data_2WNA # _entry.id 2WNA # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 2WNA pdb_00002wna 10.2210/pdb2wna/pdb PDBE EBI-40348 ? ? WWPDB D_1290040348 ? ? # 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 2010-02-16 2 'Structure model' 1 1 2011-05-08 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-05-08 # _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 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_database_status 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' pdbx_struct_special_symmetry 7 4 'Structure model' struct_conn 8 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_database_status.status_code_sf' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.value' 7 4 'Structure model' '_struct_conn.pdbx_dist_value' 8 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 9 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 10 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 11 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 12 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2WNA _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2009-07-07 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _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 'Schlegel, M.K.' 1 'Essen, L.-O.' 2 'Meggers, E.' 3 # 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 'Atomic Resolution Duplex Structure of the Simplified Nucleic Acid Gna.' 'Chem.Commun.(Camb.)' 46 1094 ? 2010 ? UK 1359-7345 ? ? 20126724 10.1039/B916851F 1 'Duplex Structure of a Minimal Nucleic Acid.' J.Am.Chem.Soc. 130 8158 ? 2008 JACSAT US 0002-7863 0004 ? 18529005 10.1021/JA802788G # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Schlegel, M.K.' 1 ? primary 'Essen, L.-O.' 2 ? primary 'Meggers, E.' 3 ? 1 'Schlegel, M.K.' 4 ? 1 'Essen, L.-O.' 5 ? 1 'Meggers, E.' 6 ? # 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 GNA 1636.884 1 ? ? ? ;SYNTHETIC GLYCOL NUCLEIC ACID, 3'-(S)-((ZGU)P(ZBC)P(ZGU)P(ZCY)P(ZGU)P(ZCY))-2' ; 2 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 2 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 4 water nat water 18.015 58 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(ZGU)(ZBC)(ZGU)(ZCY)(ZGU)(ZCY)' _entity_poly.pdbx_seq_one_letter_code_can GCGCGC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COBALT HEXAMMINE(III)' NCO 3 'MAGNESIUM ION' MG 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ZGU n 1 2 ZBC n 1 3 ZGU n 1 4 ZCY n 1 5 ZGU n 1 6 ZCY 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 'HOMO SAPIENS' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # 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 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 ZBC 'RNA linking' n '(2S)-3-(4-AMINO-5-BROMO-2-OXOPYRIMIDIN-1(2H)-YL)-2-HYDROXYPROPYL DIHYDROGEN PHOSPHATE' ? 'C7 H11 Br N3 O6 P' 344.057 ZCY 'RNA linking' n "(S)-1'-(2',3'-DIHYDROXYPROPYL)-CYTOSINE" ? 'C7 H12 N3 O6 P' 265.160 ZGU 'RNA linking' n "(S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE" ? 