data_3ZD5 # _entry.id 3ZD5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3ZD5 pdb_00003zd5 10.2210/pdb3zd5/pdb PDBE EBI-54903 ? ? WWPDB D_1290054903 ? ? # 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 2012-12-12 2 'Structure model' 1 1 2013-03-06 3 'Structure model' 1 2 2019-03-13 4 'Structure model' 1 3 2024-05-08 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' Other 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Experimental preparation' 6 3 'Structure model' Other 7 3 'Structure model' 'Source and taxonomy' 8 4 'Structure model' 'Data collection' 9 4 'Structure model' 'Database references' 10 4 'Structure model' 'Derived calculations' 11 4 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' citation 2 3 'Structure model' exptl_crystal_grow 3 3 'Structure model' pdbx_database_proc 4 3 'Structure model' pdbx_database_status 5 3 'Structure model' pdbx_entity_src_syn 6 3 'Structure model' pdbx_seq_map_depositor_info 7 3 'Structure model' struct_biol 8 3 'Structure model' struct_conn 9 4 'Structure model' chem_comp_atom 10 4 'Structure model' chem_comp_bond 11 4 'Structure model' database_2 12 4 'Structure model' pdbx_database_status 13 4 'Structure model' struct_conn # 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_abbrev' 2 3 'Structure model' '_citation.page_last' 3 3 'Structure model' '_citation.pdbx_database_id_DOI' 4 3 'Structure model' '_citation.title' 5 3 'Structure model' '_exptl_crystal_grow.method' 6 3 'Structure model' '_exptl_crystal_grow.temp' 7 3 'Structure model' '_pdbx_database_status.recvd_author_approval' 8 3 'Structure model' '_pdbx_entity_src_syn.ncbi_taxonomy_id' 9 3 'Structure model' '_pdbx_entity_src_syn.organism_scientific' 10 3 'Structure model' '_pdbx_seq_map_depositor_info.one_letter_code_mod' 11 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 4 'Structure model' '_database_2.pdbx_DOI' 13 4 'Structure model' '_database_2.pdbx_database_accession' 14 4 'Structure model' '_pdbx_database_status.status_code_sf' 15 4 'Structure model' '_struct_conn.pdbx_dist_value' 16 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 17 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 18 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 19 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 20 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 21 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 22 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 23 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 24 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 25 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' # _pdbx_database_PDB_obs_spr.id SPRSDE _pdbx_database_PDB_obs_spr.date 2012-12-12 _pdbx_database_PDB_obs_spr.pdb_id 3ZD5 _pdbx_database_PDB_obs_spr.replace_pdb_id 2GOZ _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3ZD5 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2012-11-24 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 3ZP8 unspecified 'HIGH-RESOLUTION FULL-LENGTH HAMMERHEAD RIBOZYME' PDB 3ZD4 unspecified 'FULL-LENGTH HAMMERHEAD RIBOZYME WITH G12A SUBSTITUTION AT THE GENERAL BASE POSITION' # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Martick, M.' 1 ? 'Scott, W.G.' 2 ? # _citation.id primary _citation.title 'Tertiary contacts distant from the active site prime a ribozyme for catalysis.' _citation.journal_abbrev Cell _citation.journal_volume 126 _citation.page_first 309 _citation.page_last 320 _citation.year 2006 _citation.journal_id_ASTM CELLB5 _citation.country US _citation.journal_id_ISSN 0092-8674 _citation.journal_id_CSD 0998 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16859740 _citation.pdbx_database_id_DOI 10.1016/j.cell.2006.06.036 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Martick, M.' 1 ? primary 'Scott, W.G.' 2 ? # 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, ENZYME STRAND' 13941.326 1 ? ? ? ? 2 polymer syn 'HAMMERHEAD RIBOZYME, SUBSTRATE STRAND' 6491.608 1 ? ? ? ? 3 water nat water 18.015 34 ? ? ? ? # 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 yes '(GDP)GAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACGAAACGCC' GGAUGUACUACCAGCUGAUGAGUCCCAAAUAGGACGAAACGCC A ? 