data_5DH6 # _entry.id 5DH6 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 5DH6 pdb_00005dh6 10.2210/pdb5dh6/pdb WWPDB D_1000213172 ? ? # 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 2015-10-07 2 'Structure model' 1 1 2015-11-04 3 'Structure model' 1 2 2017-09-27 4 'Structure model' 1 3 2019-12-25 5 'Structure model' 1 4 2024-03-06 # _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' 'Author supporting evidence' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Author supporting evidence' 6 5 'Structure model' 'Data collection' 7 5 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' citation 2 3 'Structure model' pdbx_audit_support 3 3 'Structure model' pdbx_struct_oper_list 4 4 'Structure model' pdbx_audit_support 5 5 'Structure model' chem_comp_atom 6 5 'Structure model' chem_comp_bond 7 5 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_citation.journal_id_CSD' 2 3 'Structure model' '_pdbx_audit_support.funding_organization' 3 3 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 4 4 'Structure model' '_pdbx_audit_support.funding_organization' 5 5 'Structure model' '_database_2.pdbx_DOI' 6 5 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5DH6 _pdbx_database_status.recvd_initial_deposition_date 2015-08-29 _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.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 5DH7 PDB . unspecified 5DH8 PDB . unspecified 5DI2 PDB . unspecified 5DI4 PDB . # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Mir, A.' 1 'Chen, J.' 2 'Neau, D.' 3 'Golden, B.L.' 4 # _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 Biochemistry _citation.journal_id_ASTM BICHAW _citation.journal_id_CSD 0033 _citation.journal_id_ISSN 0006-2960 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 54 _citation.language ? _citation.page_first 6369 _citation.page_last 6381 _citation.title 'Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.' _citation.year 2015 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.biochem.5b00824 _citation.pdbx_database_id_PubMed 26398724 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mir, A.' 1 ? primary 'Chen, J.' 2 ? primary 'Robinson, K.' 3 ? primary 'Lendy, E.' 4 ? primary 'Goodman, J.' 5 ? primary 'Neau, D.' 6 ? primary 'Golden, B.L.' 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 'hammerhead ribozyme' 15484.287 1 ? ? ? ? 2 polymer syn "5'-R(*GP*GP*GP*CP*GP*U)-D(P*C)-R(P*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP*CP*A)-3'" 6437.895 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 5 ? ? ? ? 4 water nat water 18.015 8 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no GGGUACUUAAGCCCACUGAUGAGUCGCUGGGAUGCGACAAAACGCCCA GGGUACUUAAGCCCACUGAUGAGUCGCUGGGAUGCGACAAAACGCCCA A ? 2 'polydeoxyribonucleotide/polyribonucleotide hybrid' no no 'GGGCGU(DC)UGGGCAGUACCCA' GGGCGUCUGGGCAGUACCCA B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 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 G n 1 2 G n 1 3 G n 1 4 U n 1 5 A n 1 6 C n 1 7 U n 1 8 U n 1 9 A n 1 10 A n 1 11 G n 1 12 C n 1 13 C n 1 14 C n 1 15 A n 1 16 C n 1 17 U n 1 18 G n 1 19 A n 1 20 U n 1 21 G n 1 22 A n 1 23 G n 1 24 U n 1 25 C n 1 26 G n 1 27 C n 1 28 U n 1 29 G n 1 30 G n 1 31 G n 1 32 A n 1 33 U n 1 34 G n 1 35 C n 1 36 G n 1 37 A n 1 38 C n 1 39 A n 1 40 A n 1 41 A n 1 42 A n 1 43 C n 1 44 G n 1 45 C n 1 46 C n 1 47 C n 1 48 A n 2 1 G n 2 2 G n 2 3 G n 2 4 C n 2 5 G n 2 6 U n 2 7 DC n 2 8 U n 2 9 G n 2 10 G n 2 11 G n 2 12 C n 2 13 A n 2 14 G n 2 15 U n 2 16 A n 2 17 C n 2 18 C n 2 19 C n 2 20 A n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 48 'synthetic construct' ? 