'C8 H12 N5 O6 P' 305.185 # 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 ZGU 1 1 1 ZGU ZGU A . n A 1 2 ZBC 2 2 2 ZBC ZBC A . n A 1 3 ZGU 3 3 3 ZGU ZGU A . n A 1 4 ZCY 4 4 4 ZCY ZCY A . n A 1 5 ZGU 5 5 5 ZGU ZGU A . n A 1 6 ZCY 6 6 6 ZCY ZCY A . 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 B 2 NCO 1 1001 1001 NCO NCO A . C 2 NCO 1 1002 1002 NCO NCO A . D 3 MG 1 1003 1003 MG MG A . E 4 HOH 1 2001 2001 HOH HOH A . E 4 HOH 2 2002 2002 HOH HOH A . E 4 HOH 3 2003 2003 HOH HOH A . E 4 HOH 4 2004 2004 HOH HOH A . E 4 HOH 5 2005 2005 HOH HOH A . E 4 HOH 6 2006 2006 HOH HOH A . E 4 HOH 7 2007 2007 HOH HOH A . E 4 HOH 8 2008 2008 HOH HOH A . E 4 HOH 9 2009 2009 HOH HOH A . E 4 HOH 10 2010 2010 HOH HOH A . E 4 HOH 11 2011 2011 HOH HOH A . E 4 HOH 12 2012 2012 HOH HOH A . E 4 HOH 13 2013 2013 HOH HOH A . E 4 HOH 14 2014 2014 HOH HOH A . E 4 HOH 15 2015 2015 HOH HOH A . E 4 HOH 16 2016 2016 HOH HOH A . E 4 HOH 17 2017 2017 HOH HOH A . E 4 HOH 18 2018 2018 HOH HOH A . E 4 HOH 19 2019 2019 HOH HOH A . E 4 HOH 20 2020 2020 HOH HOH A . E 4 HOH 21 2021 2021 HOH HOH A . E 4 HOH 22 2022 2022 HOH HOH A . E 4 HOH 23 2023 2023 HOH HOH A . E 4 HOH 24 2024 2024 HOH HOH A . E 4 HOH 25 2025 2025 HOH HOH A . E 4 HOH 26 2026 2026 HOH HOH A . E 4 HOH 27 2027 2027 HOH HOH A . E 4 HOH 28 2028 2028 HOH HOH A . E 4 HOH 29 2029 2029 HOH HOH A . E 4 HOH 30 2030 2030 HOH HOH A . E 4 HOH 31 2031 2031 HOH HOH A . E 4 HOH 32 2032 2032 HOH HOH A . E 4 HOH 33 2033 2033 HOH HOH A . E 4 HOH 34 2034 2034 HOH HOH A . E 4 HOH 35 2035 2035 HOH HOH A . E 4 HOH 36 2036 2036 HOH HOH A . E 4 HOH 37 2037 2037 HOH HOH A . E 4 HOH 38 2038 2038 HOH HOH A . E 4 HOH 39 2039 2039 HOH HOH A . E 4 HOH 40 2040 2040 HOH HOH A . E 4 HOH 41 2041 2041 HOH HOH A . E 4 HOH 42 2042 2042 HOH HOH A . E 4 HOH 43 2043 2043 HOH HOH A . E 4 HOH 44 2044 2044 HOH HOH A . E 4 HOH 45 2045 2045 HOH HOH A . E 4 HOH 46 2046 2046 HOH HOH A . E 4 HOH 47 2047 2047 HOH HOH A . E 4 HOH 48 2048 2048 HOH HOH A . E 4 HOH 49 2049 2049 HOH HOH A . E 4 HOH 50 2050 2050 HOH HOH A . E 4 HOH 51 2051 2051 HOH HOH A . E 4 HOH 52 2052 2052 HOH HOH A . E 4 HOH 53 2053 2053 HOH HOH A . E 4 HOH 54 2054 2054 HOH HOH A . E 4 HOH 55 2055 2055 HOH HOH A . E 4 HOH 56 2056 2056 HOH HOH A . E 4 HOH 57 2057 2057 HOH HOH A . E 4 HOH 58 2058 2058 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0019 ? 1 XDS 'data reduction' . ? 2 XSCALE 'data scaling' . ? 3 SHELXE phasing . ? 4 # _cell.entry_id 2WNA _cell.length_a 20.420 _cell.length_b 42.000 _cell.length_c 28.670 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2WNA _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 # _exptl.entry_id 2WNA _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.41 _exptl_crystal.density_percent_sol 12.73 _exptl_crystal.description 'LOW AND HIGH RESOLUTION DATA MERGED FROM SAME CRYSTAL. DATA RECORDING OCCURED AT PEAK WAVELENGTH OF BROMINE' # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;DROP: 2 MM G(BR)CGCGC, 10% 2-METHYL-2,4-PENTANEDIOL, 40 MM SODIUM CACODYLATE (PH 5.5), 20 MM COBALT HEXAMINE, 80 MM SODIUM CHLORIDE, 20 MM MAGNESIUM CHLORIDE RESERVOIR: 35 % MPD ; # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date 2008-11-25 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.91826 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 _diffrn_source.pdbx_wavelength 0.91826 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2WNA _reflns.observed_criterion_sigma_I -3.