . ? 1_655 ? 15 AC1 17 HOH F . ? HOH B 68 . ? 4_556 ? 16 AC1 17 HOH F . ? HOH B 69 . ? 4_556 ? 17 AC1 17 HOH F . ? HOH B 76 . ? 4_556 ? 18 AC2 11 DG A 4 ? DG A 4 . ? 4_466 ? 19 AC2 11 DT A 5 ? DT A 5 . ? 4_466 ? 20 AC2 11 DG A 6 ? DG A 6 . ? 1_555 ? 21 AC2 11 HOH E . ? HOH A 46 . ? 4_466 ? 22 AC2 11 HOH E . ? HOH A 80 . ? 4_466 ? 23 AC2 11 DC B 3 ? DC B 9 . ? 1_555 ? 24 AC2 11 DG B 4 ? DG B 10 . ? 1_555 ? 25 AC2 11 HOH F . ? HOH B 47 . ? 1_555 ? 26 AC2 11 HOH F . ? HOH B 82 . ? 1_555 ? 27 AC2 11 HOH F . ? HOH B 83 . ? 1_555 ? 28 AC2 11 HOH F . ? HOH B 84 . ? 1_555 ? # _database_PDB_matrix.entry_id 2F8W _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 2F8W _atom_sites.fract_transf_matrix[1][1] 0.054290 _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] 0.032531 _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] 0.023159 _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 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 CYT A . n A 1 2 DA 2 2 2 DA ADE 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 DT 5 5 5 DT THY 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 DA 2 8 8 DA ADE 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 DT 5 11 11 DT THY 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 SPM 1 13 13 SPM SP A . D 3 13D 1 85 85 13D Z5 B . E 4 HOH 1 14 14 HOH WAT A . E 4 HOH 2 15 15 HOH WAT A . E 4 HOH 3 17 17 HOH WAT A . E 4 HOH 4 18 18 HOH WAT A . E 4 HOH 5 19 19 HOH WAT A . E 4 HOH 6 21 21 HOH WAT A . E 4 HOH 7 26 26 HOH WAT A . E 4 HOH 8 28 28 HOH WAT A . E 4 HOH 9 29 29 HOH WAT A . E 4 HOH 10 30 30 HOH WAT A . E 4 HOH 11 33 33 HOH WAT A . E 4 HOH 12 34 34 HOH WAT A . E 4 HOH 13 35 35 HOH WAT A . E 4 HOH 14 36 36 HOH WAT A . E 4 HOH 15 37 37 HOH WAT A . E 4 HOH 16 39 39 HOH WAT A . E 4 HOH 17 41 41 HOH WAT A . E 4 HOH 18 42 42 HOH WAT A . E 4 HOH 19 45 45 HOH WAT A . E 4 HOH 20 46 46 HOH WAT A . E 4 HOH 21 50 50 HOH WAT A . E 4 HOH 22 51 51 HOH WAT A . E 4 HOH 23 52 52 HOH WAT A . E 4 HOH 24 54 54 HOH WAT A . E 4 HOH 25 56 56 HOH WAT A . E 4 HOH 26 59 59 HOH WAT A . E 4 HOH 27 63 63 HOH WAT A . E 4 HOH 28 64 64 HOH WAT A . E 4 HOH 29 65 65 HOH WAT A . E 4 HOH 30 71 71 HOH WAT A . E 4 HOH 31 73 73 HOH WAT A . E 4 HOH 32 74 74 HOH WAT A . E 4 HOH 33 75 75 HOH WAT A . E 4 HOH 34 77 77 HOH WAT A . E 4 HOH 35 78 78 HOH WAT A . E 4 HOH 36 79 79 HOH WAT A . E 4 HOH 37 80 80 HOH WAT A . E 4 HOH 38 81 81 HOH WAT A . F 4 HOH 1 16 16 HOH WAT B . F 4 HOH 2 20 20 HOH WAT B . F 4 HOH 3 22 22 HOH WAT B . F 4 HOH 4 23 23 HOH WAT B . F 4 HOH 5 24 24 HOH WAT B . F 4 HOH 6 25 25 HOH WAT B . F 4 HOH 7 27 27 HOH WAT B . F 4 HOH 8 31 31 HOH WAT B . F 4 HOH 9 32 32 HOH WAT B . F 4 HOH 10 38 38 HOH WAT B . F 4 HOH 11 40 40 HOH WAT B . F 4 HOH 12 43 43 HOH WAT