data_2H9S # _entry.id 2H9S # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2H9S pdb_00002h9s 10.2210/pdb2h9s/pdb NDB UD0070 ? ? RCSB RCSB038108 ? ? WWPDB D_1000038108 ? ? # 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 2006-12-12 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2019-07-24 5 'Structure model' 1 4 2024-02-14 # _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' Advisory 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' 7 5 'Structure model' Advisory 8 5 'Structure model' 'Data collection' 9 5 'Structure model' 'Database references' 10 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' pdbx_struct_special_symmetry 2 4 'Structure model' pdbx_unobs_or_zero_occ_residues 3 4 'Structure model' software 4 4 'Structure model' struct_conn 5 5 'Structure model' chem_comp_atom 6 5 'Structure model' chem_comp_bond 7 5 'Structure model' database_2 8 5 'Structure model' pdbx_struct_conn_angle 9 5 'Structure model' pdbx_unobs_or_zero_occ_residues 10 5 'Structure model' struct_conn 11 5 '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' '_software.classification' 2 4 'Structure model' '_software.name' 3 4 'Structure model' '_software.version' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 5 'Structure model' '_database_2.pdbx_DOI' 6 5 'Structure model' '_database_2.pdbx_database_accession' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.value' 10 5 'Structure model' '_struct_conn.pdbx_dist_value' 11 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 12 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 13 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 14 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2H9S _pdbx_database_status.recvd_initial_deposition_date 2006-06-11 _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.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 'Egli, M.' 1 'Pallan, P.S.' 2 # _citation.id primary _citation.title ;Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system. ; _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 128 _citation.page_first 10847 _citation.page_last 10856 _citation.year 2006 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16910680 _citation.pdbx_database_id_DOI 10.1021/ja062548x # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Egli, M.' 1 ? primary 'Pallan, P.S.' 2 ? primary 'Pattanayek, R.' 3 ? primary 'Wilds, C.J.' 4 ? primary 'Lubini, P.' 5 ? primary 'Minasov, G.' 6 ? primary 'Dobler, M.' 7 ? primary 'Leumann, C.J.' 8 ? primary 'Eschenmoser, A.' 9 ? # 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(*(XCT)P*(XGU)P*(XAD)P*(XAD)P*(XTH)P*(XTH)P*(XCT)P*(XGU))-3'" 2538.831 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 3 water nat water 18.015 72 ? ? ? ? # _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 '(XCT)(XGU)(XAD)(XAD)(XTH)(XTH)(XCT)(XGU)' _entity_poly.pdbx_seq_one_letter_code_can CGAATTCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 XCT n 1 2 XGU n 1 3 XAD n 1 4 XAD n 1 5 XTH n 1 6 XTH n 1 7 XCT n 1 8 XGU 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 'Chemically Synthesized' # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 XAD 'DNA linking' n '9-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-9H-PURIN-6-AMINE' ;2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL ADENINE ; 'C11 H16 N5 O6 P' 345.248 XCT 'DNA linking' n '4-AMINO-1-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)PYRIMIDIN-2(1H)-ONE' ;2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL CYTOSINE ; 'C10 H16 N3 O7 P' 321.224 XGU 'DNA linking' n '2-AMINO-9-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE' ;2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL GUANINE ; 'C11 H16 N5 O7 P' 361.248 XTH 'DNA linking' n '1-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE' ;2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL THYMINE ; 'C11 H17 N2 O8 P' 336.235 # 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 XCT 1 1 1 XCT XCT A . n A 1 2 XGU 2 2 2 XGU XGU A . n A 1 3 XAD 3 3 3 XAD XAD A . n A 1 4 XAD 4 4 4 XAD XAD A . n A 1 5 XTH 5 5 5 XTH XTH A . n A 1 6 XTH 6 6 6 XTH XTH A . n A 1 7 XCT 7 7 7 XCT XCT A . n A 1 8 XGU 8 8 8 XGU XGU A . n B 1 1 XCT 1 9 9 XCT XCT B . n B 1 2 XGU 2 10 10 XGU XGU B . n B 1 3 XAD 3 11 11 XAD XAD B . n B 1 4 XAD 4 12 12 XAD XAD B . n B 1 5 XTH 5 13 13 XTH XTH B . n B 1 6 XTH 6 14 14 XTH XTH B . n B 1 7 XCT 7 15 15 XCT XCT B . n B 1 8 XGU 8 16 16 XGU XGU 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 1 200 200 MG MO6 A . D 3 HOH 1 201 200 HOH MO6 A . D 3 HOH 2 202 200 HOH MO6 A . D 3 HOH 3 203 200 HOH MO6 A . D 3 HOH 4 204 200 HOH MO6 A . D 3 HOH 5 205 200 HOH MO6 A . D 3 HOH 6 206 1 HOH HOH A . D 3 HOH 7 207 3 HOH HOH A . D 3 HOH 8 208 4 HOH HOH A . D 3 HOH 9 209 9 HOH HOH A . D 3 HOH 10 210 10 HOH HOH A . D 3 HOH 11 211 11 HOH HOH A . D 3 HOH 12 212 16 HOH HOH A . D 3 HOH 13 213 19 HOH HOH A . D 3 HOH 14 214 20 HOH HOH A . D 3 HOH 15 215 29 HOH HOH A . D 3 HOH 16 216 32 HOH HOH A . D 3 HOH 17 217 33 HOH HOH A . D 3 HOH 18 218 34 HOH HOH A . D 3 HOH 19 219 37 HOH HOH A . D 3 HOH 20 220 38 HOH HOH A . D 3 HOH 21 221 41 HOH HOH A . D 3 HOH 22 222 48 HOH HOH A . D 3 HOH 23 223 55 HOH HOH A . D 3 HOH 24 224 56 HOH HOH A . D 3 HOH 25 225 65 HOH HOH A . D 3 HOH 26 226 66 HOH HOH A . D 3 HOH 27 227 67 HOH HOH A . D 3 HOH 28 228 69 HOH HOH A . D 3 HOH 29 229 70 HOH HOH A . D 3 HOH 30 230 71 HOH HOH A . E 3 HOH 1 17 2 HOH HOH B . E 3 HOH 2 18 5 HOH HOH B . E 3 HOH 3 19 6 HOH HOH B . E 3 HOH 4 20 7 HOH HOH B . E 3 HOH 5 21 8 HOH HOH B . E 3 HOH 6 22 12 HOH HOH B . E 3 HOH 7 23 13 HOH HOH B . E 3 HOH 8 24 14 HOH HOH B . E 3 HOH 9 25 17 HOH HOH B . E 3 HOH 10 26 18 HOH HOH B . E 3 HOH 11 27 21 HOH HOH B . E 3 HOH 12 28 22 HOH HOH B . E 3 HOH 13 29 23 HOH HOH B . E 3 HOH 14 30 24 HOH HOH B . E 3 HOH 15 31 25 HOH HOH B . E 3 HOH 16 32 26 HOH HOH B . E 3 HOH 17 33 27 HOH HOH B . E 3 HOH 18 34 28 HOH HOH B . E 3 HOH 19 35 30 HOH HOH B . E 3 HOH 20 36 31 HOH HOH B . E 3 HOH 21 37 35 HOH HOH B . E 3 HOH 22 38 36 HOH HOH B . E 3 HOH 23 39 39 HOH HOH B . E 3 HOH 24 40 40 HOH HOH B . E 3 HOH 25 41 43 HOH HOH B . E 3 HOH 26 42 45 HOH HOH B . E 3 HOH 27 43 46 HOH HOH B . E 3 HOH 28 44 47 HOH HOH B . E 3 HOH 29 45 49 HOH HOH B . E 3 HOH 30 46 50 HOH HOH B . E 3 HOH 31 47 51 HOH HOH B . E 3 HOH 32 48 52 HOH HOH B . E 3 HOH 33 49 53 HOH HOH B . E 3 HOH 34 50 54 HOH HOH B . E 3 HOH 35 51 57 HOH HOH B . E 3 HOH 36 52 58 HOH HOH B . E 3 HOH 37 53 59 HOH HOH B . E 3 HOH 38 54 60 HOH HOH B . E 3 HOH 39 55 61 HOH HOH B . E 3 HOH 40 56 62 HOH HOH B . E 3 HOH 41 57 63 HOH HOH B . E 3 HOH 42 58 64 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.0 ? 