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 21.00 _reflns.d_resolution_high 0.96 _reflns.number_obs 30224 _reflns.number_all ? _reflns.percent_possible_obs 98.2 _reflns.pdbx_Rmerge_I_obs 0.06 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 17.70 _reflns.B_iso_Wilson_estimate 4.6 _reflns.pdbx_redundancy 3.99 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 0.96 _reflns_shell.d_res_low 1.02 _reflns_shell.percent_possible_all 0.9 _reflns_shell.Rmerge_I_obs 0.13 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 7.20 _reflns_shell.pdbx_redundancy ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2WNA _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 7025 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.00 _refine.ls_d_res_high 0.97 _refine.ls_percent_reflns_obs 97.93 _refine.ls_R_factor_obs 0.10648 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.10503 _refine.ls_R_factor_R_free 0.12726 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 7.1 _refine.ls_number_reflns_R_free 533 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.984 _refine.correlation_coeff_Fo_to_Fc_free 0.973 _refine.B_iso_mean 6.688 _refine.aniso_B[1][1] 0.51 _refine.aniso_B[2][2] 0.07 _refine.aniso_B[3][3] -0.57 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GNA DUPLEX OF TYPE N FORMED WITH SYMMETRY- EQUIVALENT MOLECULE' _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.020 _refine.pdbx_overall_ESU_R_Free 0.021 _refine.overall_SU_ML 0.011 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 0.434 _refine.overall_SU_R_Cruickshank_DPI ? _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 103 _refine_hist.pdbx_number_atoms_ligand 15 _refine_hist.number_atoms_solvent 58 _refine_hist.number_atoms_total 176 _refine_hist.d_res_high 0.97 _refine_hist.d_res_low 8.00 # 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_bond_refined_d 0.006 0.021 ? 150 'X-RAY DIFFRACTION' ? r_bond_other_d 0.000 0.020 ? 53 'X-RAY DIFFRACTION' ? r_angle_refined_deg 3.530 3.000 ? 220 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.698 3.000 ? 118 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.048 0.200 ? 6 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.009 0.020 ? 64 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.000 0.020 ? 23 'X-RAY DIFFRACTION' ? r_nbd_refined 0.081 0.300 ? 11 'X-RAY DIFFRACTION' ? r_nbd_other 0.296 0.300 ? 47 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.265 0.500 ? 42 'X-RAY DIFFRACTION' ? r_nbtor_other 0.076 0.500 ? 30 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.450 0.500 ? 46 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.143 0.500 ? 1 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.144 0.300 ? 13 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.449 0.300 ? 39 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.321 0.500 ? 