data_7KVT # _entry.id 7KVT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _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 7KVT pdb_00007kvt 10.2210/pdb7kvt/pdb WWPDB D_1000253153 ? ? # 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 2022-01-19 2 'Structure model' 1 1 2022-02-16 3 'Structure model' 1 2 2024-05-22 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' # 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 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' chem_comp_atom 4 3 'Structure model' chem_comp_bond # 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 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation.year' 5 2 'Structure model' '_citation_author.identifier_ORCID' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7KVT _pdbx_database_status.recvd_initial_deposition_date 2020-11-28 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Truong, L.' 1 ? ;Ferre-D'Amare, A.R. ; 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Nat.Chem.Biol. _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1552-4469 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 18 _citation.language ? _citation.page_first 191 _citation.page_last 198 _citation.title 'The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41589-021-00931-2 _citation.pdbx_database_id_PubMed 34937911 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Truong, L.' 1 ? primary 'Kooshapur, H.' 2 ? primary 'Dey, S.K.' 3 ? primary 'Li, X.' 4 ? primary 'Tjandra, N.' 5 ? primary 'Jaffrey, S.R.' 6 ? primary ;Ferre-D'Amare, A.R. ; 7 ? # 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 'Squash RNA aptamer bound to DFHBI-1T with iridium (III) ions' 26986.906 1 ? ? ? ? 2 non-polymer syn '(5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one' 320.215 1 ? ? ? ? 3 non-polymer syn 'IRIDIUM HEXAMMINE ION' 294.400 3 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 5 water nat water 18.015 6 ? ? ? ? # _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 ;(GTP)GGAAGAUACAAGGUGAGCCCAAUAAUAUGGUUUGGGUUAGGAUAGGAAGUAGAGCCUUAAACUCUCUAAGCGGUA UCUUCCC ; _entity_poly.pdbx_seq_one_letter_code_can ;GGGAAGAUACAAGGUGAGCCCAAUAAUAUGGUUUGGGUUAGGAUAGGAAGUAGAGCCUUAAACUCUCUAAGCGGUAUCUU CCC ; _entity_poly.pdbx_strand_id B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '(5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one' 2ZY 3 'IRIDIUM HEXAMMINE ION' IRI 4 'MAGNESIUM ION' MG 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GTP n 1 2 G n 1 3 G n 1 4 A n 1 5 A n 1 6 G n 1 7 A n 1 8 U n 1 9 A n 1 10 C n 1 11 A n 1 12 A n 1 13 G n 1 14 G n 1 15 U n 1 16 G n 1 17 A n 1 18 G n 1 19 C n 1 20 C n 1 21 C n 1 22 A n 1 23 A n 1 24 U n 1 25 A n 1 26 A n 1 27 U n 1 28 A n 1 29 U n 1 30 G n 1 31 G n 1 32 U n 1 33 U n 1 34 U n 1 35 G n 1 36 G n 1 37 G n 1 38 U n 1 39 U n 1 40 A n 1 41 G n 1 42 G n 1 43 A n 1 44 U n 1 45 A n 1 46 G n 1 47 G n 1 48 A n 1 49 A n 1 50 G n 1 51 U n 1 52 A n 1 53 G n 1 54 A n 1 55 G n 1 56 C n 1 57 C n 1 58 U n 1 59 U n 1 60 A n 1 61 A n 1 62 A n 1 63 C n 1 64 U n 1 65 C n 1 66 U n 1 67 C n 1 68 U n 1 69 A n 1 70 A n 1 71 G n 1 72 C n 1 73 G n 1 74 G n 1 75 U n 1 76 A n 1 77 U n 1 78 C n 1 79 U n 1 80 U n 1 81 C n 1 82 C n 1 83 C 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 83 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _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 2ZY non-polymer . '(5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one' ? 'C13 H9 F5 N2 O2' 320.215 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 GTP non-polymer n "GUANOSINE-5'-TRIPHOSPHATE" ? 'C10 H16 N5 O14 P3' 523.180 HOH non-polymer . WATER ? 'H2 O' 18.015 IRI non-polymer . 'IRIDIUM HEXAMMINE ION' ? 'H18 Ir N6 3' 294.400 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 GTP 1 1 1 GTP GTP B . n A 1 2 G 2 2 2 G G B . n A 1 3 G 3 3 3 G G B . n A 1 4 A 4 4 4 A A B . n A 1 5 A 5 5 5 A A B . n A 1 6 G 6 6 6 G G B . n A 1 7 A 7 7 7 A A B . n A 1 8 U 8 8 8 U U B . n A 1 9 A 9 9 9 A A B . n A 1 10 C 10 10 10 C C B . n A 1 11 A 11 11 11 A A B . n A 1 12 A 12 12 12 A A B . n A 1 13 G 13 13 13 G G B . n A 1 14 G 14 14 14 G G B . n A 1 15 U 15 15 15 U U B . n A 1 16 G 16 16 16 G G B . n A 1 17 A 17 17 17 A A B . n A 1 18 G 18 18 18 G G B . n A 1 19 C 19 19 19 C C B . n A 1 20 C 20 20 20 C C B . n A 1 21 C 21 21 21 C C B . n A 1 22 A 22 22 22 A A B . n A 1 23 A 23 23 23 A A B . n A 1 24 U 24 24 24 U U B . n A 1 25 A 25 25 25 A A B . n A 1 26 A 26 26 26 A A B . n A 1 27 U 27 27 27 U U B . n A 1 28 A 28 28 28 A A B . n A 1 29 U 29 29 29 U U B . n A 1 30 G 30 30 30 G G B . n A 1 31 G 31 31 31 G G B . n A 1 32 U 32 32 32 U U B . n A 1 33 U 33 33 33 U U B . n A 1 34 U 34 34 34 U U B . n A 1 35 G 35 35 35 G G B . n A 1 36 G 36 36 36 G G B . n A 1 37 G 37 37 37 G G B . n A 1 38 U 38 38 38 U U B . n A 1 39 U 39 39 39 U U B . n A 1 40 A 40 40 40 A A B . n A 1 41 G 41 41 41 G G B . n A 1 42 G 42 42 42 G G B . n A 1 43 A 43 43 43 A A B . n A 1 44 U 44 44 44 U U B . n A 1 45 A 45 45 45 A A B . n A 1 46 G 46 46 46 G G B . n A 1 47 G 47 47 47 G G B . n A 1 48 A 48 48 48 A A B . n A 1 49 A 49 49 49 A A B . n A 1 50 G 50 50 50 G G B . n A 1 51 U 51 51 51 U U B . n A 1 52 A 52 52 52 A A B . n A 1 53 G 53 53 53 G G B . n A 1 54 A 54 54 54 A A B . n A 1 55 G 55 55 55 G G B . n A 1 56 C 56 56 56 C C B . n A 1 57 C 57 57 57 C C B . n A 1 58 U 58 58 58 U U B . n A 1 59 U 59 59 59 U U B . n A 1 60 A 60 60 60 A A B . n A 1 61 A 61 61 61 A A B . n A 1 62 A 62 62 62 A A B . n A 1 63 C 63 63 63 C C B . n A 1 64 U 64 64 64 U U B . n A 1 65 C 65 65 65 C C B . n A 1 66 U 66 66 66 U U B . n A 1 67 C 67 67 67 C C B . n A 1 68 U 68 68 68 U U B . n A 1 69 A 69 69 69 A A B . n A 1 70 A 70 70 70 A A B . n A 1 71 G 71 71 71 G G B . n A 1 72 C 72 72 72 C C B . n A 1 73 G 73 73 73 G G B . n A 1 74 G 74 74 74 G G B . n A 1 75 U 75 75 75 U U B . n A 1 76 A 76 76 76 A A B . n A 1 77 U 77 77 77 U U B . n A 1 78 C 78 78 78 C C B . n A 1 79 U 79 79 79 U U B . n A 1 80 U 80 80 80 U U B . n A 1 81 C 81 81 81 C C B . n A 1 82 C 82 82 82 C C B . n A 1 83 C 83 83 83 C C 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 B 2 2ZY 1 101 1 2ZY DFH B . C 3 IRI 1 102 201 IRI IRI B . D 3 IRI 1 103 301 IRI IRI B . E 3 IRI 1 104 401 IRI IRI B . F 4 MG 1 105 501 MG MG B . G 4 MG 1 106 100 MG MG B . H 5 HOH 1 201 105 HOH HOH B . H 5 HOH 2 202 104 HOH HOH B . H 5 HOH 3 203 106 HOH HOH B . H 5 HOH 4 204 101 HOH HOH B . H 5 HOH 5 205 103 HOH HOH B . H 5 HOH 6 206 102 HOH HOH B . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.17.1_3660 1 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 2 # _cell.entry_id 7KVT _cell.length_a 103.900 _cell.length_b 103.900 _cell.length_c 51.699 _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 7KVT _symmetry.space_group_name_H-M 'P 42 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 7KVT _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.59 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 52.42 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 294 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '40 mM Na cacodylate pH 7.0, 80 mM NaCl, 12 mM spermine hydrochloride, 36% (v/v) MPD, 40 mM NaI, and 1 mM iridium (III) hexammine' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2019-11-01 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.105 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'APS BEAMLINE 24-ID-C' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.105 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 24-ID-C _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate 81.37 _reflns.entry_id 7KVT _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.73 _reflns.d_resolution_low 46.5 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 7929 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 99.9 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 24.7 _reflns.pdbx_Rmerge_I_obs 0.064 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 69.6 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? # _reflns_shell.d_res_high 2.73 _reflns_shell.d_res_low 2.90 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 1386 _reflns_shell.percent_possible_all ? _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs 3.114 _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 7KVT _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 7929 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.360 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 46.47 _refine.ls_d_res_high 2.73 _refine.ls_percent_reflns_obs 99.9 _refine.ls_R_factor_obs 0.213 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.209 _refine.ls_R_factor_R_free 0.251 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.980 _refine.ls_number_reflns_R_free 791 _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 71.10 _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 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'GEOSTD + MONOMER LIBRARY + CDL V1.2' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.408 _refine.pdbx_overall_phase_error 28.374 _refine.overall_SU_B ? _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 1788 _refine_hist.pdbx_number_atoms_ligand 45 _refine_hist.number_atoms_solvent 6 _refine_hist.number_atoms_total 1839 _refine_hist.d_res_high 2.73 _refine_hist.d_res_low 46.47 # 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 f_bond_d 0.007 ? ? 2047 'X-RAY DIFFRACTION' ? f_angle_d 1.513 ? ? 3212 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 16.586 ? ? 999 'X-RAY DIFFRACTION' ? f_chiral_restr 0.062 ? ? 414 'X-RAY DIFFRACTION' ? f_plane_restr 0.008 ? ? 85 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.number_reflns_obs 'X-RAY DIFFRACTION' . 2.7300 2.9000 1155 0.3338 100.00 0.4399 . . 128 . . . . 'X-RAY DIFFRACTION' . 2.9000 3.1200 1153 0.2898 100.00 0.3737 . . 128 . . . . 'X-RAY DIFFRACTION' . 3.1300 3.4400 1175 0.2303 100.00 0.2841 . . 129 . . . . 'X-RAY DIFFRACTION' . 3.4400 3.9400 1169 0.2275 100.00 0.2515 . . 130 . . . . 'X-RAY DIFFRACTION' . 3.9400 4.9600 1202 0.2118 100.00 0.2697 . . 134 . . . . 'X-RAY DIFFRACTION' . 4.9600 46.4700 1284 0.1717 100.00 0.1961 . . 142 . . . . # _struct.entry_id 7KVT _struct.title 'Crystal structure of Squash RNA aptamer in complex with DFHBI-1T with iridium (III) ions' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7KVT _struct_keywords.text 'fluorogenic aptamer, adenine riboswitch, RNA' _struct_keywords.pdbx_keywords RNA # 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 3 ? D N N 3 ? E N N 3 ? F N N 4 ? G N N 4 ? H N N 5 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7KVT _struct_ref.pdbx_db_accession 7KVT _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7KVT _struct_ref_seq.pdbx_strand_id B _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 83 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7KVT _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 83 _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 83 # _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # _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,G,H # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _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 both ? A GTP 1 "O3'" ? ? ? 1_555 A G 2 P ? ? B GTP 1 B G 2 1_555 ? ? ? ? ? ? ? 1.546 ? ? metalc1 metalc ? ? A G 42 OP2 ? ? ? 1_555 F MG . MG ? ? B G 42 B MG 105 1_555 ? ? ? ? ? ? ? 2.340 ? ? metalc2 metalc ? ? A A 45 OP2 ? ? ? 1_555 F MG . MG ? ? B A 45 B MG 105 1_555 ? ? ? ? ? ? ? 1.870 ? ? metalc3 metalc ? ? A G 46 O6 ? ? ? 1_555 F MG . MG ? ? B G 46 B MG 105 1_555 ? ? ? ? ? ? ? 2.112 ? ? metalc4 metalc ? ? G MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 106 B HOH 201 1_555 ? ? ? ? ? ? ? 1.757 ? ? metalc5 metalc ? ? G MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 106 B HOH 202 1_555 ? ? ? ? ? ? ? 