1 HKL-2000 'data reduction' . ? 2 CNS refinement . ? 3 DENZO 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 CNS phasing . ? 6 # _cell.entry_id 2H9S _cell.length_a 38.940 _cell.length_b 38.940 _cell.length_c 133.850 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 24 _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 2H9S _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? # _exptl.entry_id 2H9S _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.88 _exptl_crystal.density_percent_sol 57.36 _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 290 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;1.5 mM homo-DNA, 8 mM Sodium Cacodylate (pH 7.0), 6 mM Magnesium Chloride, 12% MPD (2-methyl-2,4-pentanediol), VAPOR DIFFUSION, SITTING DROP, temperature 290K ; _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 'Magnesium Chloride' ? ? ? 1 3 1 'MPD (2-methyl-2,4-pentanediol)' ? ? ? 1 4 1 H2O ? ? ? 1 5 2 'Sodium Cacodylate' ? ? ? 1 6 2 'Magnesium Chloride' ? ? ? 1 7 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 110 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2000-03-06 _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 'Double crystal Si(111) cryogenically cooled monochromator' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 5ID-B' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 5ID-B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.00 # _reflns.entry_id 2H9S _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 1.75 _reflns.d_resolution_low 20.0 _reflns.number_all ? _reflns.number_obs 6688 _reflns.percent_possible_obs 99.2 _reflns.pdbx_Rmerge_I_obs 0.035 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 9.9 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 12.9 _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 1.75 _reflns_shell.d_res_low 1.81 _reflns_shell.percent_possible_all 98.9 _reflns_shell.Rmerge_I_obs 0.22 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 9.9 _reflns_shell.pdbx_redundancy 12.7 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 638 _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 2H9S _refine.ls_d_res_high 1.75 _refine.ls_d_res_low 20.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 6688 _refine.ls_number_reflns_obs 6652 _refine.ls_number_reflns_R_free 658 _refine.ls_percent_reflns_obs 99.5 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.24 _refine.ls_R_factor_R_work 0.24 _refine.ls_R_factor_R_free 0.28 _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 MAD _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _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 Anisotropic _refine.B_iso_mean ? _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_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 364 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 67 _refine_hist.number_atoms_total 437 _refine_hist.d_res_high 1.75 _refine_hist.d_res_low 20.0 # 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 r_angle_refined_deg 1.17 ? ? ? 