32630 'This RNA was made by in vitro transcription' 2 1 sample 1 20 'synthetic construct' ? 32630 'synthesized oligonucleotide' # 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 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 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 G 1 1 1 G G A . n A 1 2 G 2 2 2 G G A . n A 1 3 G 3 3 3 G G A . n A 1 4 U 4 4 4 U U A . n A 1 5 A 5 5 5 A A A . n A 1 6 C 6 6 6 C C A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 C 12 12 12 C C A . n A 1 13 C 13 13 13 C C A . n A 1 14 C 14 14 14 C C A . n A 1 15 A 15 15 15 A A A . n A 1 16 C 16 16 16 C C A . n A 1 17 U 17 17 17 U U A . n A 1 18 G 18 18 18 G G A . n A 1 19 A 19 19 19 A A A . n A 1 20 U 20 20 20 U U A . n A 1 21 G 21 21 21 G G A . n A 1 22 A 22 22 22 A A A . n A 1 23 G 23 23 23 G G A . n A 1 24 U 24 24 24 U U A . n A 1 25 C 25 25 25 C C A . n A 1 26 G 26 26 26 G G A . n A 1 27 C 27 27 27 C C A . n A 1 28 U 28 28 28 U U A . n A 1 29 G 29 29 29 G G A . n A 1 30 G 30 30 30 G G A . n A 1 31 G 31 31 31 G G A . n A 1 32 A 32 32 32 A A A . n A 1 33 U 33 33 33 U U A . n A 1 34 G 34 34 34 G G A . n A 1 35 C 35 35 35 C C A . n A 1 36 G 36 36 36 G G A . n A 1 37 A 37 37 37 A A A . n A 1 38 C 38 38 38 C C A . n A 1 39 A 39 39 39 A A A . n A 1 40 A 40 40 40 A A A . n A 1 41 A 41 41 41 A A A . n A 1 42 A 42 42 42 A A A . n A 1 43 C 43 43 43 C C A . n A 1 44 G 44 44 44 G G A . n A 1 45 C 45 45 45 C C A . n A 1 46 C 46 46 46 C C A . n A 1 47 C 47 47 47 C C A . n A 1 48 A 48 48 48 A A A . n B 2 1 G 1 1 1 G G B . n B 2 2 G 2 2 2 G G B . n B 2 3 G 3 3 3 G G B . n B 2 4 C 4 4 4 C C B . n B 2 5 G 5 5 5 G G B . n B 2 6 U 6 6 6 U U B . n B 2 7 DC 7 7 7 DC DC B . n B 2 8 U 8 8 8 U U B . n B 2 9 G 9 9 9 G G B . n B 2 10 G 10 10 10 G G B . n B 2 11 G 11 11 11 G G B . n B 2 12 C 12 12 12 C C B . n B 2 13 A 13 13 13 A A B . n B 2 14 G 14 14 14 G G B . n B 2 15 U 15 15 15 U U B . n B 2 16 A 16 16 16 A A B . n B 2 17 C 17 17 17 C C B . n B 2 18 C 18 18 18 C C B . n B 2 19 C 19 19 19 C C B . n B 2 20 A 20 20 20 A A B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 MG 1 101 1 MG MG A . D 3 MG 1 102 3 MG MG A . E 3 MG 1 103 4 MG MG A . F 3 MG 1 104 5 MG MG A . G 3 MG 1 101 2 MG MG B . H 4 HOH 1 201 4 HOH HOH A . H 4 HOH 2 202 6 HOH HOH A . H 4 HOH 3 203 2 HOH HOH A . H 4 HOH 4 204 1 HOH HOH A . I 4 HOH 1 201 3 HOH HOH B . I 4 HOH 2 202 8 HOH HOH B . I 4 HOH 3 203 7 HOH HOH B . I 4 HOH 4 204 5 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 ? ? ? 1.9_1692 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 5DH6 _cell.details ? _cell.formula_units_Z ? _cell.length_a 81.405 _cell.length_a_esd ? _cell.length_b 85.964 _cell.length_b_esd ? _cell.length_c 102.969 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DH6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.pdbx_full_space_group_name_H-M ? # _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 5DH6 _exptl.crystals_number ? _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 4.11 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 70.06 _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, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 5.