1.783 ? ? metalc6 metalc ? ? G MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 106 B HOH 203 1_555 ? ? ? ? ? ? ? 1.760 ? ? metalc7 metalc ? ? G MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 106 B HOH 204 1_555 ? ? ? ? ? ? ? 1.776 ? ? metalc8 metalc ? ? G MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 106 B HOH 205 1_555 ? ? ? ? ? ? ? 1.779 ? ? metalc9 metalc ? ? G MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 106 B HOH 206 1_555 ? ? ? ? ? ? ? 1.777 ? ? hydrog1 hydrog ? ? A GTP 1 N1 ? ? ? 1_555 A C 83 N3 ? ? B GTP 1 B C 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A GTP 1 N2 ? ? ? 1_555 A C 83 O2 ? ? B GTP 1 B C 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A GTP 1 O6 ? ? ? 1_555 A C 83 N4 ? ? B GTP 1 B C 83 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 82 N3 ? ? B G 2 B C 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 82 O2 ? ? B G 2 B C 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 82 N4 ? ? B G 2 B C 82 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 81 N3 ? ? B G 3 B C 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 81 O2 ? ? B G 3 B C 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 81 N4 ? ? B G 3 B C 81 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 A U 80 N3 ? ? B A 4 B U 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 A U 80 O4 ? ? B A 4 B U 80 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 A U 79 N3 ? ? B A 5 B U 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 A U 79 O4 ? ? B A 5 B U 79 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 6 N1 ? ? ? 1_555 A C 78 N3 ? ? B G 6 B C 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N2 ? ? ? 1_555 A C 78 O2 ? ? B G 6 B C 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 O6 ? ? ? 1_555 A C 78 N4 ? ? B G 6 B C 78 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 7 N1 ? ? ? 1_555 A U 77 N3 ? ? B A 7 B U 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 7 N6 ? ? ? 1_555 A U 77 O4 ? ? B A 7 B U 77 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 8 N3 ? ? ? 1_555 A A 76 N1 ? ? B U 8 B A 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 8 O4 ? ? ? 1_555 A A 76 N6 ? ? B U 8 B A 76 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 9 N1 ? ? ? 1_555 A U 75 N3 ? ? B A 9 B U 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A A 9 N6 ? ? ? 1_555 A U 75 O4 ? ? B A 9 B U 75 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 N3 ? ? ? 1_555 A G 74 N1 ? ? B C 10 B G 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 10 N4 ? ? ? 1_555 A G 74 O6 ? ? B C 10 B G 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 10 O2 ? ? ? 1_555 A G 74 N2 ? ? B C 10 B G 74 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A A 12 N1 ? ? ? 1_555 A G 41 N2 ? ? B A 12 B G 41 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog27 hydrog ? ? A G 13 N2 ? ? ? 1_555 A A 70 N3 ? ? B G 13 B A 70 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog28 hydrog ? ? A U 15 N3 ? ? ? 1_555 A A 69 N7 ? ? B U 15 B A 69 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog29 hydrog ? ? A U 15 O2 ? ? ? 1_555 A A 69 N6 ? ? B U 15 B A 69 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog30 hydrog ? ? A G 16 N2 ? ? ? 1_555 A A 49 N1 ? ? B G 16 B A 49 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog31 hydrog ? ? A G 16 N3 ? ? ? 1_555 A A 49 N6 ? ? B G 16 B A 49 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog32 hydrog ? ? A A 17 N1 ? ? ? 1_555 A U 68 N3 ? ? B A 17 B U 68 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog33 hydrog ? ? A G 18 N1 ? ? ? 1_555 A U 38 O2 ? ? B G 18 B U 38 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog34 hydrog ? ? A G 18 O6 ? ? ? 1_555 A U 38 N3 ? ? B G 18 B U 38 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog35 hydrog ? ? A C 19 N3 ? ? ? 1_555 A G 37 N1 ? ? B C 19 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 19 N4 ? ? ? 1_555 A G 37 O6 ? ? B C 19 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 19 O2 ? ? ? 1_555 A G 37 N2 ? ? B C 19 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 20 N3 ? ? ? 1_555 A G 36 N1 ? ? B C 20 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 20 N4 ? ? ? 1_555 A G 36 O6 ? ? B C 20 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 20 O2 ? ? ? 1_555 A G 36 N2 ? ? B C 20 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 21 N3 ? ? ? 1_555 A G 35 N1 ? ? B C 21 B G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 21 N4 ? ? ? 1_555 A G 35 O6 ? ? B C 21 B G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 21 O2 ? ? ? 1_555 A G 35 N2 ? ? B C 21 B G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A A 22 N1 ? ? ? 1_555 A U 34 N3 ? ? B A 22 B U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A A 22 N6 ? ? ? 1_555 A U 34 O4 ? ? B A 22 B U 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A A 23 N1 ? ? ? 1_555 A U 33 N3 ? ? B A 23 B U 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A A 23 N6 ? ? ? 1_555 A U 33 O4 ? ? B A 23 B U 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A U 24 N3 ? ? ? 1_555 A U 32 O4 ? ? B U 24 B U 32 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog49 hydrog ? ? A U 24 O2 ? ? ? 1_555 A U 32 N3 ? ? B U 24 B U 32 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog50 hydrog ? ? A A 26 N1 ? ? ? 1_555 A A 62 N6 ? ? B A 26 B A 62 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog51 hydrog ? ? A A 26 N6 ? ? ? 1_555 A A 62 N7 ? ? B A 26 B A 62 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog52 hydrog ? ? A U 27 N3 ? ? ? 1_555 A A 61 N1 ? ? B U 27 B A 61 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog53 hydrog ? ? A A 28 N6 ? ? ? 1_555 A A 60 N1 ? ? B A 28 B A 60 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog54 hydrog ? ? A A 28 N7 ? ? ? 1_555 A A 60 N6 ? ? B A 28 B A 60 1_555 ? ? ? ? ? ? TYPE_5_PAIR ? ? ? hydrog55 hydrog ? ? A G 30 O6 ? ? ? 1_555 A C 57 N4 ? ? B G 30 B C 57 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog56 hydrog ? ? A G 31 N1 ? ? ? 