'X-RAY DIFFRACTION' ? r_bond_refined_d 0.015 ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 2H9S _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 2H9S _struct.title ;Crystal Structure of Homo-DNA and Nature's Choice of Pentose over Hexose in the Genetic System ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2H9S _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;Homo-DNA, Homo-DNA crystal structure, 2', 3'-Di-deoxy-beta- D-glucopyranose, Hexose nucleic acid, Glucopyranosyl nucleic acid, Dideoxyglucopyranose Octamer, DNA ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2H9S _struct_ref.pdbx_db_accession 2H9S _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 2H9S A 1 ? 8 ? 2H9S 1 ? 8 ? 1 8 2 1 2H9S B 1 ? 8 ? 2H9S 9 ? 16 ? 9 16 # _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 # _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_ _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 one ? A XCT 1 "O4'" ? ? ? 1_555 A XGU 2 P ? ? A XCT 1 A XGU 2 1_555 ? ? ? ? ? ? ? 1.637 ? ? covale2 covale one ? A XGU 2 "O4'" ? ? ? 1_555 A XAD 3 P ? ? A XGU 2 A XAD 3 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale3 covale one ? A XAD 3 "O4'" ? ? ? 1_555 A XAD 4 P ? ? A XAD 3 A XAD 4 1_555 ? ? ? ? ? ? ? 1.580 ? ? covale4 covale one ? A XAD 4 "O4'" ? ? ? 1_555 A XTH 5 P ? ? A XAD 4 A XTH 5 1_555 ? ? ? ? ? ? ? 1.590 ? ? covale5 covale one ? A XTH 5 "O4'" ? ? ? 1_555 A XTH 6 P ? ? A XTH 5 A XTH 6 1_555 ? ? ? ? ? ? ? 1.592 ? ? covale6 covale one ? A XTH 6 "O4'" ? ? ? 1_555 A XCT 7 P ? ? A XTH 6 A XCT 7 1_555 ? ? ? ? ? ? ? 1.584 ? ? covale7 covale one ? A XCT 7 "O4'" ? ? ? 1_555 A XGU 8 P ? ? A XCT 7 A XGU 8 1_555 ? ? ? ? ? ? ? 1.579 ? ? covale8 covale one ? B XCT 1 "O4'" ? ? ? 1_555 B XGU 2 P ? ? B XCT 9 B XGU 10 1_555 ? ? ? ? ? ? ? 1.572 ? ? covale9 covale one ? B XGU 2 "O4'" ? ? ? 1_555 B XAD 3 P ? ? B XGU 10 B XAD 11 1_555 ? ? ? ? ? ? ? 1.579 ? ? covale10 covale one ? B XAD 3 "O4'" ? ? ? 1_555 B XAD 4 P ? ? B XAD 11 B XAD 12 1_555 ? ? ? ? ? ? ? 1.569 ? ? covale11 covale one ? B XAD 4 "O4'" ? ? ? 1_555 B XTH 5 P ? ? B XAD 12 B XTH 13 1_555 ? ? ? ? ? ? ? 1.589 ? ? covale12 covale one ? B XTH 5 "O4'" A ? ? 1_555 B XTH 6 P A ? B XTH 13 B XTH 14 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale13 covale one ? B XTH 5 "O4'" B ? ? 1_555 B XTH 6 P B ? B XTH 13 B XTH 14 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale14 covale one ? B XTH 6 "O4'" A ? ? 1_555 B XCT 7 P A ? B XTH 14 B XCT 15 1_555 ? ? ? ? ? ? ? 1.586 ? ? covale15 covale one ? B XTH 6 "O4'" B ? ? 1_555 B XCT 7 P B ? B XTH 14 B XCT 15 1_555 ? ? ? ? ? ? ? 1.591 ? ? covale16 covale one ? B XCT 7 "O4'" ? ? ? 1_555 B XGU 8 P ? ? B XCT 15 B XGU 16 1_555 ? ? ? ? ? ? ? 1.603 ? ? metalc1 metalc ? ? A XGU 2 OP1 ? ? ? 1_555 C MG . MG ? ? A XGU 2 A MG 200 1_555 ? ? ? ? ? ? ? 2.103 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 200 A HOH 201 1_555 ? ? ? ? ? ? ? 2.102 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 200 A HOH 202 1_555 ? ? ? ? ? ? ? 2.091 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 200 A HOH 203 1_555 ? ? ? ? ? ? ? 2.086 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 200 A HOH 204 1_555 ? ? ? ? ? ? ? 2.029 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 D HOH . O ? ? A MG 200 A HOH 205 1_555 ? ? ? ? ? ? ? 2.106 ? ? hydrog1 hydrog ? ? A XCT 1 N3 ? ? ? 1_555 B XGU 8 N1 ? ? A XCT 1 B XGU 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A XCT 1 N4 ? ? ? 