B . F 4 HOH 13 44 44 HOH WAT B . F 4 HOH 14 47 47 HOH WAT B . F 4 HOH 15 48 48 HOH WAT B . F 4 HOH 16 49 49 HOH WAT B . F 4 HOH 17 53 53 HOH WAT B . F 4 HOH 18 55 55 HOH WAT B . F 4 HOH 19 57 57 HOH WAT B . F 4 HOH 20 58 58 HOH WAT B . F 4 HOH 21 60 60 HOH WAT B . F 4 HOH 22 61 61 HOH WAT B . F 4 HOH 23 62 62 HOH WAT B . F 4 HOH 24 66 66 HOH WAT B . F 4 HOH 25 67 67 HOH WAT B . F 4 HOH 26 68 68 HOH WAT B . F 4 HOH 27 69 69 HOH WAT B . F 4 HOH 28 70 70 HOH WAT B . F 4 HOH 29 72 72 HOH WAT B . F 4 HOH 30 76 76 HOH WAT B . F 4 HOH 31 82 82 HOH WAT B . F 4 HOH 32 83 83 HOH WAT B . F 4 HOH 33 84 84 HOH WAT B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # 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 2006-01-31 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2018-04-04 5 'Structure model' 1 4 2018-04-18 6 'Structure model' 1 5 2023-08-30 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 5 'Structure model' 'Data collection' 5 6 'Structure model' 'Data collection' 6 6 'Structure model' 'Database references' 7 6 'Structure model' 'Derived calculations' 8 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' diffrn_source 2 5 'Structure model' diffrn_detector 3 6 'Structure model' chem_comp_atom 4 6 'Structure model' chem_comp_bond 5 6 'Structure model' database_2 6 6 'Structure model' pdbx_initial_refinement_model 7 6 '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' '_diffrn_source.type' 2 5 'Structure model' '_diffrn_detector.detector' 3 6 'Structure model' '_database_2.pdbx_DOI' 4 6 'Structure model' '_database_2.pdbx_database_accession' 5 6 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 6 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 6 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CAD4 'data collection' . ? 1 CAD4 'data reduction' 'associated program' ? 2 X-PLOR 'model building' . ? 3 X-PLOR refinement . ? 4 CAD4 'data scaling' . ? 5 X-PLOR phasing . ? 6 # _pdbx_database_remark.id 600 _pdbx_database_remark.text ;HETEROGEN Ligand Z5 in the manuscript is labeled as 13D in the coordinate file. ; # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 O _pdbx_validate_close_contact.auth_asym_id_1 B _pdbx_validate_close_contact.auth_comp_id_1 HOH _pdbx_validate_close_contact.auth_seq_id_1 44 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 66 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.09 # 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 ? ? 112.66 108.30 4.36 0.30 N 2 1 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 110.90 108.30 2.60 0.30 N 3 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.19 108.30 2.89 0.30 N 4 1 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 119.04 122.90 -3.86 0.60 N 5 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 110.40 108.30 2.10 0.30 N 6 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 110.44 108.30 2.14 0.30 N 7 1 N1 B DC 9 ? ? C2 B DC 9 ? ? O2 B DC 9 ? ? 