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '33% MPD, 0.4 M potassium chloride, 50 mM potassium acetate, 10 mM MgCl2, pH 5.0, and 0.5mM spermine' _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_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MARMOSAIC 300 mm CCD' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-11-14 # _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 0.976 _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 21-ID-D' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.976 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 21-ID-D _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 5DH6 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.784 _reflns.d_resolution_low 50 _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 9318 _reflns.number_obs 9318 _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 99.5 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 14.3 _reflns.pdbx_Rmerge_I_obs 0.078 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 61.7 _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_R_split ? # _reflns_shell.d_res_high 2.784 _reflns_shell.d_res_low 2.85 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs 6.3 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.percent_possible_all 96.7 _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 0.655 _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 15.0 _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_R_split ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 5DH6 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 2.784 _refine.ls_d_res_low 28.407 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 9231 _refine.ls_number_reflns_R_free 920 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.82 _refine.ls_percent_reflns_R_free 9.97 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2139 _refine.ls_R_factor_R_free 0.2416 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2108 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.35 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.11 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 27.65 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.37 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _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 1454 _refine_hist.pdbx_number_atoms_ligand 5 _refine_hist.number_atoms_solvent 8 _refine_hist.number_atoms_total 1467 _refine_hist.d_res_high 2.784 _refine_hist.d_res_low 28.407 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.002 ? 1626 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.470 ? 2532 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 10.131 ? 807 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.023 ? 338 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.003 ? 68 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free 'X-RAY DIFFRACTION' 2.7843 2.9310 . . 126 1141 96.00 . . . 0.3602 . 0.3527 . . . . . . . . . . 'X-RAY DIFFRACTION' 2.9310 3.1144 . . 134 1160 98.00 . . . 0.3306 . 0.2607 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.1144 3.3545 . . 121 1158 98.00 . . . 0.2336 . 0.2231 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.3545 3.6915 . . 131 1193 99.00 . . . 0.2585 . 0.2065 . . . . . . . . . . 'X-RAY DIFFRACTION' 3.6915 4.2241 . . 137 1190 100.00 . . . 0.2107 . 0.1871 . . . . . . . . . . 'X-RAY DIFFRACTION' 4.2241 5.3162 . . 133 1196 100.00 . . . 0.2054 . 0.1849 . . . . . . . . . . 'X-RAY DIFFRACTION' 5.3162 28.4086 . . 138 1273 100.00 . . . 0.2373 . 