1_555 B XGU 8 O6 ? ? A XCT 1 B XGU 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A XCT 1 O2 ? ? ? 1_555 B XGU 8 N2 ? ? A XCT 1 B XGU 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A XGU 2 N1 ? ? ? 1_555 B XCT 7 N3 ? ? A XGU 2 B XCT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A XGU 2 N2 ? ? ? 1_555 B XCT 7 O2 ? ? A XGU 2 B XCT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A XGU 2 O6 ? ? ? 1_555 B XCT 7 N4 ? ? A XGU 2 B XCT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A XAD 4 N1 ? ? ? 1_555 B XTH 5 N3 ? ? A XAD 4 B XTH 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A XAD 4 N6 ? ? ? 1_555 B XTH 5 O4 ? ? A XAD 4 B XTH 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A XTH 5 N3 ? ? ? 1_555 B XAD 4 N1 ? ? A XTH 5 B XAD 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A XTH 5 O4 ? ? ? 1_555 B XAD 4 N6 ? ? A XTH 5 B XAD 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A XCT 7 N3 ? ? ? 1_555 B XGU 2 N1 ? ? A XCT 7 B XGU 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A XCT 7 N4 ? ? ? 1_555 B XGU 2 O6 ? ? A XCT 7 B XGU 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A XCT 7 O2 ? ? ? 1_555 B XGU 2 N2 ? ? A XCT 7 B XGU 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A XGU 8 N1 ? ? ? 1_555 B XCT 1 N3 ? ? A XGU 8 B XCT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A XGU 8 N2 ? ? ? 1_555 B XCT 1 O2 ? ? A XGU 8 B XCT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A XGU 8 O6 ? ? ? 1_555 B XCT 1 N4 ? ? A XGU 8 B XCT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP1 ? A XGU 2 ? A XGU 2 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 201 ? 1_555 90.8 ? 2 OP1 ? A XGU 2 ? A XGU 2 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 202 ? 1_555 88.1 ? 3 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 202 ? 1_555 89.4 ? 4 OP1 ? A XGU 2 ? A XGU 2 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 203 ? 1_555 90.4 ? 5 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 203 ? 1_555 178.1 ? 6 O ? D HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 203 ? 1_555 89.2 ? 7 OP1 ? A XGU 2 ? A XGU 2 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 91.8 ? 8 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 91.3 ? 9 O ? D HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 179.4 ? 10 O ? D HOH . ? A HOH 203 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 204 ? 1_555 90.1 ? 11 OP1 ? A XGU 2 ? A XGU 2 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 205 ? 1_555 177.7 ? 12 O ? D HOH . ? A HOH 201 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 205 ? 1_555 88.0 ? 13 O ? D HOH . ? A HOH 202 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 205 ? 1_555 90.0 ? 14 O ? D HOH . ? A HOH 203 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 205 ? 1_555 90.7 ? 15 O ? D HOH . ? A HOH 204 ? 1_555 MG ? C MG . ? A MG 200 ? 1_555 O ? D HOH . ? A HOH 205 ? 1_555 90.1 ? # _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 200 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 8 _struct_site.details 'BINDING SITE FOR RESIDUE MG A 200' # 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 8 XGU A 2 ? XGU A 2 . ? 1_555 ? 2 AC1 8 HOH D . ? HOH A 202 . ? 1_555 ? 3 AC1 8 HOH D . ? HOH A 202 . ? 12_565 ? 4 AC1 8 HOH D . ? HOH A 203 . ? 12_565 ? 