122.75 118.90 3.85 0.60 N 8 1 "O4'" B DT 11 ? ? "C1'" B DT 11 ? ? N1 B DT 11 ? ? 111.13 108.30 2.83 0.30 N 9 1 C6 B DT 11 ? ? C5 B DT 11 ? ? C7 B DT 11 ? ? 119.15 122.90 -3.75 0.60 N 10 1 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 112.46 108.30 4.16 0.30 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DA A 2 ? ? 0.060 'SIDE CHAIN' 2 1 DG A 6 ? ? 0.070 'SIDE CHAIN' 3 1 DC B 9 ? ? 0.062 'SIDE CHAIN' 4 1 DG B 12 ? ? 0.064 '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 13D CA C N N 1 13D CB C N N 2 13D CC C N N 3 13D ND N N N 4 13D NAA N N N 5 13D HAC1 H N N 6 13D HAC2 H N N 7 13D HBC1 H N N 8 13D HBC2 H N N 9 13D HCC1 H N N 10 13D HCC2 H N N 11 13D HDN1 H N N 12 13D HDN2 H N N 13 13D HAA1 H N N 14 13D HAA2 H N N 15 DA OP3 O N N 16 DA P P N N 17 DA OP1 O N N 18 DA OP2 O N N 19 DA "O5'" O N N 20 DA "C5'" C N N 21 DA "C4'" C N R 22 DA "O4'" O N N 23 DA "C3'" C N S 24 DA "O3'" O N N 25 DA "C2'" C N N 26 DA "C1'" C N R 27 DA N9 N Y N 28 DA C8 C Y N 29 DA N7 N Y N 30 DA C5 C Y N 31 DA C6 C Y N 32 DA N6 N N N 33 DA N1 N Y N 34 DA C2 C Y N 35 DA N3 N Y N 36 DA C4 C Y N 37 DA HOP3 H N N 38 DA HOP2 H N N 39 DA "H5'" H N N 40 DA "H5''" H N N 41 DA "H4'" H N N 42 DA "H3'" H N N 43 DA "HO3'" H N N 44 DA "H2'" H N N 45 DA "H2''" H N N 46 DA "H1'" H N N 47 DA H8 H N N 48 DA H61 H N N 49 DA H62 H N N 50 DA H2 H N N 51 DC OP3 O N N 52 DC P P N N 53 DC OP1 O N N 54 DC OP2 O N N 55 DC "O5'" O N N 56 DC "C5'" C N N 57 DC "C4'" C N R 58 DC "O4'" O N N 59 DC "C3'" C N S 60 DC "O3'" O N N 61 DC "C2'" C N N 62 DC "C1'" C N R 63 DC N1 N N N 64 DC C2 C N N 65 DC O2 O N N 66 DC N3 N N N 67 DC C4 C N N 68 DC N4 N N N 69 DC C5 C N N 70 DC C6 C N N 71 DC HOP3 H N N 72 DC HOP2 H N N 73 DC "H5'" H N N 74 DC "H5''" H N N 75 DC "H4'" H N N 76 DC "H3'" H N N 77 DC "HO3'" H N N 78 DC "H2'" H N N 79 DC "H2''" H N N 80 DC "H1'" H N N 81 DC H41 H N N 82 DC H42 H N N 83 DC H5 H N N 84 DC H6 H N N 85 DG OP3 O N N 86 DG P P N N 87 DG OP1 O N N 88 DG OP2 O N N 89 DG "O5'" O N N 90 DG "C5'" C N N 91 DG "C4'" C N R 92 DG "O4'" O N N 93 DG "C3'" C N S 94 DG "O3'" O N N 95 DG "C2'" C N N 96 DG "C1'" C N R 97 DG N9 N Y N 98 DG C8 C Y N 99 DG N7 N Y N 100 DG C5 C Y N 101 DG C6 C N N 102 DG O6 O N N 103 DG N1 N N N 104 DG C2 C N N 105 DG N2 N N N 106 DG N3 N N N 107 DG C4 C Y N 108 DG HOP3 H N N 109 DG HOP2 H N N 110 DG "H5'" H N N 111 DG "H5''" H N N 112 DG "H4'" H N N 113 DG "H3'" H N N 114 DG "HO3'" H N N 115 DG "H2'" H N N 116 DG "H2''" H N N 117 DG "H1'" H N N 118 DG H8 H N N 119 DG H1 H N N 120 DG H21 H