0.2078 . . . . . . . . . . # _struct.entry_id 5DH6 _struct.title 'Two divalent metal ions and conformational changes play roles in the hammerhead ribozyme cleavage reaction-G12A mutant in Mg2+' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 5DH6 _struct_keywords.text 'ribozyme, hammerhead, 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 3 ? G N N 3 ? H N N 4 ? I N N 4 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 5DH6 5DH6 ? 1 ? 1 2 PDB 5DH6 5DH6 ? 2 ? 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 5DH6 A 1 ? 48 ? 5DH6 1 ? 48 ? 1 48 2 2 5DH6 B 1 ? 19 ? 5DH6 1 ? 19 ? 1 19 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2310 ? 1 MORE -37 ? 1 'SSA (A^2)' 12190 ? # _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,I # _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 metalc1 metalc ? ? A G 30 O6 ? ? ? 1_555 D MG . MG ? ? A G 30 A MG 102 1_555 ? ? ? ? ? ? ? 2.742 ? ? metalc2 metalc ? ? A A 41 OP2 ? ? ? 1_555 E MG . MG ? ? A A 41 A MG 103 1_555 ? ? ? ? ? ? ? 2.478 ? ? metalc3 metalc ? ? B G 3 O6 ? ? ? 1_555 G MG . MG ? ? B G 3 B MG 101 1_555 ? ? ? ? ? ? ? 2.780 ? ? hydrog1 hydrog ? ? A U 7 N3 ? ? ? 1_555 B A 13 N7 ? ? A U 7 B A 13 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog2 hydrog ? ? A U 7 O2 ? ? ? 1_555 B A 13 N6 ? ? A U 7 B A 13 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog3 hydrog ? ? A A 10 N1 ? ? ? 1_555 A G 29 N2 ? ? A A 10 A G 29 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog4 hydrog ? ? A A 10 N6 ? ? ? 1_555 A G 29 N3 ? ? A A 10 A G 29 1_555 ? ? ? ? ? ? TYPE_10_PAIR ? ? ? hydrog5 hydrog ? ? A G 11 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 11 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 11 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 11 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 11 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 11 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 12 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 12 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 12 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 13 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 13 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 13 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 14 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 14 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 14 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 14 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 14 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 14 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 15 N1 ? ? ? 1_555 B U 8 N3 ? ? A A 15 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 15 N6 ? ? ? 1_555 B U 8 O4 ? ? A A 15 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 16 N3 ? ? ? 1_555 A G 21 N1 ? ? A C 16 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 16 N4 ? ? ? 1_555 A G 21 O6 ? ? A C 16 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 16 O2 ? ? ? 1_555 A G 21 N2 ? ? A C 16 A G 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 18 N2 ? ? ? 1_555 A A 41 N1 ? ? A G 18 A A 41 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog23 hydrog ? ? A A 22 N6 ? ? ? 1_555 A A 39 N3 ? ? A A 22 A A 39 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog24 hydrog ? ? A G 23 N1 ? ? ? 1_555 A C 38 N3 ? ? A G 23 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 23 N2 ? ? ? 1_555 A C 38 O2 ? ? A G 23 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 23 O6 ? ? ? 1_555 A C 38 N4 ? ? A G 23 A C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A U 24 N3 ? ? ? 