58 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 2.224 2.000 ? 218 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 2.798 3.000 ? 203 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 1.253 3.000 ? 405 'X-RAY DIFFRACTION' ? r_sphericity_free 10.469 3.000 ? 59 'X-RAY DIFFRACTION' ? r_sphericity_bonded 5.229 3.000 ? 184 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 0.965 _refine_ls_shell.d_res_low 0.990 _refine_ls_shell.number_reflns_R_work 423 _refine_ls_shell.R_factor_R_work 0.161 _refine_ls_shell.percent_reflns_obs 83.88 _refine_ls_shell.R_factor_R_free 0.169 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 40 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 2WNA _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 2WNA _struct.title ;Crystal structure of the GNA 3'-G(Br)CGCGC-2' ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2WNA _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA, GNA, NUCLEIC ACID, GLYCOL NUCLEIC ACID, WATSON-CRICK BASE PAIR' # 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 2 ? C N N 2 ? D N N 3 ? E N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2WNA _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession 2WNA _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2WNA _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 2WNA _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 6 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # 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' 3_855 -x+3,y,-z+1/2 -1.0000000000 0.0000000000 0.0000000000 61.2600000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 14.3350000000 # _struct_biol.id 1 # 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 ZGU 1 O2G ? ? ? 1_555 A ZBC 2 P ? ? A ZGU 1 A ZBC 2 1_555 ? ? ? ? ? ? ? 1.582 ? ? covale2 covale one ? A ZBC 2 O2G ? ? ? 1_555 A ZGU 3 P ? ? A ZBC 2 A ZGU 3 1_555 ? ? ? ? ? ? ? 1.590 ? ? covale3 covale one ? A ZGU 3 O2G ? ? ? 1_555 A ZCY 4 P ? ? A ZGU 3 A ZCY 4 1_555 ? ? ? ? ? ? ? 1.587 ? ? covale4 covale one ? A ZCY 4 O2G ? ? ? 1_555 A ZGU 5 P ? ? A ZCY 4 A ZGU 5 1_555 ? ? ? ? ? ? ? 1.583 ? ? covale5 covale one ? A ZGU 5 O2G ? ? ? 1_555 A ZCY 6 P ? ? A ZGU 5 A ZCY 6 1_555 ? ? ? ? ? ? ? 1.595 ? ? metalc1 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 1003 A HOH 2005 1_555 ? ? ? ? ? ? ? 1.847 ? ? metalc2 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 1003 A HOH 2006 4_576 ? ? ? ? ? ? ? 2.303 ? ? metalc3 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 1003 A HOH 2009 1_555 ? ? ? ? ? ? ? 2.133 ? ? metalc4 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 1003 A HOH 2010 1_555 ? ? ? ? ? ? ? 2.088 ? ? hydrog1 hydrog ? ? A ZGU 1 N1 ? ? ? 1_555 A ZCY 6 N3 ? ? A ZGU 1 A ZCY 6 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A ZGU 1 N2 ? ? ? 1_555 A ZCY 6 O2 ? ? A ZGU 1 A ZCY 6 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A ZGU 1 O6 ? ? ? 1_555 A ZCY 6 N4 ? ? A ZGU 1 A ZCY 6 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A ZBC 2 N3 ? ? ? 1_555 A ZGU 5 N1 ? ? A ZBC 2 A ZGU 5 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A ZBC 2 N4 ? ? ? 