1_555 A C 56 N3 ? ? B G 31 B C 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A G 31 N2 ? ? ? 1_555 A C 56 O2 ? ? B G 31 B C 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A G 31 O6 ? ? ? 1_555 A C 56 N4 ? ? B G 31 B C 56 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A G 31 N2 ? ? ? 1_555 A A 62 N1 ? ? B G 31 B A 62 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog60 hydrog ? ? A G 31 N3 ? ? ? 1_555 A A 62 N6 ? ? B G 31 B A 62 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog61 hydrog ? ? A U 39 N3 ? ? ? 1_555 A A 48 N7 ? ? B U 39 B A 48 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog62 hydrog ? ? A U 39 O2 ? ? ? 1_555 A A 48 N6 ? ? B U 39 B A 48 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog63 hydrog ? ? A G 41 N1 ? ? ? 1_555 A G 47 N7 ? ? B G 41 B G 47 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog64 hydrog ? ? A G 41 N2 ? ? ? 1_555 A G 47 O6 ? ? B G 41 B G 47 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog65 hydrog ? ? A G 42 N7 ? ? ? 1_555 A G 46 N1 ? ? B G 42 B G 46 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog66 hydrog ? ? A G 42 O6 ? ? ? 1_555 A G 46 N2 ? ? B G 42 B G 46 1_555 ? ? ? ? ? ? TYPE_7_PAIR ? ? ? hydrog67 hydrog ? ? A G 42 O6 ? ? ? 1_555 A C 72 N4 ? ? B G 42 B C 72 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog68 hydrog ? ? A A 43 N6 ? ? ? 1_555 A U 75 O2 ? ? B A 43 B U 75 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog69 hydrog ? ? A U 44 O4 ? ? ? 1_555 A G 74 N2 ? ? B U 44 B G 74 1_555 ? ? ? ? ? ? 'U-G MISPAIR' ? ? ? hydrog70 hydrog ? ? A A 45 N6 ? ? ? 1_555 A G 71 O6 ? ? B A 45 B G 71 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog71 hydrog ? ? A A 45 N1 ? ? ? 1_555 A G 74 N2 ? ? B A 45 B G 74 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog72 hydrog ? ? A G 46 N2 ? ? ? 1_555 A G 73 O6 ? ? B G 46 B G 73 1_555 ? ? ? ? ? ? 'G-G MISPAIR' ? ? ? hydrog73 hydrog ? ? A G 47 N1 ? ? ? 1_555 A C 72 N3 ? ? B G 47 B C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog74 hydrog ? ? A G 47 N2 ? ? ? 1_555 A C 72 O2 ? ? B G 47 B C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog75 hydrog ? ? A G 47 O6 ? ? ? 1_555 A C 72 N4 ? ? B G 47 B C 72 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog76 hydrog ? ? A A 48 N3 ? ? ? 1_555 A A 69 N6 ? ? B A 48 B A 69 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog77 hydrog ? ? A G 50 N1 ? ? ? 1_555 A C 67 N3 ? ? B G 50 B C 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog78 hydrog ? ? A G 50 N2 ? ? ? 1_555 A C 67 O2 ? ? B G 50 B C 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog79 hydrog ? ? A G 50 O6 ? ? ? 1_555 A C 67 N4 ? ? B G 50 B C 67 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog80 hydrog ? ? A A 52 N1 ? ? ? 1_555 A U 66 N3 ? ? B A 52 B U 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog81 hydrog ? ? A A 52 N6 ? ? ? 1_555 A U 66 O4 ? ? B A 52 B U 66 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog82 hydrog ? ? A G 53 N1 ? ? ? 1_555 A C 65 N3 ? ? B G 53 B C 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog83 hydrog ? ? A G 53 N2 ? ? ? 1_555 A C 65 O2 ? ? B G 53 B C 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog84 hydrog ? ? A G 53 O6 ? ? ? 1_555 A C 65 N4 ? ? B G 53 B C 65 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog85 hydrog ? ? A A 54 N1 ? ? ? 1_555 A U 64 N3 ? ? B A 54 B U 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog86 hydrog ? ? A A 54 N6 ? ? ? 1_555 A U 64 O4 ? ? B A 54 B U 64 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog87 hydrog ? ? A G 55 N1 ? ? ? 1_555 A C 63 N3 ? ? B G 55 B C 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog88 hydrog ? ? A G 55 N2 ? ? ? 1_555 A C 63 O2 ? ? B G 55 B C 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog89 hydrog ? ? A G 55 O6 ? ? ? 1_555 A C 63 N4 ? ? B G 55 B C 63 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog90 hydrog ? ? A C 57 O2 ? ? ? 1_555 A A 61 N6 ? ? B C 57 B A 61 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? # 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 OP2 ? A G 42 ? B G 42 ? 1_555 MG ? F MG . ? B MG 105 ? 1_555 OP2 ? A A 45 ? B A 45 ? 1_555 119.4 ? 2 OP2 ? A G 42 ? B G 42 ? 1_555 MG ? F MG . ? B MG 105 ? 1_555 O6 ? A G 46 ? B G 46 ? 1_555 77.7 ? 3 OP2 ? A A 45 ? B A 45 ? 1_555 MG ? F MG . ? B MG 105 ? 1_555 O6 ? A G 46 ? B G 46 ? 1_555 95.2 ? 4 O ? H HOH . ? B HOH 201 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 202 ? 1_555 131.0 ? 5 O ? H HOH . ? B HOH 201 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 203 ? 1_555 87.4 ? 6 O ? H HOH . ? B HOH 202 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 203 ? 1_555 74.3 ? 7 O ? H HOH . ? B HOH 201 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 204 ? 1_555 94.1 ? 8 O ? H HOH . ? B HOH 202 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 204 ? 1_555 129.7 ? 9 O ? H HOH . ? B HOH 203 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 204 ? 1_555 89.5 ? 10 O ? H HOH . ? B HOH 201 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 205 ? 1_555 64.5 ? 11 O ? H HOH . ? B HOH 202 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 205 ? 1_555 93.4 ? 12 O ? H HOH . ? B HOH 203 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 205 ? 1_555 129.9 ? 13 O ? H HOH . ? B HOH 204 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 205 ? 1_555 130.6 ? 14 O ? H HOH . ? B HOH 201 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 206 ? 1_555 133.9 ? 15 O ? H HOH . ? B HOH 202 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 206 ? 1_555 86.4 ? 16 O ? H HOH . ? B HOH 203 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 206 ? 1_555 134.1 ? 17 O ? H HOH . ? B HOH 204 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 206 ? 1_555 71.3 ? 18 O ? H HOH . ? B HOH 205 ? 1_555 MG ? G MG . ? B MG 106 ? 1_555 O ? H HOH . ? B HOH 206 ? 