1_555 A A 37 N1 ? ? A U 24 A A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A U 24 O4 ? ? ? 1_555 A A 37 N6 ? ? A U 24 A A 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 25 N3 ? ? ? 1_555 A G 36 N1 ? ? A C 25 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 25 N4 ? ? ? 1_555 A G 36 O6 ? ? A C 25 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A C 25 O2 ? ? ? 1_555 A G 36 N2 ? ? A C 25 A G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 26 N1 ? ? ? 1_555 A C 35 N3 ? ? A G 26 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 26 N2 ? ? ? 1_555 A C 35 O2 ? ? A G 26 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 26 O6 ? ? ? 1_555 A C 35 N4 ? ? A G 26 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 27 N3 ? ? ? 1_555 A G 34 N1 ? ? A C 27 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 27 N4 ? ? ? 1_555 A G 34 O6 ? ? A C 27 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 27 O2 ? ? ? 1_555 A G 34 N2 ? ? A C 27 A G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A U 28 N3 ? ? ? 1_555 A A 32 N7 ? ? A U 28 A A 32 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog39 hydrog ? ? A U 28 O2 ? ? ? 1_555 A A 32 N6 ? ? A U 28 A A 32 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog40 hydrog ? ? A A 40 N6 ? ? ? 1_555 B DC 7 O2 ? ? A A 40 B DC 7 1_555 ? ? ? ? ? ? 'A-DC MISPAIR' ? ? ? hydrog41 hydrog ? ? A A 41 N6 ? ? ? 1_555 B DC 7 O2 ? ? A A 41 B DC 7 1_555 ? ? ? ? ? ? 'A-DC MISPAIR' ? ? ? hydrog42 hydrog ? ? A A 42 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 42 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A A 42 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 42 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 43 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 43 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 43 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 43 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 43 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 43 B G 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 44 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 44 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 44 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 44 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A G 44 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 44 B C 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 45 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 45 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A C 45 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 45 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A C 45 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 45 B G 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A C 46 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 46 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A C 46 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 46 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A C 46 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 46 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A C 47 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 47 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A C 47 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 47 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A C 47 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 47 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # 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 MG 101 ? 