N N 121 DG H22 H N N 122 DT OP3 O N N 123 DT P P N N 124 DT OP1 O N N 125 DT OP2 O N N 126 DT "O5'" O N N 127 DT "C5'" C N N 128 DT "C4'" C N R 129 DT "O4'" O N N 130 DT "C3'" C N S 131 DT "O3'" O N N 132 DT "C2'" C N N 133 DT "C1'" C N R 134 DT N1 N N N 135 DT C2 C N N 136 DT O2 O N N 137 DT N3 N N N 138 DT C4 C N N 139 DT O4 O N N 140 DT C5 C N N 141 DT C7 C N N 142 DT C6 C N N 143 DT HOP3 H N N 144 DT HOP2 H N N 145 DT "H5'" H N N 146 DT "H5''" H N N 147 DT "H4'" H N N 148 DT "H3'" H N N 149 DT "HO3'" H N N 150 DT "H2'" H N N 151 DT "H2''" H N N 152 DT "H1'" H N N 153 DT H3 H N N 154 DT H71 H N N 155 DT H72 H N N 156 DT H73 H N N 157 DT H6 H N N 158 HOH O O N N 159 HOH H1 H N N 160 HOH H2 H N N 161 SPM N1 N N N 162 SPM C2 C N N 163 SPM C3 C N N 164 SPM C4 C N N 165 SPM N5 N N N 166 SPM C6 C N N 167 SPM C7 C N N 168 SPM C8 C N N 169 SPM C9 C N N 170 SPM N10 N N N 171 SPM C11 C N N 172 SPM C12 C N N 173 SPM C13 C N N 174 SPM N14 N N N 175 SPM HN11 H N N 176 SPM HN12 H N N 177 SPM H21 H N N 178 SPM H22 H N N 179 SPM H31 H N N 180 SPM H32 H N N 181 SPM H41 H N N 182 SPM H42 H N N 183 SPM HN5 H N N 184 SPM H61 H N N 185 SPM H62 H N N 186 SPM H71 H N N 187 SPM H72 H N N 188 SPM H81 H N N 189 SPM H82 H N N 190 SPM H91 H N N 191 SPM H92 H N N 192 SPM HN0 H N N 193 SPM H111 H N N 194 SPM H112 H N N 195 SPM H121 H N N 196 SPM H122 H N N 197 SPM H131 H N N 198 SPM H132 H N N 199 SPM HN41 H N N 200 SPM HN42 H N N 201 # 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 13D CA CB sing N N 1 13D CA NAA sing N N 2 13D CA HAC1 sing N N 3 13D CA HAC2 sing N N 4 13D CB CC sing N N 5 13D CB HBC1 sing N N 6 13D CB HBC2 sing N N 7 13D CC ND sing N N 8 13D CC HCC1 sing N N 9 13D CC HCC2 sing N N 10 13D ND HDN1 sing N N 11 13D ND HDN2 sing N N 12 13D NAA HAA1 sing N N 13 13D NAA HAA2 sing N N 14 DA OP3 P sing N N 15 DA OP3 HOP3 sing N N 16 DA P OP1 doub N N 17 DA P OP2 sing N N 18 DA P "O5'" sing N N 19 DA OP2 HOP2 sing N N 20 DA "O5'" "C5'" sing N N 21 DA "C5'" "C4'" sing N N 22 DA "C5'" "H5'" sing N N 23 DA "C5'" "H5''" sing N N 24 DA "C4'" "O4'" sing N N 25 DA "C4'" "C3'" sing N N 26 DA "C4'" "H4'" sing N N 27 DA "O4'" "C1'" sing N N 28 DA "C3'" "O3'" sing N N 29 DA "C3'" "C2'" sing N N 30 DA "C3'" "H3'" sing N N 31 DA "O3'" "HO3'" sing N N 32 DA "C2'" "C1'" sing N N 33 DA "C2'" "H2'" sing N N 34 DA "C2'" "H2''" sing N N 35 DA "C1'" N9 sing N N 36 DA "C1'" "H1'" sing N N 37 DA N9 C8 sing Y N 38 DA N9 C4 sing Y N 39 DA C8 N7 doub Y N 40 DA C8 H8 sing N N 41 DA N7 C5 sing Y N 42 DA C5 C6 sing Y N 43 DA C5 C4 doub Y N 44 DA C6 N6 sing N N 45 DA C6 N1 doub Y N 46 DA N6 H61 sing N N 47 DA N6 H62 sing N N 48 DA N1 C2 sing Y N 49 DA C2 N3 doub Y N 50 DA C2 H2 sing N N 51 DA N3 C4 sing Y N 52 DC OP3 P