1_555 91.7 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O B HOH 201 ? ? O B HOH 205 ? ? 1.89 2 1 O B HOH 204 ? ? O B HOH 206 ? ? 2.07 3 1 O B HOH 202 ? ? O B HOH 203 ? ? 2.14 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 "O2'" _pdbx_validate_symm_contact.auth_asym_id_1 B _pdbx_validate_symm_contact.auth_comp_id_1 G _pdbx_validate_symm_contact.auth_seq_id_1 3 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 "O2'" _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 G _pdbx_validate_symm_contact.auth_seq_id_2 3 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 7_643 _pdbx_validate_symm_contact.dist 2.05 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 C8 _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 G _pdbx_validate_rmsd_bond.auth_seq_id_1 71 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 N9 _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 G _pdbx_validate_rmsd_bond.auth_seq_id_2 71 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.421 _pdbx_validate_rmsd_bond.bond_target_value 1.374 _pdbx_validate_rmsd_bond.bond_deviation 0.047 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.007 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 C5 B G 13 ? ? C6 B G 13 ? ? N1 B G 13 ? ? 108.41 111.50 -3.09 0.50 N 2 1 "O5'" B G 14 ? ? P B G 14 ? ? OP2 B G 14 ? ? 100.23 105.70 -5.47 0.90 N 3 1 C5 B G 14 ? ? N7 B G 14 ? ? C8 B G 14 ? ? 101.01 104.30 -3.29 0.50 N 4 1 "O4'" B A 17 ? ? "C1'" B A 17 ? ? N9 B A 17 ? ? 113.83 108.50 5.33 0.70 N 5 1 N1 B A 17 ? ? C2 B A 17 ? ? N3 B A 17 ? ? 132.94 129.30 3.64 0.50 N 6 1 C2 B A 17 ? ? N3 B A 17 ? ? C4 B A 17 ? ? 105.02 110.60 -5.58 0.50 N 7 1 "O4'" B G 30 ? ? "C1'" B G 30 ? ? N9 B G 30 ? ? 113.53 108.50 5.03 0.70 N 8 1 C4 B G 30 ? ? C5 B G 30 ? ? N7 B G 30 ? ? 114.45 110.80 3.65 0.40 N 9 1 C5 B G 30 ? ? N7 B G 30 ? ? C8 B G 30 ? ? 99.08 104.30 -5.22 0.50 N 10 1 N7 B G 30 ? ? C8 B G 30 ? ? N9 B G 30 ? ? 117.83 113.10 4.73 0.50 N 11 1 C8 B G 30 ? ? N9 B G 30 ? ? C4 B G 30 ? ? 103.14 106.40 -3.26 0.40 N 12 1 C6 B G 30 ? ? C5 B G 30 ? ? N7 B G 30 ? ? 126.06 130.40 -4.34 0.60 N 13 1 "O4'" B A 61 ? ? "C1'" B A 61 ? ? N9 B A 61 ? ? 112.74 108.50 4.24 0.70 N 14 1 N3 B C 63 ? ? C2 B C 63 ? ? O2 B C 63 ? ? 117.66 121.90 -4.24 0.70 N 15 1 C5 B G 71 ? ? N7 B G 71 ? ? C8 B G 71 ? ? 99.12 104.30 -5.18 0.50 N 16 1 N7 B G 71 ? ? C8 B G 71 ? ? N9 B G 71 ? ? 118.09 113.10 4.99 0.50 N 17 1 C8 B G 71 ? ? N9 B G 71 ? ? C4 B G 71 ? ? 102.12 106.40 -4.28 0.40 N 18 1 N3 B G 71 ? ? C4 B G 71 ? ? N9 B G 71 ? ? 121.22 126.00 -4.78 0.60 N # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -y+1/2,x+1/2,z+1/2 3 y+1/2,-x+1/2,z+1/2 4 x+1/2,-y+1/2,-z+1/2 5 -x+1/2,y+1/2,-z+1/2 6 -x,-y,z 7 y,x,-z 8 -y,-x,-z # _pdbx_entry_details.entry_id 7KVT _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # 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 2ZY O18 O N N 1 2ZY C15 C N N 2 2ZY N14 N N N 3 2ZY C16 C N N 4 2ZY C19 C N N 5 2ZY C13 C N N 6 2ZY C17 C N N 7 2ZY C11 C N N 8 2ZY N12 N N N 9 2ZY C10 C N N 10 2ZY C2 C Y N 11 2ZY C1 C Y N 12 2ZY C6 C Y N 13 2ZY F8 F N N 14 2ZY C5 C Y N 15 2ZY O9 O N N 16 2ZY C4 C Y N 17 2ZY F7 F N N 18 2ZY C3 C Y N 19 2ZY F20 F N N 20 2ZY F21 F N N 21 2ZY F22 F N N 22 2ZY H1 H N N 23 2ZY H2 H N N 24 2ZY H4 H N N 25 2ZY H5 H N N 26 2ZY H6 H N N 27 2ZY H7 H N N 28 2ZY H9 H N N 29 2ZY H10 H N N 30 2ZY H11 H N N 31 A OP3 O N N 32 A P P N N 33 A OP1 O N N 34 A OP2 O N N 35 A "O5'" O N N 36 A "C5'" C N N 37 A "C4'" C N R 38 A "O4'" O N N 39 A "C3'" C N S 40 A "O3'" O N N 41 A "C2'" C N R 42 A "O2'" O N N 43 A "C1'" C N R 44 A N9 N Y N 45 A C8 C Y N 46 A N7 N Y N 47 A C5 C Y N 48 A C6 C Y N 49 A N6 N N N 50 A N1 N Y N 51 A C2 C Y N 52 A N3 N Y N 53 A C4 C Y N 54 A HOP3 H N N 55 A HOP2 H N N 56 A "H5'" H N N 57 A "H5''" H N N 58 A "H4'" H N N 59 A "H3'" H N N 60 A "HO3'" H N N 61 A "H2'" H N N 62 A "HO2'" H N N 63 A "H1'" H N N 64 A H8 H N N 65 A H61 H N N 66 A H62 H N N 67 A H2 H N N 68 C OP3 O N N 69 C P P N N 70 C OP1 O N N 71 C OP2 O N N 72 C "O5'" O N N 73 C "C5'" C N N 74 C "C4'" C N R 75 C "O4'" O N N 76 C "C3'" C N S 77 C "O3'" O N N 78 C "C2'" C N R 79 C "O2'" O N N 80 C "C1'" C N R 81 C N1 N N N 82 C C2 C N N 83 C O2 O N N 84 C N3 N N N 85 C C4 C N N 86 C N4 N N N 87 C C5 C N N 88 C C6 C N N 89 C HOP3 H N N 90 C HOP2 H N N 91 C "H5'" H N N 92 C "H5''" H N N 93 C "H4'" H N N 94 C "H3'" H N N 95 C "HO3'" H N N 96 C "H2'" H N N 97 C "HO2'" H N N 98 C "H1'" H N N 99 C H41 H N N 100 C H42 H N N 101 C H5 H N N 102 C H6 H N N 103 G OP3 O N N 104 G P P N N 105 G OP1 O N N 106 G OP2 O N N 107 G "O5'" O N N 108 G "C5'" C N N 109 G "C4'" C N R 110 G "O4'" O N N 111 G "C3'" C N S 112 G "O3'" O N N 113 G "C2'" C N R 114 G "O2'" O N N 115 G "C1'" C N R 116 G N9 N Y N 117 G C8 C Y N 118 G N7 N Y N 119 G C5 C Y N 120 G C6 C N N 121 G O6 O N N 122 G N1 N N N 123 G C2 C N N 124 G N2 N N N 125 G N3 N N N 126 G C4 C Y N 127 G HOP3 H N N 128 G HOP2 H N N 129 G "H5'" H N N 130 G "H5''" H N N 131 G "H4'" H N N 132 G "H3'" H N N 133 G "HO3'" H N N 134 G "H2'" H N N 135 G "HO2'" H N N 136 G "H1'" H N N 137 G H8 H N N 138 G H1 H N N 139 G H21 H N N 140 G H22 H N N 141 GTP PG P N N 142 GTP O1G O N N 143 GTP O2G O N N 144 GTP O3G O N N 145 GTP O3B O N N 146 GTP PB P N N 147 GTP O1B O N N 148 GTP O2B O N N 149 GTP O3A O N N 150 GTP PA P N N 151 GTP O1A O N N 152 GTP O2A O N N 153 GTP "O5'" O N N 154 GTP "C5'" C N N 155 GTP "C4'" C N R 156 GTP "O4'" O N N 157 GTP "C3'" C N S 158 GTP "O3'" O N N 159 GTP "C2'" C N R 160 GTP "O2'" O N N 161 GTP "C1'" C N R 162 GTP N9 N Y N 163 GTP C8 C Y N 164 GTP N7 N Y N 165 GTP C5 C Y N 166 GTP C6 C N N 167 GTP O6 O N N 168 GTP N1 N N N 169 GTP C2 C N N 170 GTP N2 N N N 171 GTP N3 N N N 172 GTP C4 C Y N 173 GTP HOG2 H N N 174 GTP HOG3 H N N 175 GTP HOB2 H N N 176 GTP HOA2 H N N 177 GTP "H5'" H N N 178 GTP "H5''" H N N 179 GTP "H4'" H N N 180 GTP "H3'" H N N 181 GTP "HO3'" H N N 182 GTP "H2'" H N N 183 GTP "HO2'" H N N 184 GTP "H1'" H N