1_555 A ZGU 5 O6 ? ? A ZBC 2 A ZGU 5 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A ZBC 2 O2 ? ? ? 1_555 A ZGU 5 N2 ? ? A ZBC 2 A ZGU 5 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A ZGU 3 N1 ? ? ? 1_555 A ZCY 4 N3 ? ? A ZGU 3 A ZCY 4 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A ZGU 3 N2 ? ? ? 1_555 A ZCY 4 O2 ? ? A ZGU 3 A ZCY 4 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A ZGU 3 O6 ? ? ? 1_555 A ZCY 4 N4 ? ? A ZGU 3 A ZCY 4 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A ZCY 4 N3 ? ? ? 1_555 A ZGU 3 N1 ? ? A ZCY 4 A ZGU 3 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A ZCY 4 N4 ? ? ? 1_555 A ZGU 3 O6 ? ? A ZCY 4 A ZGU 3 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A ZCY 4 O2 ? ? ? 1_555 A ZGU 3 N2 ? ? A ZCY 4 A ZGU 3 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A ZGU 5 N1 ? ? ? 1_555 A ZBC 2 N3 ? ? A ZGU 5 A ZBC 2 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A ZGU 5 N2 ? ? ? 1_555 A ZBC 2 O2 ? ? A ZGU 5 A ZBC 2 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A ZGU 5 O6 ? ? ? 1_555 A ZBC 2 N4 ? ? A ZGU 5 A ZBC 2 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A ZCY 6 N3 ? ? ? 1_555 A ZGU 1 N1 ? ? A ZCY 6 A ZGU 1 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A ZCY 6 N4 ? ? ? 1_555 A ZGU 1 O6 ? ? A ZCY 6 A ZGU 1 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A ZCY 6 O2 ? ? ? 1_555 A ZGU 1 N2 ? ? A ZCY 6 A ZGU 1 3_855 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? E HOH . ? A HOH 2005 ? 1_555 MG ? D MG . ? A MG 1003 ? 1_555 O ? E HOH . ? A HOH 2006 ? 4_576 90.4 ? 2 O ? E HOH . ? A HOH 2005 ? 1_555 MG ? D MG . ? A MG 1003 ? 1_555 O ? E HOH . ? A HOH 2009 ? 1_555 102.7 ? 3 O ? E HOH . ? A HOH 2006 ? 4_576 MG ? D MG . ? A MG 1003 ? 1_555 O ? E HOH . ? A HOH 2009 ? 1_555 164.5 ? 4 O ? E HOH . ? A HOH 2005 ? 1_555 MG ? D MG . ? A MG 1003 ? 1_555 O ? E HOH . ? A HOH 2010 ? 1_555 72.6 ? 5 O ? E HOH . ? A HOH 2006 ? 4_576 MG ? D MG . ? A MG 1003 ? 1_555 O ? E HOH . ? A HOH 2010 ? 1_555 97.0 ? 6 O ? E HOH . ? A HOH 2009 ? 1_555 MG ? D MG . ? A MG 1003 ? 1_555 O ? E HOH . ? A HOH 2010 ? 1_555 94.8 ? # 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 NCO 1001 ? 11 'BINDING SITE FOR RESIDUE NCO A 1001' AC2 Software A NCO 1002 ? 15 'BINDING SITE FOR RESIDUE NCO A 1002' AC3 Software A MG 1003 ? 5 'BINDING SITE FOR RESIDUE MG A 1003' # 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 11 ZGU A 3 ? ZGU A 3 . ? 4_475 ? 2 AC1 11 ZCY A 6 ? ZCY A 6 . ? 1_555 ? 3 AC1 11 HOH E . ? HOH A 2023 . ? 4_475 ? 4 AC1 11 HOH E . ? HOH A 2034 . ? 1_455 ? 5 AC1 11 HOH E . ? HOH A 2035 . ? 1_455 ? 6 AC1 11 HOH E . ? HOH A 2046 . ? 1_555 ? 7 AC1 11 HOH E . ? HOH A 2047 . ? 1_555 ? 8 AC1 11 HOH E . ? HOH A 2049 . ? 1_555 ? 9 AC1 11 HOH E . ? HOH A 2050 . ? 1_555 ? 10 AC1 11 HOH E . ? HOH A 2051 . ? 1_555 ? 11 AC1 11 HOH E . ? HOH A 2052 . ? 1_555 ? 12 AC2 15 ZBC A 2 ? ZBC A 2 . ? 5_445 ? 13 AC2 15 ZGU A 5 ? ZGU A 5 . ? 8_465 ? 14 AC2 15 ZGU A 5 ? ZGU A 5 . ? 1_555 ? 15 AC2 15 ZCY A 6 ? ZCY A 6 . ? 8_465 ? 16 AC2 15 ZCY A 6 ? ZCY A 6 . ? 