3 'binding site for residue MG A 101' AC2 Software A MG 102 ? 2 'binding site for residue MG A 102' AC3 Software A MG 103 ? 1 'binding site for residue MG A 103' AC4 Software B MG 101 ? 2 'binding site for residue MG B 101' # 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 3 G A 29 ? G A 29 . ? 1_555 ? 2 AC1 3 G A 31 ? G A 31 . ? 1_555 ? 3 AC1 3 C B 19 ? C B 19 . ? 5_545 ? 4 AC2 2 G A 30 ? G A 30 . ? 1_555 ? 5 AC2 2 G A 31 ? G A 31 . ? 1_555 ? 6 AC3 1 A A 41 ? A A 41 . ? 1_555 ? 7 AC4 2 G B 2 ? G B 2 . ? 1_555 ? 8 AC4 2 G B 3 ? G B 3 . ? 1_555 ? # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 202 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id I _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 DC OP3 O N N 73 DC P P N N 74 DC OP1 O N N 75 DC OP2 O N N 76 DC "O5'" O N N 77 DC "C5'" C N N 78 DC "C4'" C N R 79 DC "O4'" O N N 80 DC "C3'" C N S 81 DC "O3'" O N N 82 DC "C2'" C N N 83 DC "C1'" C N R 84 DC N1 N N N 85 DC C2 C N N 86 DC O2 O N N 87 DC N3 N N N 88 DC C4 C N N 89 DC N4 N N N 90 DC C5 C N N 91 DC C6 C N N 92 DC HOP3 H N N 93 DC HOP2 H N N 94 DC "H5'" H N N 95 DC "H5''" H N N 96 DC "H4'" H N N 97 DC "H3'" H N N 98 DC "HO3'" H N N 99 DC "H2'" H N N 100 DC "H2''" H N N 101 DC "H1'" H N N 102 DC H41 H N N 103 DC H42 H N N 104 DC H5 H N N 105 DC H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 MG MG MG N N 148 U OP3 O N N 149 U P P N N 150 U OP1 O N N 151 U OP2 O N N 152 U "O5'" O N N 153 U "C5'" C N N 154 U "C4'" C N R 155 U "O4'" O N N 156 U "C3'" C N S 157 U "O3'" O N N 158 U "C2'" C N R 159 U "O2'" O N N 160 U "C1'" C N R 161 U N1 N N N 162 U C2 C N N 163 U O2 O N N 164 U N3 N N N 165 U C4 C N N 166 U O4 O N N 167 U C5 C N N 168 U C6 C N N 169 U HOP3 H N N 170 U HOP2 H N N 171 U "H5'" H N N 172 U "H5''" H N N 173 U "H4'" H N N 174 U "H3'" H N N 175 U "HO3'" H N N 176 U "H2'" H N N 177 U "HO2'" H N N 178 U "H1'" H N N 179 U H3 H N N 180 U H5 H N N 181 U H6 H N N 182 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 DC OP3 P sing N N 76 DC OP3 HOP3 sing N N 77 DC P OP1 doub N N 78 DC P OP2 sing N N 79 DC P "O5'" sing N N 80 DC OP2 HOP2 sing N N 81 DC "O5'" "C5'" sing N N 82 DC "C5'" "C4'" sing N N 83 DC "C5'" "H5'" sing N N 84 DC "C5'" "H5''" sing N N 85 DC "C4'" "O4'" sing N N 86 DC "C4'" "C3'" sing N N 87 DC "C4'" "H4'" sing N N 88 DC "O4'" "C1'" sing N N 89 DC "C3'" "O3'" sing N N 90 DC "C3'" "C2'" sing N N 91 DC "C3'" "H3'" sing N N 92 DC "O3'" "HO3'" sing N N 93 DC "C2'" "C1'" sing N N 94 DC "C2'" "H2'" sing N N 95 DC "C2'" "H2''" sing N N 96 DC "C1'" N1 sing N N 97 DC "C1'" "H1'" sing N N 98 DC N1 C2 sing N N 99 DC N1 C6 sing N N 100 DC C2 O2 doub N N 101 DC C2 N3 sing N N 102 DC N3 C4 doub N N 103 DC C4 N4 sing N N 104 DC C4 C5 sing N N 105 DC N4 H41 sing N N 106 DC N4 H42 sing N N 107 DC C5 C6 doub N N 108 DC C5 H5 sing N N 109 DC C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 HOH O H1 sing N N 151 HOH O H2 sing N N 152 U OP3 P sing N N 153 U OP3 HOP3 sing N N 154 U P OP1 doub N N 155 U P OP2 sing N N 156 U P "O5'" sing N N 157 U OP2 HOP2 sing N N 158 U "O5'" "C5'" sing N N 159 U "C5'" "C4'" sing N N 160 U "C5'" "H5'" sing N N 161 U "C5'" "H5''" sing N N 162 U "C4'" "O4'" sing N N 163 U "C4'" "C3'" sing N N 164 U "C4'" "H4'" sing N N 165 U "O4'" "C1'" sing N N 166 U "C3'" "O3'" sing N N 167 U "C3'" "C2'" sing N N 168 U "C3'" "H3'" sing N N 169 U "O3'" "HO3'" sing N N 170 