N 185 GTP H8 H N N 186 GTP HN1 H N N 187 GTP HN21 H N N 188 GTP HN22 H N N 189 HOH O O N N 190 HOH H1 H N N 191 HOH H2 H N N 192 IRI IR IR N N 193 IRI N1 N N N 194 IRI N2 N N N 195 IRI N3 N N N 196 IRI N4 N N N 197 IRI N5 N N N 198 IRI N6 N N N 199 IRI HN11 H N N 200 IRI HN12 H N N 201 IRI HN13 H N N 202 IRI HN21 H N N 203 IRI HN22 H N N 204 IRI HN23 H N N 205 IRI HN31 H N N 206 IRI HN32 H N N 207 IRI HN33 H N N 208 IRI HN41 H N N 209 IRI HN42 H N N 210 IRI HN43 H N N 211 IRI HN51 H N N 212 IRI HN52 H N N 213 IRI HN53 H N N 214 IRI HN61 H N N 215 IRI HN62 H N N 216 IRI HN63 H N N 217 MG MG MG N N 218 U OP3 O N N 219 U P P N N 220 U OP1 O N N 221 U OP2 O N N 222 U "O5'" O N N 223 U "C5'" C N N 224 U "C4'" C N R 225 U "O4'" O N N 226 U "C3'" C N S 227 U "O3'" O N N 228 U "C2'" C N R 229 U "O2'" O N N 230 U "C1'" C N R 231 U N1 N N N 232 U C2 C N N 233 U O2 O N N 234 U N3 N N N 235 U C4 C N N 236 U O4 O N N 237 U C5 C N N 238 U C6 C N N 239 U HOP3 H N N 240 U HOP2 H N N 241 U "H5'" H N N 242 U "H5''" H N N 243 U "H4'" H N N 244 U "H3'" H N N 245 U "HO3'" H N N 246 U "H2'" H N N 247 U "HO2'" H N N 248 U "H1'" H N N 249 U H3 H N N 250 U H5 H N N 251 U H6 H N N 252 # 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 2ZY F20 C19 sing N N 1 2ZY F22 C19 sing N N 2 2ZY C19 F21 sing N N 3 2ZY C19 C16 sing N N 4 2ZY C16 N14 sing N N 5 2ZY O18 C15 doub N N 6 2ZY C15 N14 sing N N 7 2ZY C15 C11 sing N N 8 2ZY N14 C13 sing N N 9 2ZY C10 C11 doub N Z 10 2ZY C10 C2 sing N N 11 2ZY C11 N12 sing N N 12 2ZY C13 C17 sing N N 13 2ZY C13 N12 doub N N 14 2ZY C1 C2 doub Y N 15 2ZY C1 C6 sing Y N 16 2ZY C2 C3 sing Y N 17 2ZY F8 C6 sing N N 18 2ZY C6 C5 doub Y N 19 2ZY C3 C4 doub Y N 20 2ZY C5 C4 sing Y N 21 2ZY C5 O9 sing N N 22 2ZY C4 F7 sing N N 23 2ZY C16 H1 sing N N 24 2ZY C16 H2 sing N N 25 2ZY C17 H4 sing N N 26 2ZY C17 H5 sing N N 27 2ZY C17 H6 sing N N 28 2ZY C10 H7 sing N N 29 2ZY C1 H9 sing N N 30 2ZY O9 H10 sing N N 31 2ZY C3 H11 sing N N 32 A OP3 P sing N N 33 A OP3 HOP3 sing N N 34 A P OP1 doub N N 35 A P OP2 sing N N 36 A P "O5'" sing N N 37 A OP2 HOP2 sing N N 38 A "O5'" "C5'" sing N N 39 A "C5'" "C4'" sing N N 40 A "C5'" "H5'" sing N N 41 A "C5'" "H5''" sing N N 42 A "C4'" "O4'" sing N N 43 A "C4'" "C3'" sing N N 44 A "C4'" "H4'" sing N N 45 A "O4'" "C1'" sing N N 46 A "C3'" "O3'" sing N N 47 A "C3'" "C2'" sing N N 48 A "C3'" "H3'" sing N N 49 A "O3'" "HO3'" sing N N 50 A "C2'" "O2'" sing N N 51 A "C2'" "C1'" sing N N 52 A "C2'" "H2'" sing N N 53 A "O2'" "HO2'" sing N N 54 A "C1'" N9 sing N N 55 A "C1'" "H1'" sing N N 56 A N9 C8 sing Y N 57 A N9 C4 sing Y N 58 A C8 N7 doub Y N 59 A C8 H8 sing N N 60 A N7 C5 sing Y N 61 A C5 C6 sing Y N 62 A C5 C4 doub Y N 63 A C6 N6 sing N N 64 A C6 N1 doub Y N 65 A N6 H61 sing N N 66 A N6 H62 sing N N 67 A N1 C2 sing Y N 68 A C2 N3 doub Y N 69 A C2 H2 sing N N 70 A N3 C4 sing Y N 71 C OP3 P sing N N 72 C OP3 HOP3 sing N N 73 C P OP1 doub N N 74 C P OP2 sing N N 75 C P "O5'" sing N N 76 C OP2 HOP2 sing N N 77 C "O5'" "C5'" sing N N 78 C "C5'" "C4'" sing N N 79 C "C5'" "H5'" sing N N 80 C "C5'" "H5''" sing N N 81 C "C4'" "O4'" sing N N 82 C "C4'" "C3'" sing N N 83 C "C4'" "H4'" sing N N 84 C "O4'" "C1'" sing N N 85 C "C3'" "O3'" sing N N 86 C "C3'" "C2'" sing N N 87 C "C3'" "H3'" sing N N 88 C "O3'" "HO3'" sing N N 89 C "C2'" "O2'" sing N N 90 C "C2'" "C1'" sing N N 91 C "C2'" "H2'" sing N N 92 C "O2'" "HO2'" sing N N 93 C "C1'" N1 sing N N 94 C "C1'" "H1'" sing N N 95 C N1 C2 sing N N 96 C N1 C6 sing N N 97 C C2 O2 doub N N 98 C C2 N3 sing N N 99 C N3 C4 doub N N 100 C C4 N4 sing N N 101 C C4 C5 sing N N 102 C N4 H41 sing N N 103 C N4 H42 sing N N 104 C C5 C6 doub N N 105 C C5 H5 sing N N 106 C C6 H6 sing N N 107 G OP3 P sing N N 108 G OP3 HOP3 sing N N 109 G P OP1 doub N N 110 G P OP2 sing N N 111 G P "O5'" sing N N 112 G OP2 HOP2 sing N N 113 G "O5'" "C5'" sing N N 114 G "C5'" "C4'" sing N N 115 G "C5'" "H5'" sing N N 116 G "C5'" "H5''" sing N N 117 G "C4'" "O4'" sing N N 118 G "C4'" "C3'" sing N N 119 G "C4'" "H4'" sing N N 120 G "O4'" "C1'" sing N N 121 G "C3'" "O3'" sing N N 122 G "C3'" "C2'" sing N N 123 G "C3'" "H3'" sing N N 124 G "O3'" "HO3'" sing N N 125 G "C2'" "O2'" sing N N 126 G "C2'" "C1'" sing N N 127 G "C2'" "H2'" sing N N 128 G "O2'" "HO2'" sing N N 129 G "C1'" N9 sing N N 130 G "C1'" "H1'" sing N N 131 G N9 C8 sing Y N 132 G N9 C4 sing Y N 133 G C8 N7 doub Y N 134 G C8 H8 sing N N 135 G N7 C5 sing Y N 136 G C5 C6 sing N N 137 G C5 C4 doub Y N 138 G C6 O6 doub N N 139 G C6 N1 sing N N 140 G N1 C2 sing N N 141 G N1 H1 sing N N 142 G C2 N2 sing N N 143 G C2 N3 doub N N 144 G N2 H21 sing N N 145 G N2 H22 sing N N 146 G N3 C4 sing N N 147 GTP PG O1G doub N N 148 GTP PG O2G sing N N 149 GTP PG O3G sing N N 150 GTP PG O3B sing N N 151 GTP O2G HOG2 sing N N 152 GTP O3G HOG3 sing N N 153 GTP O3B PB sing N N 154 GTP PB O1B doub N N 155 GTP PB O2B sing N N 156 GTP PB O3A sing N N 157 GTP O2B HOB2 sing N N 158 GTP O3A PA sing N N 159 GTP PA O1A doub N N 160 GTP PA O2A sing N N 161 GTP PA "O5'" sing N N 162 GTP O2A HOA2 sing N N 163 GTP "O5'" "C5'" sing N N 164 GTP "C5'" "C4'" sing N N 165 GTP "C5'" "H5'" sing N N 166 GTP "C5'" "H5''" sing N N 167 GTP "C4'" "O4'" sing N N 168 GTP "C4'" "C3'" sing N N 169 GTP "C4'" "H4'" sing N N 170 GTP "O4'" "C1'" sing N N 171 GTP "C3'" "O3'" sing N N 172 GTP "C3'" "C2'" sing N N 173 GTP "C3'" "H3'" sing N N 174 GTP "O3'" "HO3'" sing N N 175 GTP "C2'" "O2'" sing N N 176 GTP "C2'" "C1'" sing N N 177 GTP "C2'" "H2'" sing N N 178 GTP "O2'" "HO2'" sing N N 179 GTP "C1'" N9 sing N N 180 GTP "C1'" "H1'" sing N N 181 GTP N9 C8 sing Y N 182 GTP N9 C4 sing Y N 183 GTP C8 N7 doub Y N 184 GTP C8 H8 sing N N 185 GTP N7 C5 sing Y N 186 GTP C5 C6 sing N N 187 GTP C5 C4 doub Y N 188 GTP C6 O6 doub N N 189 GTP C6 N1 sing N N 190 GTP N1 C2 sing N N 191 GTP N1 HN1 sing N N 192 GTP C2 N2 sing N N 193 GTP C2 N3 doub N N 194 GTP N2 HN21 sing N N 195 GTP N2 HN22 sing