1_555 ? 17 AC2 15 HOH E . ? HOH A 2002 . ? 5_445 ? 18 AC2 15 HOH E . ? HOH A 2020 . ? 5_445 ? 19 AC2 15 HOH E . ? HOH A 2021 . ? 5_445 ? 20 AC2 15 HOH E . ? HOH A 2053 . ? 1_555 ? 21 AC2 15 HOH E . ? HOH A 2054 . ? 1_555 ? 22 AC2 15 HOH E . ? HOH A 2055 . ? 3_755 ? 23 AC2 15 HOH E . ? HOH A 2055 . ? 1_555 ? 24 AC2 15 HOH E . ? HOH A 2056 . ? 1_555 ? 25 AC2 15 HOH E . ? HOH A 2057 . ? 1_555 ? 26 AC2 15 HOH E . ? HOH A 2058 . ? 1_555 ? 27 AC3 5 HOH E . ? HOH A 2005 . ? 1_555 ? 28 AC3 5 HOH E . ? HOH A 2006 . ? 4_576 ? 29 AC3 5 HOH E . ? HOH A 2007 . ? 4_576 ? 30 AC3 5 HOH E . ? HOH A 2009 . ? 1_555 ? 31 AC3 5 HOH E . ? HOH A 2010 . ? 1_555 ? # 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 HN63 A NCO 1001 ? B O A HOH 2047 ? ? 0.95 2 1 N6 A NCO 1001 ? B O A HOH 2047 ? ? 1.26 3 1 HN62 A NCO 1001 ? B O A HOH 2047 ? ? 1.29 4 1 N1 A NCO 1001 ? B O A HOH 2052 ? ? 1.99 # 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 ZGU 1 A ZGU 1 ? G "(S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE" 2 A ZBC 2 A ZBC 2 ? C ? 3 A ZGU 3 A ZGU 3 ? G "(S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE" 4 A ZCY 4 A ZCY 4 ? C "(S)-1'-(2',3'-DIHYDROXYPROPYL)-CYTOSINE" 5 A ZGU 5 A ZGU 5 ? G "(S)-1'-(2',3'-DIHYDROXYPROPYL)-GUANINE" 6 A ZCY 6 A ZCY 6 ? C "(S)-1'-(2',3'-DIHYDROXYPROPYL)-CYTOSINE" # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id NCO _pdbx_struct_special_symmetry.auth_seq_id 1001 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id B _pdbx_struct_special_symmetry.label_comp_id NCO _pdbx_struct_special_symmetry.label_seq_id . # _pdbx_entry_details.entry_id 2WNA _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ;(S)-1'-(2',3'-DIHYDROXYPROPYL)-5-BROMO-CYTOSINE (ZBC): ZCY ANALOG BEARING A BROMINE AT C5 COBALT HEXAMMINE(III) (NCO): COBALT HEXAMINNE COMPLEXES SHOW DISORDER, CHARGE +3 MAGNESIUM ION (MG): CHARGE +2 ; _pdbx_entry_details.sequence_details 'CYTOSINE A2 IS BROMINATED AT C5 FOR SAD ANALYSIS' _pdbx_entry_details.has_ligand_of_interest ? # loop_ _pdbx_distant_solvent_atoms.id _pdbx_distant_solvent_atoms.PDB_model_num _pdbx_distant_solvent_atoms.auth_atom_id _pdbx_distant_solvent_atoms.label_alt_id _pdbx_distant_solvent_atoms.auth_asym_id _pdbx_distant_solvent_atoms.auth_comp_id _pdbx_distant_solvent_atoms.auth_seq_id _pdbx_distant_solvent_atoms.PDB_ins_code _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance _pdbx_distant_solvent_atoms.neighbor_ligand_distance 1 1 O ? A HOH 2009 ? 5.95 . 2 1 O ? A HOH 2011 ? 6.45 . 3 1 O ? A HOH 2012 ? 6.28 . # 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 NCO CO CO N N 5 NCO N1 N N N 6 NCO N2 N N N 7 NCO N3 N N N 8 NCO N4 N N N 9 NCO N5 N N N 10 NCO N6 N N N 11 NCO HN11 H N N 12 NCO HN12 H N N 13 NCO HN13 H N N 14 NCO HN21 H N N 15 NCO HN22 H N N 16 NCO HN23 H N N 17 NCO HN31 H N N 18 NCO HN32 H N N 19 NCO HN33 H N N 20 NCO HN41 H N N 21 NCO HN42 H N N 22 NCO HN43 H N N 23 NCO HN51 H N N 24 NCO HN52 H N N 25 NCO HN53 H N N 26 NCO HN61 H N N 27 NCO HN62 H N N 28 NCO HN63 H N N 29 ZBC P P N N 30 ZBC BR5 BR N N 31 ZBC C5 C N N 32 ZBC C4 C N N 33 ZBC N4 