U "C2'" "O2'" sing N N 171 U "C2'" "C1'" sing N N 172 U "C2'" "H2'" sing N N 173 U "O2'" "HO2'" sing N N 174 U "C1'" N1 sing N N 175 U "C1'" "H1'" sing N N 176 U N1 C2 sing N N 177 U N1 C6 sing N N 178 U C2 O2 doub N N 179 U C2 N3 sing N N 180 U N3 C4 sing N N 181 U N3 H3 sing N N 182 U C4 O4 doub N N 183 U C4 C5 sing N N 184 U C5 C6 doub N N 185 U C5 H5 sing N N 186 U C6 H6 sing N N 187 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 5DH6 'double helix' 5DH6 'a-form double helix' 5DH6 'hairpin loop' 5DH6 '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 U 7 1_555 B A 13 1_555 4.235 -2.224 -0.596 -9.141 -9.909 -93.182 1 A_U7:A13_B A 7 ? B 13 ? 24 4 1 A A 10 1_555 A G 29 1_555 -3.579 3.960 0.084 -14.922 -10.052 67.457 2 A_A10:G29_A A 10 ? A 29 ? 10 6 1 A A 32 1_555 A U 28 1_555 -4.471 -2.683 0.637 0.141 7.911 -90.274 3 A_A32:U28_A A 32 ? A 28 ? 24 4 1 A G 34 1_555 A C 27 1_555 -0.341 -0.019 0.088 4.467 -9.854 2.545 4 A_G34:C27_A A 34 ? A 27 ? 19 1 1 A C 35 1_555 A G 26 1_555 -0.338 -0.078 0.042 5.951 -9.280 2.830 5 A_C35:G26_A A 35 ? A 26 ? 19 1 1 A G 36 1_555 A C 25 1_555 -0.738 0.012 0.131 -4.152 -5.902 7.102 6 A_G36:C25_A A 36 ? A 25 ? 19 1 1 A A 37 1_555 A U 24 1_555 -0.213 -0.133 0.290 1.303 -7.088 2.458 7 A_A37:U24_A A 37 ? A 24 ? 20 1 1 A C 38 1_555 A G 23 1_555 0.205 -0.093 0.395 1.104 -10.169 6.792 8 A_C38:G23_A A 38 ? A 23 ? 19 1 1 A A 39 1_555 A A 22 1_555 6.411 -1.430 0.594 -4.246 -11.120 41.467 9 A_A39:A22_A A 39 ? A 22 ? ? 5 1 A A 40 1_555 B DC 7 1_555 -6.323 -3.493 -1.311 -20.994 -3.188 -41.842 10 A_A40:DC7_B A 40 ? B 7 ? ? ? 1 A A 41 1_555 A G 18 1_555 -4.314 3.182 -0.179 46.153 -42.568 83.270 11 A_A41:G18_A A 41 ? A 18 ? ? ? 1 A A 42 1_555 B U 6 1_555 -0.041 -0.021 0.568 7.353 -7.128 0.361 12 A_A42:U6_B A 42 ? B 6 ? 20 1 1 A C 43 1_555 B G 5 1_555 -0.247 -0.191 0.278 8.850 -13.715 0.613 13 A_C43:G5_B A 43 ? B 5 ? 19 1 1 A G 44 1_555 B C 4 1_555 -0.349 -0.100 0.073 3.356 -12.546 1.788 14 A_G44:C4_B A 44 ? B 4 ? 19 1 1 A C 45 1_555 B G 3 1_555 0.042 -0.191 -0.111 6.989 -14.074 2.743 15 A_C45:G3_B A 45 ? B 3 ? 19 1 1 A C 46 1_555 B G 2 1_555 0.115 -0.030 0.197 -0.171 -12.408 3.287 16 A_C46:G2_B A 46 ? B 2 ? 19 1 1 A C 47 1_555 B G 1 1_555 -0.271 0.062 0.232 -4.824 -10.738 -4.365 17 A_C47:G1_B A 47 ? B 1 ? 19 1 1 A G 11 1_555 B C 12 1_555 -0.154 -0.164 -0.180 -6.927 -11.034 -0.848 18 A_G11:C12_B A 11 ? B 12 ? 19 1 1 A C 12 1_555 B G 11 1_555 0.122 -0.109 0.135 4.312 -7.046 2.145 19 A_C12:G11_B A 12 ? B 11 ? 19 1 1 A C 13 1_555 B G 10 1_555 -0.262 -0.127 -0.313 6.434 -12.380 -1.039 20 A_C13:G10_B A 13 ? B 10 ? 19 1 1 A C 14 1_555 B G 9 1_555 0.160 -0.282 -0.291 5.912 -13.413 -1.074 21 A_C14:G9_B A 14 ? B 9 ? 19 1 1 A A 15 1_555 B U 8 1_555 0.048 -0.131 0.057 -2.550 -8.522 -0.423 22 A_A15:U8_B A 15 ? B 8 ? 20 1 1 A C 16 1_555 A G 21 1_555 0.438 -0.201 -0.340 12.198 -1.144 -1.874 23 A_C16:G21_A A 16 ? A 21 ? 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 A 10 1_555 A G 29 1_555 A A 32 1_555 A U 28 1_555 -3.080 -2.440 -2.165 163.276 -47.162 -35.753 1.157 -1.777 1.504 24.547 84.980 -170.437 1 AA_A10A32:U28G29_AA A 10 ? A 29 ? A 32 ? A 28 ? 1 A A 32 1_555 A U 28 1_555 A G 34 1_555 A C 27 1_555 3.214 -1.539 3.249 -2.923 7.993 74.044 -1.509 -2.743 2.984 6.616 2.419 74.462 2 AA_A32G34:C27U28_AA A 32 ? A 28 ? A 34 ? A 27 ? 1 A G 34 1_555 A C 27 1_555 A C 35 1_555 A G 26 1_555 0.105 -1.541 3.116 -1.446 4.072 35.131 -3.090 -0.370 2.919 6.715 2.384 35.387 3 AA_G34C35:G26C27_AA A 34 ? A 27 ? A 35 ? A 26 ? 