N N 196 GTP N3 C4 sing N N 197 HOH O H1 sing N N 198 HOH O H2 sing N N 199 IRI IR N1 sing N N 200 IRI IR N2 sing N N 201 IRI IR N3 sing N N 202 IRI IR N4 sing N N 203 IRI IR N5 sing N N 204 IRI IR N6 sing N N 205 IRI N1 HN11 sing N N 206 IRI N1 HN12 sing N N 207 IRI N1 HN13 sing N N 208 IRI N2 HN21 sing N N 209 IRI N2 HN22 sing N N 210 IRI N2 HN23 sing N N 211 IRI N3 HN31 sing N N 212 IRI N3 HN32 sing N N 213 IRI N3 HN33 sing N N 214 IRI N4 HN41 sing N N 215 IRI N4 HN42 sing N N 216 IRI N4 HN43 sing N N 217 IRI N5 HN51 sing N N 218 IRI N5 HN52 sing N N 219 IRI N5 HN53 sing N N 220 IRI N6 HN61 sing N N 221 IRI N6 HN62 sing N N 222 IRI N6 HN63 sing N N 223 U OP3 P sing N N 224 U OP3 HOP3 sing N N 225 U P OP1 doub N N 226 U P OP2 sing N N 227 U P "O5'" sing N N 228 U OP2 HOP2 sing N N 229 U "O5'" "C5'" sing N N 230 U "C5'" "C4'" sing N N 231 U "C5'" "H5'" sing N N 232 U "C5'" "H5''" sing N N 233 U "C4'" "O4'" sing N N 234 U "C4'" "C3'" sing N N 235 U "C4'" "H4'" sing N N 236 U "O4'" "C1'" sing N N 237 U "C3'" "O3'" sing N N 238 U "C3'" "C2'" sing N N 239 U "C3'" "H3'" sing N N 240 U "O3'" "HO3'" sing N N 241 U "C2'" "O2'" sing N N 242 U "C2'" "C1'" sing N N 243 U "C2'" "H2'" sing N N 244 U "O2'" "HO2'" sing N N 245 U "C1'" N1 sing N N 246 U "C1'" "H1'" sing N N 247 U N1 C2 sing N N 248 U N1 C6 sing N N 249 U C2 O2 doub N N 250 U C2 N3 sing N N 251 U N3 C4 sing N N 252 U N3 H3 sing N N 253 U C4 O4 doub N N 254 U C4 C5 sing N N 255 U C5 C6 doub N N 256 U C5 H5 sing N N 257 U C6 H6 sing N N 258 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7KVT 'double helix' 7KVT 'a-form double helix' 7KVT 'bulge loop' 7KVT 'mismatched base pair' 7KVT 'internal loop' 7KVT 'quadruple helix' 7KVT 'three-way junction' # 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 GTP 1 1_555 A C 83 1_555 0.045 -0.141 -0.017 1.446 -5.776 -3.205 1 B_GTP1:C83_B B 1 ? B 83 ? 19 1 1 A G 2 1_555 A C 82 1_555 0.027 -0.075 -0.235 -6.814 -12.064 1.764 2 B_G2:C82_B B 2 ? B 82 ? 19 1 1 A G 3 1_555 A C 81 1_555 -0.318 0.171 -0.161 -13.546 -12.487 6.917 3 B_G3:C81_B B 3 ? B 81 ? 19 1 1 A A 4 1_555 A U 80 1_555 -0.003 -0.083 0.114 -6.835 -12.408 0.727 4 B_A4:U80_B B 4 ? B 80 ? 20 1 1 A A 5 1_555 A U 79 1_555 0.342 0.163 0.237 -4.190 -14.706 4.082 5 B_A5:U79_B B 5 ? B 79 ? 20 1 1 A G 6 1_555 A C 78 1_555 -0.325 -0.168 0.125 0.337 -17.675 2.024 6 B_G6:C78_B B 6 ? B 78 ? 19 1 1 A A 7 1_555 A U 77 1_555 0.373 0.062 0.311 -3.843 -15.325 -1.269 7 B_A7:U77_B B 7 ? B 77 ? 20 1 1 A U 8 1_555 A A 76 1_555 0.474 -0.308 0.646 -10.864 -9.779 -3.416 8 B_U8:A76_B B 8 ? B 76 ? 20 1 1 A A 9 1_555 A U 75 1_555 -0.010 0.088 0.372 0.729 -10.341 8.614 9 B_A9:U75_B B 9 ? B 75 ? 20 1 1 A C 10 1_555 A G 74 1_555 0.316 -0.019 0.050 14.546 -4.334 -2.253 10 B_C10:G74_B B 10 ? B 74 ? 19 1 1 A A 45 1_555 A G 71 1_555 1.179 3.404 -0.354 -9.526 -39.323 -104.557 11 B_A45:G71_B B 45 ? B 71 ? ? ? 1 A G 46 1_555 A G 42 1_555 5.769 -0.880 -0.072 1.884 0.080 -110.210 12 B_G46:G42_B B 46 ? B 42 ? 7 4 1 A G 47 1_555 A C 72 1_555 -0.307 -0.414 -0.106 3.429 -11.756 1.329 13 B_G47:C72_B B 47 ? B 72 ? 19 1 1 A A 70 1_555 A G 13 1_555 -1.000 -7.925 -0.484 -18.997 6.209 -127.709 14 B_A70:G13_B B 70 ? B 13 ? ? 6 1 A U 15 1_555 A A 69 1_555 4.504 -1.958 0.753 -19.635 22.927 -98.815 15 B_U15:A69_B B 15 ? B 69 ? 24 4 1 A G 16 1_555 A A 49 1_555 3.079 -4.109 -0.820 4.364 14.424 -72.953 16 B_G16:A49_B B 16 ? B 49 ? 10 6 1 A A 17 1_555 A U 68 1_555 -0.761 -3.013 0.134 -17.710 -1.703 -164.976 17 B_A17:U68_B B 17 ? B 68 ? ? 2 1 A G 50 1_555 A C 67 1_555 0.126 -0.080 0.312 0.171 -12.839 2.555 18 B_G50:C67_B B 50 ? B 67 ? 19 1 1 A A 52 1_555 A U 66 1_555 0.556 -0.399 0.066 -3.645 -7.996 1.372 19 B_A52:U66_B B 52 ? B 66 ? 20 1 1 A G 53 1_555 A C 65 1_555 -0.109 -0.342 -0.002 -2.358 -3.697 -0.763 20 B_G53:C65_B B 53 ? B 65 ? 19 1 1 A A 54 1_555 A U 64 1_555 -0.232 -0.304 0.045 3.374 -5.222 1.411 21 B_A54:U64_B B 54 ? B 64 ? 20 1 1 A G 55 1_555 A C 63 1_555 0.278 -0.050 -0.038 -7.179 -11.354 2.616 22 B_G55:C63_B B 55 ? B 63 ? 19 1 1 A C 56 1_555 A G 31 1_555 -0.426 -0.005 0.616 -22.120 -11.519 0.047 23 B_C56:G31_B B 56 ? B 31 ? 19 1 1 A C 57 1_555 A G 30 1_555 0.134 2.062 1.072 -18.440 -1.072 -106.639 24 B_C57:G30_B B 57 ? B 30 ? ? ? 1 A A 60 1_555 A A 28 1_555 4.096 1.332 0.387 7.971 10.771 -111.765 25 B_A60:A28_B B 60 ? B 28 ? 5 4 1 A U 32 1_555 A U 24 1_555 -2.916 -2.012 -0.216 -9.399 -6.905 7.096 26 B_U32:U24_B B 32 ? B 24 ? 16 1 1 A U 33 1_555 A A 23 1_555 0.264 -0.350 -0.112 0.932 -7.048 1.115 27 B_U33:A23_B B 33 ? B 23 ? 20 1 1 A U 34 1_555 A A 22 1_555 -0.821 -0.081 0.035 6.335 -3.147 -0.444 28 B_U34:A22_B B 34 ? B 22 ? 20 1 1 A G 35 1_555 A C 21 1_555 0.039 -0.292 0.424 3.335 -14.211 3.546 29 B_G35:C21_B B 35 ? B 21 ? 19 1 1 A G 36 1_555 A C 20 1_555 -0.180 -0.471 0.354 -0.581 -1.797 2.559 30 B_G36:C20_B B 36 ? B 20 ? 19 1 1 A G 37 1_555 A C 19 1_555 -0.412 -0.120 -0.203 -13.800 -21.877 -1.187 31 B_G37:C19_B B 37 ? B 19 ? 19 1 1 A U 38 1_555 A G 18 1_555 2.569 -0.485 0.633 -20.313 2.539 -3.231 32 B_U38:G18_B B 38 ? B 18 ? 28 1 1 A U 39 1_555 A A 48 1_555 4.629 -2.116 -0.047 20.458 -13.173 -88.181 33 B_U39:A48_B B 39 ? B 48 ? 24 4 # 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 GTP 1 1_555 A C 83 1_555 A G 2 1_555 A C 82 1_555 -0.008 -1.819 3.372 2.952 9.152 34.426 -4.240 0.424 2.803 15.101 -4.870 35.705 1 BB_GTP1G2:C82C83_BB B 1 ? B 83 ? B 2 ? B 82 ? 1 A G 2 1_555 A C 82 1_555 A G 3 1_555 A C 81 1_555 0.444 -1.987 3.414 1.315 8.710 27.453 -5.856 -0.611 2.687 17.782 -2.684 28.806 2 BB_G2G3:C81C82_BB B 2 ? B 82 ? B 3 ? B 81 ? 1 A G 3 1_555 A C 81 1_555 A A 4 1_555 A U 80 1_555 -0.428 -1.533 3.110 -1.095 1.914 31.935 -3.104 0.591 3.028 3.474 1.988 32.009 3 BB_G3A4:U80C81_BB B 3 ? B 81 ? B 4 ? B 80 ? 1 A A 4 1_555 A U 80 1_555 A A 5 1_555 A U 79 1_555 -0.052 -1.172 3.242 0.512 2.072 34.119 -2.316 0.168 3.167 3.528 -0.871 34.184 4 BB_A4A5:U79U80_BB B 4 ? B 80 ? B 5 ? B 79 ? 