N N N 34 ZBC N3 N N N 35 ZBC C2 C N N 36 ZBC O2 O N N 37 ZBC C6 C N N 38 ZBC N1 N N N 39 ZBC C1G C N N 40 ZBC C2G C N S 41 ZBC O2G O N N 42 ZBC C3G C N N 43 ZBC O3G O N N 44 ZBC O1P O N N 45 ZBC O2P O N N 46 ZBC OXT O N N 47 ZBC H2P H N N 48 ZBC HXT H N N 49 ZBC H6 H N N 50 ZBC H41N H N N 51 ZBC H42N H N N 52 ZBC H1G1 H N N 53 ZBC H1G2 H N N 54 ZBC H2G H N N 55 ZBC HA H N N 56 ZBC H3G1 H N N 57 ZBC H3G2 H N N 58 ZCY O2 O N N 59 ZCY C2 C N N 60 ZCY N3 N N N 61 ZCY C4 C N N 62 ZCY N4 N N N 63 ZCY C5 C N N 64 ZCY C6 C N N 65 ZCY N1 N N N 66 ZCY C1G C N N 67 ZCY C2G C N S 68 ZCY O2G O N N 69 ZCY C3G C N N 70 ZCY O3G O N N 71 ZCY P P N N 72 ZCY O2P O N N 73 ZCY O1P O N N 74 ZCY OXT O N N 75 ZCY H4N1 H N N 76 ZCY H4N2 H N N 77 ZCY H5 H N N 78 ZCY H6 H N N 79 ZCY H1G1 H N N 80 ZCY H1G2 H N N 81 ZCY H2G H N N 82 ZCY H3G1 H N N 83 ZCY H3G2 H N N 84 ZCY H2P H N N 85 ZCY H2 H N N 86 ZCY HXT H N N 87 ZGU P P N N 88 ZGU O1P O N N 89 ZGU O2P O N N 90 ZGU O3G O N N 91 ZGU C3G C N N 92 ZGU C2G C N S 93 ZGU O2G O N N 94 ZGU C1G C N N 95 ZGU N9 N Y N 96 ZGU C8 C Y N 97 ZGU N7 N Y N 98 ZGU C4 C Y N 99 ZGU C5 C Y N 100 ZGU N3 N N N 101 ZGU C2 C N N 102 ZGU N2 N N N 103 ZGU N1 N N N 104 ZGU C6 C N N 105 ZGU O6 O N N 106 ZGU OXT O N N 107 ZGU H1P H N N 108 ZGU HOT H N N 109 ZGU H3G1 H N N 110 ZGU H3G2 H N N 111 ZGU H2G H N N 112 ZGU HA H N N 113 ZGU H1G1 H N N 114 ZGU H1G2 H N N 115 ZGU H8 H N N 116 ZGU H2N1 H N N 117 ZGU H2N2 H N N 118 ZGU H1 H N N 119 # 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 NCO CO N1 sing N N 3 NCO CO N2 sing N N 4 NCO CO N3 sing N N 5 NCO CO N4 sing N N 6 NCO CO N5 sing N N 7 NCO CO N6 sing N N 8 NCO N1 HN11 sing N N 9 NCO N1 HN12 sing N N 10 NCO N1 HN13 sing N N 11 NCO N2 HN21 sing N N 12 NCO N2 HN22 sing N N 13 NCO N2 HN23 sing N N 14 NCO N3 HN31 sing N N 15 NCO N3 HN32 sing N N 16 NCO N3 HN33 sing N N 17 NCO N4 HN41 sing N N 18 NCO N4 HN42 sing N N 19 NCO N4 HN43 sing N N 20 NCO N5 HN51 sing N N 21 NCO N5 HN52 sing N N 22 NCO N5 HN53 sing N N 23 NCO N6 HN61 sing N N 24 NCO N6 HN62 sing N N 25 NCO N6 HN63 sing N N 26 ZBC P O3G sing N N 27 ZBC P O1P doub N N 28 ZBC P O2P sing N N 29 ZBC P OXT sing N N 30 ZBC BR5 C5 sing N N 31 ZBC C5 C4 sing N N 32 ZBC C5 C6 doub N N 33 ZBC C4 N4 sing N N 34 ZBC C4 N3 doub N N 35 ZBC N3 C2 sing N N 36 ZBC C2 O2 doub N N 37 ZBC C2 N1 sing N N 38 ZBC C6 N1 sing N N 39 ZBC N1 C1G sing N N 40 ZBC C1G C2G sing N N 41 ZBC C2G O2G sing N N 42 ZBC C2G C3G sing N N 43 ZBC C3G O3G sing N N 44 ZBC O2P H2P sing N N 45 ZBC OXT HXT sing N N 46 ZBC C6 H6 sing N N 47 ZBC N4 H41N sing N N 48 ZBC N4 H42N sing N N 49 ZBC C1G H1G1 sing N N 50 ZBC C1G H1G2 sing N N 51 ZBC C2G H2G sing N N 52 ZBC O2G HA sing N N 53 ZBC C3G H3G1 sing N N 54 ZBC C3G H3G2 sing N N 55 ZCY O2 C2 doub N N 56 ZCY C2 N3 sing N N 57 ZCY C2 N1 sing N N 58 ZCY N3 C4 doub N N 59 ZCY C4 N4 sing N N 60 ZCY C4 C5 sing N N 61 ZCY C5 C6 doub N N 62 ZCY C6 N1 sing N N 63 ZCY N1 C1G sing N N 64 ZCY C1G C2G sing N N 65 ZCY C2G O2G sing N N 66 ZCY C2G C3G sing N N 67 ZCY O2G H2G sing N N 68 ZCY C3G O3G sing N N 69 ZCY O3G P sing N N 70 ZCY P O2P sing