sing N N 53 DC OP3 HOP3 sing N N 54 DC P OP1 doub N N 55 DC P OP2 sing N N 56 DC P "O5'" sing N N 57 DC OP2 HOP2 sing N N 58 DC "O5'" "C5'" sing N N 59 DC "C5'" "C4'" sing N N 60 DC "C5'" "H5'" sing N N 61 DC "C5'" "H5''" sing N N 62 DC "C4'" "O4'" sing N N 63 DC "C4'" "C3'" sing N N 64 DC "C4'" "H4'" sing N N 65 DC "O4'" "C1'" sing N N 66 DC "C3'" "O3'" sing N N 67 DC "C3'" "C2'" sing N N 68 DC "C3'" "H3'" sing N N 69 DC "O3'" "HO3'" sing N N 70 DC "C2'" "C1'" sing N N 71 DC "C2'" "H2'" sing N N 72 DC "C2'" "H2''" sing N N 73 DC "C1'" N1 sing N N 74 DC "C1'" "H1'" sing N N 75 DC N1 C2 sing N N 76 DC N1 C6 sing N N 77 DC C2 O2 doub N N 78 DC C2 N3 sing N N 79 DC N3 C4 doub N N 80 DC C4 N4 sing N N 81 DC C4 C5 sing N N 82 DC N4 H41 sing N N 83 DC N4 H42 sing N N 84 DC C5 C6 doub N N 85 DC C5 H5 sing N N 86 DC C6 H6 sing N N 87 DG OP3 P sing N N 88 DG OP3 HOP3 sing N N 89 DG P OP1 doub N N 90 DG P OP2 sing N N 91 DG P "O5'" sing N N 92 DG OP2 HOP2 sing N N 93 DG "O5'" "C5'" sing N N 94 DG "C5'" "C4'" sing N N 95 DG "C5'" "H5'" sing N N 96 DG "C5'" "H5''" sing N N 97 DG "C4'" "O4'" sing N N 98 DG "C4'" "C3'" sing N N 99 DG "C4'" "H4'" sing N N 100 DG "O4'" "C1'" sing N N 101 DG "C3'" "O3'" sing N N 102 DG "C3'" "C2'" sing N N 103 DG "C3'" "H3'" sing N N 104 DG "O3'" "HO3'" sing N N 105 DG "C2'" "C1'" sing N N 106 DG "C2'" "H2'" sing N N 107 DG "C2'" "H2''" sing N N 108 DG "C1'" N9 sing N N 109 DG "C1'" "H1'" sing N N 110 DG N9 C8 sing Y N 111 DG N9 C4 sing Y N 112 DG C8 N7 doub Y N 113 DG C8 H8 sing N N 114 DG N7 C5 sing Y N 115 DG C5 C6 sing N N 116 DG C5 C4 doub Y N 117 DG C6 O6 doub N N 118 DG C6 N1 sing N N 119 DG N1 C2 sing N N 120 DG N1 H1 sing N N 121 DG C2 N2 sing N N 122 DG C2 N3 doub N N 123 DG N2 H21 sing N N 124 DG N2 H22 sing N N 125 DG N3 C4 sing N N 126 DT OP3 P sing N N 127 DT OP3 HOP3 sing N N 128 DT P OP1 doub N N 129 DT P OP2 sing N N 130 DT P "O5'" sing N N 131 DT OP2 HOP2 sing N N 132 DT "O5'" "C5'" sing N N 133 DT "C5'" "C4'" sing N N 134 DT "C5'" "H5'" sing N N 135 DT "C5'" "H5''" sing N N 136 DT "C4'" "O4'" sing N N 137 DT "C4'" "C3'" sing N N 138 DT "C4'" "H4'" sing N N 139 DT "O4'" "C1'" sing N N 140 DT "C3'" "O3'" sing N N 141 DT "C3'" "C2'" sing N N 142 DT "C3'" "H3'" sing N N 143 DT "O3'" "HO3'" sing N N 144 DT "C2'" "C1'" sing N N 145 DT "C2'" "H2'" sing N N 146 DT "C2'" "H2''" sing N N 147 DT "C1'" N1 sing N N 148 DT "C1'" "H1'" sing N N 149 DT N1 C2 sing N N 150 DT N1 C6 sing N N 151 DT C2 O2 doub N N 152 DT C2 N3 sing N N 153 DT N3 C4 sing N N 154 DT N3 H3 sing N N 155 DT C4 O4 doub N N 156 DT C4 C5 sing N N 157 DT C5 C7 sing N N 158 DT C5 C6 doub N N 159 DT C7 H71 sing N N 160 DT C7 H72 sing N N 161 DT C7 H73 sing N N 162 DT C6 H6 sing N N 163 HOH O