1 A C 35 1_555 A G 26 1_555 A G 36 1_555 A C 25 1_555 0.169 -1.911 3.307 -0.752 11.138 28.965 -5.521 -0.448 2.419 21.296 1.438 30.998 4 AA_C35G36:C25G26_AA A 35 ? A 26 ? A 36 ? A 25 ? 1 A G 36 1_555 A C 25 1_555 A A 37 1_555 A U 24 1_555 -0.096 -1.485 2.973 -1.899 7.043 33.318 -3.500 -0.097 2.615 12.104 3.264 34.085 5 AA_G36A37:U24C25_AA A 36 ? A 25 ? A 37 ? A 24 ? 1 A A 37 1_555 A U 24 1_555 A C 38 1_555 A G 23 1_555 0.720 -1.931 3.212 1.925 0.916 31.626 -3.701 -0.971 3.193 1.678 -3.527 31.696 6 AA_A37C38:G23U24_AA A 37 ? A 24 ? A 38 ? A 23 ? 1 A C 38 1_555 A G 23 1_555 A A 39 1_555 A A 22 1_555 1.795 -0.232 3.496 5.767 4.118 56.110 -0.497 -1.542 3.625 4.358 -6.103 56.520 7 AA_C38A39:A22G23_AA A 38 ? A 23 ? A 39 ? A 22 ? 1 A A 39 1_555 A A 22 1_555 A A 40 1_555 B DC 7 1_555 -1.811 -0.654 3.749 6.734 6.211 19.949 -4.197 7.449 2.680 16.829 -18.247 21.933 8 AA_A39A40:DC7A22_BA A 39 ? A 22 ? A 40 ? B 7 ? 1 A A 40 1_555 B DC 7 1_555 A A 41 1_555 A G 18 1_555 0.299 -4.392 1.657 -25.663 29.368 -17.739 2.391 -2.771 3.876 -50.054 -43.739 -42.703 9 AA_A40A41:G18DC7_AB A 40 ? B 7 ? A 41 ? A 18 ? 1 A A 41 1_555 A G 18 1_555 A A 42 1_555 B U 6 1_555 1.142 2.884 3.295 -1.753 -19.149 90.261 2.353 -0.826 2.762 -13.387 1.225 91.852 10 AA_A41A42:U6G18_BA A 41 ? A 18 ? A 42 ? B 6 ? 1 A A 42 1_555 B U 6 1_555 A C 43 1_555 B G 5 1_555 0.095 -1.270 3.349 0.816 8.451 29.678 -3.988 -0.024 2.887 16.089 -1.554 30.843 11 AA_A42C43:G5U6_BB A 42 ? B 6 ? A 43 ? B 5 ? 1 A C 43 1_555 B G 5 1_555 A G 44 1_555 B C 4 1_555 -0.323 -1.621 3.167 -1.752 14.414 31.631 -4.636 0.308 2.253 24.870 3.022 34.727 12 AA_C43G44:C4G5_BB A 43 ? B 5 ? A 44 ? B 4 ? 1 A G 44 1_555 B C 4 1_555 A C 45 1_555 B G 3 1_555 -0.178 -1.467 3.145 -1.334 6.592 34.084 -3.387 0.110 2.825 11.112 2.249 34.722 13 AA_G44C45:G3C4_BB A 44 ? B 4 ? A 45 ? B 3 ? 1 A C 45 1_555 B G 3 1_555 A C 46 1_555 B G 2 1_555 -0.164 -1.802 3.330 -3.363 8.567 32.486 -4.431 -0.237 2.781 14.944 5.865 33.730 14 AA_C45C46:G2G3_BB A 45 ? B 3 ? A 46 ? B 2 ? 1 A C 46 1_555 B G 2 1_555 A C 47 1_555 B G 1 1_555 -0.603 -1.802 3.210 -0.260 7.209 32.316 -4.287 1.018 2.759 12.755 0.461 33.091 15 AA_C46C47:G1G2_BB A 46 ? B 2 ? A 47 ? B 1 ? 1 A G 11 1_555 B C 12 1_555 A C 12 1_555 B G 11 1_555 -0.174 -1.574 2.924 -4.385 2.547 33.462 -3.067 -0.324 2.799 4.393 7.562 33.833 16 AA_G11C12:G11C12_BB A 11 ? B 12 ? A 12 ? B 11 ? 1 A C 12 1_555 B G 11 1_555 A C 13 1_555 B G 10 1_555 -0.252 -1.925 3.145 2.946 4.306 28.235 -4.768 1.115 2.786 8.732 -5.974 28.704 17 AA_C12C13:G10G11_BB A 12 ? B 11 ? A 13 ? B 10 ? 1 A C 13 1_555 B G 10 1_555 A C 14 1_555 B G 9 1_555 -0.287 -1.516 3.338 0.812 8.845 31.927 -4.091 0.635 2.820 15.704 -1.442 33.108 18 AA_C13C14:G9G10_BB A 13 ? B 10 ? A 14 ? B 9 ? 1 A C 14 1_555 B G 9 1_555 A A 15 1_555 B U 8 1_555 0.596 -1.515 3.541 -0.409 9.484 31.793 -4.280 -1.114 2.971 16.849 0.726 33.145 19 AA_C14A15:U8G9_BB A 14 ? B 9 ? A 15 ? B 8 ? 1 A A 15 1_555 B U 8 1_555 A C 16 1_555 A G 21 1_555 -1.701 -2.175 2.945 4.330 21.473 16.584 -7.426 4.160 -0.166 52.254 -10.536 27.414 20 AA_A15C16:G21U8_AB A 15 ? B 8 ? A 16 ? A 21 ? # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number R01GM095923 _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 5DH6 _atom_sites.fract_transf_matrix[1][1] 0.012284 _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] 0.011633 _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] 0.009712 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H MG N O P # loop_