N N 71 ZCY P O1P doub N N 72 ZCY N4 H4N1 sing N N 73 ZCY N4 H4N2 sing N N 74 ZCY C5 H5 sing N N 75 ZCY C6 H6 sing N N 76 ZCY C1G H1G1 sing N N 77 ZCY C1G H1G2 sing N N 78 ZCY C2G H2 sing N N 79 ZCY C3G H3G1 sing N N 80 ZCY C3G H3G2 sing N N 81 ZCY O2P H2P sing N N 82 ZCY P OXT sing N N 83 ZCY OXT HXT sing N N 84 ZGU P O1P sing N N 85 ZGU P O2P doub N N 86 ZGU P O3G sing N N 87 ZGU P OXT sing N N 88 ZGU O3G C3G sing N N 89 ZGU C3G C2G sing N N 90 ZGU C2G O2G sing N N 91 ZGU C2G C1G sing N N 92 ZGU C1G N9 sing N N 93 ZGU N9 C8 sing Y N 94 ZGU N9 C4 sing Y N 95 ZGU C8 N7 doub Y N 96 ZGU N7 C5 sing Y N 97 ZGU C4 C5 doub Y N 98 ZGU C4 N3 sing N N 99 ZGU C5 C6 sing N N 100 ZGU N3 C2 doub N N 101 ZGU C2 N2 sing N N 102 ZGU C2 N1 sing N N 103 ZGU N1 C6 sing N N 104 ZGU C6 O6 doub N N 105 ZGU O1P H1P sing N N 106 ZGU OXT HOT sing N N 107 ZGU C3G H3G1 sing N N 108 ZGU C3G H3G2 sing N N 109 ZGU C2G H2G sing N N 110 ZGU O2G HA sing N N 111 ZGU C1G H1G1 sing N N 112 ZGU C1G H1G2 sing N N 113 ZGU C8 H8 sing N N 114 ZGU N2 H2N1 sing N N 115 ZGU N2 H2N2 sing N N 116 ZGU N1 H1 sing N N 117 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2WNA 'double helix' 2WNA '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 ZGU 1 1_555 A ZCY 6 3_855 0.082 -0.130 -0.200 -1.501 -12.399 1.108 1 A_ZGU1:ZCY6_A A 1 ? A 6 ? 19 1 1 A ZBC 2 1_555 A ZGU 5 3_855 -0.139 -0.136 0.221 -4.554 1.011 3.294 2 A_ZBC2:ZGU5_A A 2 ? A 5 ? 19 1 1 A ZGU 3 1_555 A ZCY 4 3_855 0.149 -0.126 0.026 1.296 0.405 1.192 3 A_ZGU3:ZCY4_A A 3 ? A 4 ? 19 1 1 A ZCY 4 1_555 A ZGU 3 3_855 -0.149 -0.126 0.026 -1.296 0.405 1.192 4 A_ZCY4:ZGU3_A A 4 ? A 3 ? 19 1 1 A ZGU 5 1_555 A ZBC 2 3_855 0.139 -0.136 0.221 4.554 1.011 3.294 5 A_ZGU5:ZBC2_A A 5 ? A 2 ? 19 1 1 A ZCY 6 1_555 A ZGU 1 3_855 -0.082 -0.130 -0.200 1.501 -12.399 1.108 6 A_ZCY6:ZGU1_A A 6 ? A 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A ZGU 1 1_555 A ZCY 6 3_855 A ZBC 2 1_555 A ZGU 5 3_855 -0.374 -3.429 3.333 0.666 6.153 43.725 -5.110 0.557 2.844 8.213 -0.889 44.140 1 AA_ZGU1ZBC2:ZGU5ZCY6_AA A 1 ? A 6 ? A 2 ? A 5 ? 1 A ZBC 2 1_555 A ZGU 5 3_855 A ZGU 3 1_555 A ZCY 4 3_855 -0.111 -4.629 3.124 0.700 4.923 23.781 -12.263 0.442 2.132 11.781 -1.674 24.288 2 AA_ZBC2ZGU3:ZCY4ZGU5_AA A 2 ? A 5 ? A 3 ? A 4 ? 1 A ZGU 3 1_555 A ZCY 4 3_855 A ZCY 4 1_555 A ZGU 3 3_855 0.000 -2.663 3.380 0.000 7.366 48.351 -3.765 0.000 2.968 8.933 0.000 48.875 3 AA_ZGU3ZCY4:ZGU3ZCY4_AA A 3 ? A 4 ? A 4 ? A 3 ? 1 A ZCY 4 1_555 A ZGU 3 3_855 A ZGU 5 1_555 A ZBC 2 3_855 0.111 -4.629 3.124 -0.700 4.923 23.781 -12.263 -0.442 2.132 11.781 1.674 24.288 4 AA_ZCY4ZGU5:ZBC2ZGU3_AA A 4 ? A 3 ? A 5 ? A 2 ? 1 A ZGU 5 1_555 A ZBC 2 3_855 A ZCY 6 1_555 A ZGU 1 3_855 0.374 -3.429 3.333 -0.666 6.153 43.725 -5.110 -0.557 2.844 8.213 0.889 44.140 5 AA_ZGU5ZCY6:ZGU1ZBC2_AA A 5 ? A 2 ? A 6 ? A 1 ? # _atom_sites.entry_id 2WNA _atom_sites.fract_transf_matrix[1][1] 0.048972 _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] 0.023810 _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] 0.034880 _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 BR C CO H MG N O P # loop_