H1 sing N N 164 HOH O H2 sing N N 165 SPM N1 C2 sing N N 166 SPM N1 HN11 sing N N 167 SPM N1 HN12 sing N N 168 SPM C2 C3 sing N N 169 SPM C2 H21 sing N N 170 SPM C2 H22 sing N N 171 SPM C3 C4 sing N N 172 SPM C3 H31 sing N N 173 SPM C3 H32 sing N N 174 SPM C4 N5 sing N N 175 SPM C4 H41 sing N N 176 SPM C4 H42 sing N N 177 SPM N5 C6 sing N N 178 SPM N5 HN5 sing N N 179 SPM C6 C7 sing N N 180 SPM C6 H61 sing N N 181 SPM C6 H62 sing N N 182 SPM C7 C8 sing N N 183 SPM C7 H71 sing N N 184 SPM C7 H72 sing N N 185 SPM C8 C9 sing N N 186 SPM C8 H81 sing N N 187 SPM C8 H82 sing N N 188 SPM C9 N10 sing N N 189 SPM C9 H91 sing N N 190 SPM C9 H92 sing N N 191 SPM N10 C11 sing N N 192 SPM N10 HN0 sing N N 193 SPM C11 C12 sing N N 194 SPM C11 H111 sing N N 195 SPM C11 H112 sing N N 196 SPM C12 C13 sing N N 197 SPM C12 H121 sing N N 198 SPM C12 H122 sing N N 199 SPM C13 N14 sing N N 200 SPM C13 H131 sing N N 201 SPM C13 H132 sing N N 202 SPM N14 HN41 sing N N 203 SPM N14 HN42 sing N N 204 # _ndb_struct_conf_na.entry_id 2F8W _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 -0.242 -0.173 0.086 6.255 -1.394 2.616 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DA 2 1_555 B DT 5 1_555 0.049 -0.195 -0.182 -10.166 -4.376 1.376 2 A_DA2:DT11_B A 2 ? B 11 ? 20 1 1 A DC 3 1_555 B DG 4 1_555 -0.271 -0.176 0.134 1.168 4.789 2.043 3 A_DC3:DG10_B A 3 ? B 10 ? 19 1 1 A DG 4 1_555 B DC 3 1_555 0.251 -0.223 0.103 -6.702 3.214 2.533 4 A_DG4:DC9_B A 4 ? B 9 ? 19 1 1 A DT 5 1_555 B DA 2 1_555 -0.123 -0.145 0.012 7.620 -4.336 5.274 5 A_DT5:DA8_B A 5 ? B 8 ? 20 1 1 A DG 6 1_555 B DC 1 1_555 0.214 -0.163 -0.012 -1.929 -2.419 2.458 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 DA 2 1_555 B DT 5 1_555 0.208 5.718 3.856 1.003 -3.529 -11.416 -20.768 2.877 5.332 17.168 4.881 -11.989 1 AA_DC1DA2:DT11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DA 2 1_555 B DT 5 1_555 A DC 3 1_555 B DG 4 1_555 0.682 -0.436 3.208 -1.611 -3.161 -50.829 0.722 0.683 3.196 3.678 -1.874 -50.944 2 AA_DA2DC3:DG10DT11_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 -0.372 5.429 3.698 -0.963 1.109 -9.884 -33.314 -3.997 3.021 -6.392 -5.547 -9.992 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 DT 5 1_555 B DA 2 1_555 -0.342 -0.993 3.257 2.018 3.278 -50.298 0.930 -0.257 3.322 -3.851 2.370 -50.436 4 AA_DG4DT5:DA8DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DT 5 1_555 B DA 2 1_555 A DG 6 1_555 B DC 1 1_555 -0.311 5.490 3.766 3.619 -0.249 -7.482 -37.061 9.620 3.689 1.776 25.830 -8.314 5 AA_DT5DG6:DC7DA8_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 SPERMINE SPM 3 1,3-DIAMINOPROPANE 13D 4 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 1D48 _pdbx_initial_refinement_model.details 'PDB entry 1D48' #