1 A A 5 1_555 A U 79 1_555 A G 6 1_555 A C 78 1_555 0.422 -1.527 3.116 2.176 5.734 27.531 -4.355 -0.404 2.771 11.863 -4.501 28.193 5 BB_A5G6:C78U79_BB B 5 ? B 79 ? B 6 ? B 78 ? 1 A G 6 1_555 A C 78 1_555 A A 7 1_555 A U 77 1_555 -0.202 -1.250 3.179 -2.436 10.407 36.896 -3.105 0.027 2.747 16.034 3.753 38.361 6 BB_G6A7:U77C78_BB B 6 ? B 78 ? B 7 ? B 77 ? 1 A A 7 1_555 A U 77 1_555 A U 8 1_555 A A 76 1_555 -0.206 -1.488 3.460 -1.722 10.873 34.114 -3.974 0.089 2.874 17.962 2.846 35.796 7 BB_A7U8:A76U77_BB B 7 ? B 77 ? B 8 ? B 76 ? 1 A U 8 1_555 A A 76 1_555 A A 9 1_555 A U 75 1_555 0.477 -1.569 2.788 4.533 6.833 28.336 -4.263 -0.155 2.398 13.602 -9.023 29.475 8 BB_U8A9:U75A76_BB B 8 ? B 76 ? B 9 ? B 75 ? 1 A A 9 1_555 A U 75 1_555 A C 10 1_555 A G 74 1_555 0.634 -1.028 2.874 6.015 7.535 35.144 -2.551 -0.292 2.673 12.198 -9.738 36.402 9 BB_A9C10:G74U75_BB B 9 ? B 75 ? B 10 ? B 74 ? 1 A C 10 1_555 A G 74 1_555 A A 45 1_555 A G 71 1_555 0.369 4.233 2.518 3.829 -7.057 167.421 2.138 -0.181 2.491 -3.550 -1.926 167.452 10 BB_C10A45:G71G74_BB B 10 ? B 74 ? B 45 ? B 71 ? 1 A A 45 1_555 A G 71 1_555 A G 46 1_555 A G 42 1_555 2.138 1.937 3.956 14.566 2.322 38.684 2.411 -0.924 4.546 3.361 -21.079 41.300 11 BB_A45G46:G42G71_BB B 45 ? B 71 ? B 46 ? B 42 ? 1 A G 46 1_555 A G 42 1_555 A G 47 1_555 A C 72 1_555 -4.311 4.468 0.869 12.316 -16.062 -77.982 -3.270 -3.194 2.158 12.568 9.637 -80.159 12 BB_G46G47:C72G42_BB B 46 ? B 42 ? B 47 ? B 72 ? 1 A G 47 1_555 A C 72 1_555 A A 70 1_555 A G 13 1_555 0.317 1.448 4.467 5.734 -13.677 -132.435 -0.662 0.227 4.529 7.465 3.130 -132.857 13 BB_G47A70:G13C72_BB B 47 ? B 72 ? B 70 ? B 13 ? 1 A A 70 1_555 A G 13 1_555 A U 15 1_555 A A 69 1_555 -3.735 -2.078 5.563 27.677 -3.720 111.858 -1.170 2.728 4.939 -2.226 -16.559 114.133 14 BB_A70U15:A69G13_BB B 70 ? B 13 ? B 15 ? B 69 ? 1 A U 15 1_555 A A 69 1_555 A G 16 1_555 A A 49 1_555 2.166 -2.701 2.964 5.696 -9.502 35.356 -2.896 -2.598 3.831 -15.191 -9.107 36.998 15 BB_U15G16:A49A69_BB B 15 ? B 69 ? B 16 ? B 49 ? 1 A G 16 1_555 A A 49 1_555 A A 17 1_555 A U 68 1_555 0.822 -4.501 0.838 -115.244 -136.668 -177.306 2.258 0.405 0.769 68.334 -57.622 -179.971 16 BB_G16A17:U68A49_BB B 16 ? B 49 ? B 17 ? B 68 ? 1 A A 17 1_555 A U 68 1_555 A G 50 1_555 A C 67 1_555 -2.849 2.429 0.087 -159.918 -68.038 -177.928 -1.214 -1.425 0.057 34.019 -79.959 -179.888 17 BB_A17G50:C67U68_BB B 17 ? B 68 ? B 50 ? B 67 ? 1 A G 50 1_555 A C 67 1_555 A A 52 1_555 A U 66 1_555 -1.044 -1.609 3.204 0.235 6.371 41.418 -2.878 1.484 2.930 8.944 -0.329 41.884 18 BB_G50A52:U66C67_BB B 50 ? B 67 ? B 52 ? B 66 ? 1 A A 52 1_555 A U 66 1_555 A G 53 1_555 A C 65 1_555 -0.078 -2.074 3.165 1.618 4.465 28.161 -5.139 0.496 2.800 9.094 -3.296 28.550 19 BB_A52G53:C65U66_BB B 52 ? B 66 ? B 53 ? B 65 ? 1 A G 53 1_555 A C 65 1_555 A A 54 1_555 A U 64 1_555 0.491 -1.870 3.047 2.270 3.096 27.862 -4.506 -0.528 2.856 6.391 -4.685 28.120 20 BB_G53A54:U64C65_BB B 53 ? B 65 ? B 54 ? B 64 ? 1 A A 54 1_555 A U 64 1_555 A G 55 1_555 A C 63 1_555 0.781 -2.228 3.351 2.663 10.534 31.656 -5.492 -0.950 2.555 18.636 -4.711 33.423 21 BB_A54G55:C63U64_BB B 54 ? B 64 ? B 55 ? B 63 ? 1 A G 55 1_555 A C 63 1_555 A C 56 1_555 A G 31 1_555 1.981 -0.859 3.359 0.365 7.375 53.238 -1.417 -2.169 3.235 8.185 -0.405 53.711 22 BB_G55C56:G31C63_BB B 55 ? B 63 ? B 56 ? B 31 ? 1 A C 56 1_555 A G 31 1_555 A C 57 1_555 A G 30 1_555 -0.294 -1.175 2.778 1.284 8.518 84.003 -1.042 0.244 2.668 6.350 -0.957 84.361 23 BB_C56C57:G30G31_BB B 56 ? B 31 ? B 57 ? B 30 ? 1 A C 57 1_555 A G 30 1_555 A A 60 1_555 A A 28 1_555 -3.227 5.530 -0.059 14.740 174.010 -33.086 -0.872 -1.776 -5.038 -88.917 7.532 -174.855 24 BB_C57A60:A28G30_BB B 57 ? B 30 ? B 60 ? B 28 ? 1 A U 32 1_555 A U 24 1_555 A U 33 1_555 A A 23 1_555 -0.344 -1.206 3.098 0.770 -0.703 48.677 -1.412 0.473 3.108 -0.852 -0.935 48.687 25 BB_U32U33:A23U24_BB B 32 ? B 24 ? B 33 ? B 23 ? 1 A U 33 1_555 A A 23 1_555 A U 34 1_555 A A 22 1_555 -0.626 -2.535 3.223 -1.580 3.635 17.842 -9.845 1.160 2.701 11.536 5.013 18.273 26 BB_U33U34:A22A23_BB B 33 ? B 23 ? B 34 ? B 22 ? 1 A U 34 1_555 A A 22 1_555 A G 35 1_555 A C 21 1_555 -0.090 -1.641 3.199 -2.826 7.019 35.770 -3.521 -0.220 2.836 11.272 4.538 36.535 27 BB_U34G35:C21A22_BB B 34 ? B 22 ? B 35 ? B 21 ? 1 A G 35 1_555 A C 21 1_555 A G 36 1_555 A C 20 1_555 -0.328 -1.849 3.053 -2.446 8.332 30.064 -4.793 0.208 2.482 15.656 4.596 31.265 28 BB_G35G36:C20C21_BB B 35 ? B 21 ? B 36 ? B 20 ? 1 A G 36 1_555 A C 20 1_555 A G 37 1_555 A C 19 1_555 0.474 -2.056 3.413 6.755 13.889 29.823 -5.689 0.211 2.307 24.989 -12.153 33.504 29 BB_G36G37:C19C20_BB B 36 ? B 20 ? B 37 ? B 19 ? 1 A G 37 1_555 A C 19 1_555 A U 38 1_555 A G 18 1_555 0.314 -1.432 3.388 -2.406 5.423 46.356 -2.263 -0.599 3.191 6.856 3.041 46.714 30 BB_G37U38:G18C19_BB B 37 ? B 19 ? B 38 ? B 18 ? 1 A U 38 1_555 A G 18 1_555 A U 39 1_555 A A 48 1_555 -3.126 -1.727 2.221 7.707 2.773 58.126 -1.851 3.435 1.754 2.839 -7.890 58.650 31 BB_U38U39:A48G18_BB B 38 ? B 18 ? B 39 ? B 48 ? # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _space_group.name_H-M_alt 'P 42 21 2' _space_group.name_Hall 'P 4n 2n' _space_group.IT_number 94 _space_group.crystal_system tetragonal _space_group.id 1 # _atom_sites.entry_id 7KVT _atom_sites.fract_transf_matrix[1][1] 0.009625 _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] 0.009625 _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] 0.019343 _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 _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? F ? ? 8.95735 ? ? ? 7.27484 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? IR ? ? 76.48196 ? ? ? 4.24549 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? MG ? ? 9.41153 2.53737 ? ? 2.59044 63.03566 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? MG2+ ? ? 9.95820 ? ? ? 3.10187 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 7.96527 ? ? ? 9.05267 ? ? ? 0.0 ;1-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_