5 AC1 8 HOH D . ? HOH A 203 . ? 1_555 ? 6 AC1 8 HOH D . ? HOH A 204 . ? 1_555 ? 7 AC1 8 HOH D . ? HOH A 205 . ? 12_565 ? 8 AC1 8 HOH D . ? HOH A 205 . ? 1_555 ? # 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 XCT 1 A XCT 1 ? DC ? 2 A XGU 2 A XGU 2 ? DG ? 3 A XAD 3 A XAD 3 ? DA ? 4 A XAD 4 A XAD 4 ? DA ? 5 A XTH 5 A XTH 5 ? DT ? 6 A XTH 6 A XTH 6 ? DT ? 7 A XCT 7 A XCT 7 ? DC ? 8 A XGU 8 A XGU 8 ? DG ? 9 B XCT 1 B XCT 9 ? DC ? 10 B XGU 2 B XGU 10 ? DG ? 11 B XAD 3 B XAD 11 ? DA ? 12 B XAD 4 B XAD 12 ? DA ? 13 B XTH 5 B XTH 13 ? DT ? 14 B XTH 6 B XTH 14 ? DT ? 15 B XCT 7 B XCT 15 ? DC ? 16 B XGU 8 B XGU 16 ? DG ? # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 216 ? D HOH . 2 1 B HOH 53 ? E HOH . 3 1 B HOH 58 ? E HOH . # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag N _pdbx_unobs_or_zero_occ_residues.occupancy_flag 0 _pdbx_unobs_or_zero_occ_residues.auth_asym_id A _pdbx_unobs_or_zero_occ_residues.auth_comp_id HOH _pdbx_unobs_or_zero_occ_residues.auth_seq_id 201 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id D _pdbx_unobs_or_zero_occ_residues.label_comp_id HOH _pdbx_unobs_or_zero_occ_residues.label_seq_id ? # 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 HOH O O N N 1 HOH H1 H N N 2 HOH H2 H N N 3 MG MG MG N N 4 XAD OP3 O N N 5 XAD P P N N 6 XAD OP1 O N N 7 XAD OP2 O N N 8 XAD "O6'" O N N 9 XAD "C6'" C N N 10 XAD "C5'" C N R 11 XAD "C4'" C N S 12 XAD "O4'" O N N 13 XAD "C3'" C N N 14 XAD "C2'" C N N 15 XAD "C1'" C N R 16 XAD "O5'" O N N 17 XAD N9 N Y N 18 XAD C8 C Y N 19 XAD N7 N Y N 20 XAD C5 C Y N 21 XAD C4 C Y N 22 XAD C6 C Y N 23 XAD N6 N N N 24 XAD N1 N Y N 25 XAD C2 C Y N 26 XAD N3 N Y N 27 XAD HOP3 H N N 28 XAD HOP2 H N N 29 XAD "H6'1" H N N 30 XAD "H6'2" H N N 31 XAD "H5'" H N N 32 XAD "H4'" H N N 33 XAD "H4T'" H N N 34 XAD "H3'1" H N N 35 XAD "H3'2" H N N 36 XAD "H2'1" H N N 37 XAD "H2'2" H N N 38 XAD "H1'" H N N 39 XAD H8 H N N 40 XAD HN61 H N N 41 XAD HN62 H N N 42 XAD H2 H N N 43 XCT OP3 O N N 44 XCT P P N N 45 XCT OP1 O N N 46 XCT OP2 O N N 47 XCT "O6'" O N N 48 XCT "C6'" C N N 49 XCT "C5'" C N R 50 XCT "O5'" O N N 51 XCT "C4'" C N S 52 XCT "O4'" O N N 53 XCT "C3'" C N N 54 XCT "C2'" C N N 55 XCT "C1'" C N R 56 XCT N1 N N N 57 XCT C2 C N N 58 XCT O2 O N N 59 XCT C6 C N N 60 XCT C5 C N N 61 XCT C4 C N N 62 XCT N3 N N N 63 XCT N4 N N N 64 XCT HOP3 H N N 65 XCT HOP2 H N N 66 XCT "H6'1" H N N 67 XCT "H6'2" H N N 68 XCT "H5'" H N N 69 XCT "H4'" H N N 70 XCT H4T H N N 71 XCT "H3'1" H N N 72 XCT "H3'2" H N N 73 XCT "H2'1" H N N 74 XCT "H2'2" H N N 75 XCT "H1'" H N N 76 XCT H6 H N N 77 XCT H5 H N N 78 XCT HN41 H N N 79 XCT HN42 H N N 80 XGU OP3 O N N 81 XGU P P N N 82 XGU OP1 O N N 83 XGU OP2 O N N 84 XGU "O6'" O N N 85 XGU "C6'" C N N 86 XGU "C5'" C N R 87 XGU "O5'" O N N 88 XGU "C4'" C N S 89 XGU "O4'" O N N 90 XGU "C3'" C N N 91 XGU "C2'" C N N 92 XGU "C1'" C N R 93 XGU N9 N Y N 94 XGU C8 C Y N 95 XGU N7 N Y N 96 XGU C4 C Y N 97 XGU C5 C Y N 98 XGU N3 N N N 99 XGU C2 C N N 100 XGU N2 N N N 101 XGU N1 N N N 102 XGU C6 C N N 103 XGU O6 O N N 104 XGU HOP3 H N N 105 XGU HOP2 H N N 106 XGU "H6'1" H N N 107 XGU "H6'2" H N N 108 XGU "H5'" H N N 109 XGU "H4'" H N N 110 XGU "H4T'" H N N 111 XGU "H3'1" H N N 112 XGU "H3'2" H N N 113 XGU "H2'1" H N N 114 XGU "H2'2" H N N 115 XGU "H1'" H N N 116 XGU H8 H N N 117 XGU HN21 H N N 118 XGU HN22 H N N 119 XGU HN1 H N N 120 XTH OP3 O N N 121 XTH P P N N 122 XTH OP1 O N N 123 XTH OP2 O N N 124 XTH "O6'" O N N 125 XTH "C6'" C N N 126 XTH "C5'" C N R 127 XTH "C4'" C N S 128 XTH "O4'" O N N 129 XTH "C3'" C N N 130 XTH "C2'" C N N 131 XTH "C1'" C N R 132 XTH "O5'" O N N 133 XTH N1 N N N 134 XTH C2 C N N 135 XTH O2 O N N 136 XTH N3 N N N 137 XTH C4 C N N 138 XTH O4 O N N 139 XTH C5 C N N 140 XTH C5M C N N 141 XTH C6 C N N 142 XTH HOP3 H N N 143 XTH HOP2 H N N 144 XTH "H6'1" H N N 145 XTH "H6'2" H N N 146 XTH "H5'" H N N 147 XTH "H4'" H N N 148 XTH "H4T'" H N N 149 XTH "H3'1" H N N 150 XTH "H3'2" H N N 151 XTH "H2'1" H N N 152 XTH "H2'2" H N N 153 XTH "H1'" H N N 154 XTH HN3 H N N 155 XTH H71 H N N 156 XTH H72 H N N 157 XTH H73 H N N 158 XTH H6 H N N 159 # 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 HOH O H1 sing N N 1 HOH O H2 sing N N 2 XAD OP3 P sing N N 3 XAD OP3 HOP3 sing N N 4 XAD P OP1 doub N N 5 XAD P OP2 sing N N 6 XAD P "O6'" sing N N 7 XAD OP2 HOP2 sing N N 8 XAD "O6'" "C6'" sing N N 9 XAD "C6'" "C5'" sing N N 10 XAD "C6'" "H6'1" sing N N 11 XAD "C6'" "H6'2" sing N N 12 XAD "C5'" "C4'" sing N N 13 XAD "C5'" "O5'" sing N N 14 XAD "C5'" "H5'" sing N N 15 XAD "C4'" "O4'" sing N N 16 XAD "C4'" "C3'" sing N N 17 XAD "C4'" "H4'" sing N N 18 XAD "O4'" "H4T'" sing N N 19 XAD "C3'" "C2'" sing N N 20 XAD "C3'" "H3'1" sing N N 21 XAD "C3'" "H3'2" sing N N 22 XAD "C2'" "C1'" sing N N 23 XAD "C2'" "H2'1" sing N N 24 XAD "C2'" "H2'2" sing N N 25 XAD "C1'" "O5'" sing N N 26 XAD "C1'" N9 sing N N 27 XAD "C1'" "H1'" sing N N 28 XAD N9 C8 sing Y N 29 XAD N9 C4 sing Y N 30 XAD C8 N7 doub Y N 31 XAD C8 H8 sing N N 32 XAD N7 C5 sing Y N 33 XAD C5 C4 doub Y N 34 XAD C5 C6 sing Y N 35 XAD C4 N3 sing Y N 36 XAD C6 N6 sing N N 37 XAD C6 N1 doub Y N 38 XAD N6 HN61 sing N N 39 XAD N6 HN62 sing N N 40 XAD N1 C2 sing Y N 41 XAD C2 N3 doub Y N 42 XAD C2 H2 sing N N 43 XCT OP3 P sing N N 44 XCT OP3 HOP3 sing N N 45 XCT P OP1 doub N N 46 XCT P OP2 sing N N 47 XCT P "O6'" sing N N 48 XCT OP2 HOP2 sing N N 49 XCT "O6'" "C6'" sing N N 50 XCT "C6'" "C5'" sing N N 51 XCT "C6'" "H6'1" sing N N 52 XCT "C6'" "H6'2" sing N N 53 XCT "C5'" "O5'" sing N N 54 XCT "C5'" "C4'" sing N N 55 XCT "C5'" "H5'" sing N N 56 XCT "O5'" "C1'" sing N N 57 XCT "C4'" "O4'" sing N N 58 XCT "C4'" "C3'" sing N N 59 XCT "C4'" "H4'" sing N N 60 XCT "O4'" H4T sing N N 61 XCT "C3'" "C2'" sing N N 62 XCT "C3'" "H3'1" sing N N 63 XCT "C3'" "H3'2" sing N N 64 XCT "C2'" "C1'" sing N N 65 XCT "C2'" "H2'1" sing N N 66 XCT "C2'" "H2'2" sing N N 67 XCT "C1'" N1 sing N N 68 XCT "C1'" "H1'" sing N N 69 XCT N1 C2 sing N N 70 XCT N1 C6 sing N N 71 XCT C2 O2 doub N N 72 XCT C2 N3 sing N N 73 XCT C6 C5 doub N N 74 XCT C6 H6 sing N N 75 XCT C5 C4 sing N N 76 XCT C5 H5 sing N N 77 XCT C4 N3 doub N N 78 XCT C4 N4 sing N N 79 XCT N4 HN41 sing N N 80 XCT N4 HN42 sing N N 81 XGU OP3 P sing N N 82 XGU OP3 HOP3 sing N N 83 XGU P OP1 doub N N 84 XGU P OP2 sing N N 85 XGU P "O6'" sing N N 86 XGU OP2 HOP2 sing N N 87 XGU "O6'" "C6'" sing N N 88 XGU "C6'" "C5'" sing N N 89 XGU "C6'" "H6'1" sing N N 90 XGU "C6'" "H6'2" sing N N 91 XGU "C5'" "O5'" sing N N 92 XGU "C5'" "C4'" sing N N 93 XGU "C5'" "H5'" sing N N 94 XGU "O5'" "C1'" sing N N 95 XGU "C4'" "O4'" sing N N 96 XGU "C4'" "C3'" sing N N 97 XGU "C4'" "H4'" sing N N 98 XGU "O4'" "H4T'" sing N N 99 XGU "C3'" "C2'" sing N N 100 XGU "C3'" "H3'1" sing N N 101 XGU "C3'" "H3'2" sing N N 102 XGU "C2'" "C1'" sing N N 103 XGU "C2'" "H2'1" sing N N 104 XGU "C2'" "H2'2" sing N N 105 XGU "C1'" N9 sing N N 106 XGU "C1'" "H1'" sing N N 107 XGU N9 C8 sing Y N 108 XGU N9 C4 sing Y N 109 XGU C8 N7 doub Y N 110 XGU C8 H8 sing N N 111 XGU N7 C5 sing Y N 112 XGU C4 C5 doub Y N 113 XGU C4 N3 sing N N 114 XGU C5 C6 sing N N 115 XGU N3 C2 doub N N 116 XGU C2 N2 sing N N 117 XGU C2 N1 sing N N 118 XGU N2 HN21 sing N N 119 XGU N2 HN22 sing N N 120 XGU N1 C6 sing N N 121 XGU N1 HN1 sing N N 122 XGU C6 O6 doub N N 123 XTH OP3 P sing N N 124 XTH OP3 HOP3 sing N N 125 XTH P OP1 doub N N 126 XTH P OP2 sing N N 127 XTH P "O6'" sing N N 128 XTH OP2 HOP2 sing N N 129 XTH "O6'" "C6'" sing N N 130 XTH "C6'" "C5'" sing N N 131 XTH "C6'" "H6'1" sing N N 132 XTH "C6'" "H6'2" sing N N 133 XTH "C5'" "C4'" sing N N 134 XTH "C5'" "O5'" sing N N 135 XTH "C5'" "H5'" sing N N 136 XTH "C4'" "O4'" sing N N 137 XTH "C4'" "C3'" sing N N 138 XTH "C4'" "H4'" sing N N 139 XTH "O4'" "H4T'" sing N N 140 XTH "C3'" "C2'" sing N N 141 XTH "C3'" "H3'1" sing N N 142 XTH "C3'" "H3'2" sing N N 143 XTH "C2'" "C1'" sing N N 144 XTH "C2'" "H2'1" sing N N 145 XTH "C2'" "H2'2" sing N N 146 XTH "C1'" "O5'" sing N N 147 XTH "C1'" N1 sing N N 148 XTH "C1'" "H1'" sing N N 149 XTH N1 C2 sing N N 150 XTH N1 C6 sing N N 151 XTH C2 O2 doub N N 152 XTH C2 N3 sing N N 153 XTH N3 C4 sing N N 154 XTH N3 HN3 sing N N 155 XTH C4 O4 doub N N 156 XTH C4 C5 sing N N 157 XTH C5 C5M sing N N 158 XTH C5 C6 doub N N 159 XTH C5M H71 sing N N 160 XTH C5M H72 sing N N 161 XTH C5M H73 sing N N 162 XTH C6 H6 sing N N 163 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2H9S 'double helix' 2H9S 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A XCT 1 1_555 B XGU 8 1_555 0.520 -0.200 0.146 2.149 4.620 -3.220 1 A_XCT1:XGU16_B A 1 ? B 16 ? 19 1 1 A XGU 2 1_555 B XCT 7 1_555 -0.222 -0.107 0.348 -2.980 3.771 -2.761 2 A_XGU2:XCT15_B A 2 ? B 15 ? 19 1 1 A XAD 4 1_555 B XTH 5 1_555 -0.047 0.012 0.286 6.443 4.458 -0.911 3 A_XAD4:XTH13_B A 4 ? B 13 ? 20 1 1 A XTH 5 1_555 B XAD 4 1_555 -0.156 0.037 0.223 -6.712 4.865 -0.775 4 A_XTH5:XAD12_B A 5 ? B 12 ? 20 1 1 A XCT 7 1_555 B XGU 2 1_555 0.363 -0.271 0.150 11.777 9.527 -1.166 5 A_XCT7:XGU10_B A 7 ? B 10 ? 19 1 1 A XGU 8 1_555 B XCT 1 1_555 -0.255 -0.149 0.061 -12.763 -16.833 -3.761 6 A_XGU8:XCT9_B A 8 ? B 9 ? 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 XCT 1 1_555 B XGU 8 1_555 A XGU 2 1_555 B XCT 7 1_555 0.045 5.188 3.930 -0.527 17.389 -5.409 -16.746 0.130 -3.777 -72.825 -2.209 -18.212 1 AA_XCT1XGU2:XCT15XGU16_BB A 1 ? B 16 ? A 2 ? B 15 ? 1 A XAD 4 1_555 B XTH 5 1_555 A XTH 5 1_555 B XAD 4 1_555 -0.066 5.766 4.098 0.675 8.191 9.709 8.054 1.780 6.834 40.195 -3.312 12.714 2 AA_XAD4XTH5:XAD12XTH13_BB A 4 ? B 13 ? A 5 ? B 12 ? # _atom_sites.entry_id 2H9S _atom_sites.fract_transf_matrix[1][1] 0.025681 _atom_sites.fract_transf_matrix[1][2] 0.014827 _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] 0.029653 _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] 0.007471 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C MG N O P # loop_