2 polyribonucleotide no yes 'GGCGU(OMC)CUGG(5BU)AUCCAA(5BU)C(DC)' GGCGUCCUGGUAUCCAAUCC B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GDP n 1 2 G n 1 3 A n 1 4 U n 1 5 G n 1 6 U n 1 7 A n 1 8 C n 1 9 U n 1 10 A n 1 11 C n 1 12 C n 1 13 A n 1 14 G n 1 15 C n 1 16 U n 1 17 G n 1 18 A n 1 19 U n 1 20 G n 1 21 A n 1 22 G n 1 23 U n 1 24 C n 1 25 C n 1 26 C n 1 27 A n 1 28 A n 1 29 A n 1 30 U n 1 31 A n 1 32 G n 1 33 G n 1 34 A n 1 35 C n 1 36 G n 1 37 A n 1 38 A n 1 39 A n 1 40 C n 1 41 G n 1 42 C n 1 43 C n 2 1 G n 2 2 G n 2 3 C n 2 4 G n 2 5 U n 2 6 OMC n 2 7 C n 2 8 U n 2 9 G n 2 10 G n 2 11 5BU n 2 12 A n 2 13 U n 2 14 C n 2 15 C n 2 16 A n 2 17 A n 2 18 5BU n 2 19 C n 2 20 DC 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 ? ? ' Schistosoma mansoni' ? 6183 'ENZYME STRAND WAS OBTAINED BY T7 RNA TRANSCRIPTION' 2 1 sample ? ? ' Schistosoma mansoni' ? 6183 'SUBSTRATE STRAND WAS OBTAINED BY SOLID-PHASE CHEMICAL SYNTHESIS' # 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 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 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 GDP 'RNA linking' n "GUANOSINE-5'-DIPHOSPHATE" ? 'C10 H15 N5 O11 P2' 443.201 HOH non-polymer . WATER ? 'H2 O' 18.015 OMC 'RNA linking' n "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O8 P' 337.223 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 GDP 1 1 1 GDP GDP A . n A 1 2 G 2 2 2 G G A . n A 1 3 A 3 3 3 A A A . n A 1 4 U 4 4 4 U U A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 A 7 7 7 A A A . n A 1 8 C 8 8 8 C C A . n A 1 9 U 9 9 9 U U A . n A 1 10 A 10 10 10 A A A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 A 13 13 13 A A A . n A 1 14 G 14 14 14 G G A . n A 1 15 C 15 15 15 C C A . n A 1 16 U 16 16 16 U U A . n A 1 17 G 17 17 17 G G A . n A 1 18 A 18 18 18 A A A . n A 1 19 U 19 19 19 U U A . n A 1 20 G 20 20 20 G G A . n A 1 21 A 21 21 21 A A A . n A 1 22 G 22 22 22 G G A . n A 1 23 U 23 23 23 U U A . n A 1 24 C 24 24 24 C C A . n A 1 25 C 25 25 25 C C A . n A 1 26 C 26 26 26 C C A . n A 1 27 A 27 27 27 A A A . n A 1 28 A 28 28 28 A A A . n A 1 29 A 29 29 29 A A A . n A 1 30 U 30 30 30 U U A . n A 1 31 A 31 31 31 A A A . n A 1 32 G 32 32 32 G G A . n A 1 33 G 33 33 33 G G A . n A 1 34 A 34 34 34 A A 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 A 38 38 38 A A A . n A 1 39 A 39 39 39 A A A . n A 1 40 C 40 40 40 C C A . n A 1 41 G 41 41 41 G G A . n A 1 42 C 42 42 42 C C A . n A 1 43 C 43 43 43 C C 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 C 3 3 3 C C B . n B 2 4 G 4 4 4 G G B . n B 2 5 U 5 5 5 U U B . n B 2 6 OMC 6 6 6 OMC OMC B . n B 2 7 C 7 7 7 C C 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 5BU 11 11 11 5BU 5BU B . n B 2 12 A 12 12 12 A A B . n B 2 13 U 13 13 13 U U B . n B 2 14 C 14 14 14 C C B . n B 2 15 C 15 15 15 C C B . n B 2 16 A 16 16 16 A A B . n B 2 17 A 17 17 17 A A B . n B 2 18 5BU 18 18 18 5BU 5BU B . n B 2 19 C 19 19 19 C C B . n B 2 20 DC 20 20 20 DC DC 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 HOH 1 2001 2001 HOH HOH A . C 3 HOH 2 2002 2002 HOH HOH A . C 3 HOH 3 2003 2003 HOH HOH A . C 3 HOH 4 2004 2004 HOH HOH A . C 3 HOH 5 2005 2005 HOH HOH A . C 3 HOH 6 2006 2006 HOH HOH A . C 3 HOH 7 2007 2007 HOH HOH A . C 3 HOH 8 2008 2008 HOH HOH A . C 3 HOH 9 2009 2009 HOH HOH A . C 3 HOH 10 2010 2010 HOH HOH A . C 3 HOH 11 2011 2011 HOH HOH A . C 3 HOH 12 2012 2012 HOH HOH A . C 3 HOH 13 2013 2013 HOH HOH A . C 3 HOH 14 2014 2014 HOH HOH A . C 3 HOH 15 2015 2015 HOH HOH A . C 3 HOH 16 2016 2016 HOH HOH A . C 3 HOH 17 2017 2017 HOH HOH A . C 3 HOH 18 2018 2018 HOH HOH A . C 3 HOH 19 2019 2019 HOH HOH A . D 3 HOH 1 2001 2001 HOH HOH B . D 3 HOH 2 2002 2002 HOH HOH B . D 3 HOH 3 2003 2003 HOH HOH B . D 3 HOH 4 2004 2004 HOH HOH B . D 3 HOH 5 2005 2005 HOH HOH B . D 3 HOH 6 2006 2006 HOH HOH B . D 3 HOH 7 2007 2007 HOH HOH B . D 3 HOH 8 2008 2008 HOH HOH B . D 3 HOH 9 2009 2009 HOH HOH B . D 3 HOH 10 2010 2010 HOH HOH B . D 3 HOH 11 2011 2011 HOH HOH B . D 3 HOH 12 2012 2012 HOH HOH B . D 3 HOH 13 2013 2013 HOH HOH B . D 3 HOH 14 2014 2014 HOH HOH B . D 3 HOH 15 2015 2015 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language PHENIX refinement '(PHENIX.REFINE)' ? 1 ? ? ? ? ADSC 'data reduction' . ? 2 ? ? ? ? MOSFLM 'data scaling' . ? 3 ? ? ? ? CNS phasing . ? 4 ? ? ? ? # _cell.entry_id 3ZD5 _cell.length_a 49.886 _cell.length_b 69.210 _cell.length_c 60.076 _cell.angle_alpha 90.00 _cell.angle_beta 111.83 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZD5 _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 # _exptl.entry_id 3ZD5 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.36 _exptl_crystal.density_percent_sol 47.78 _exptl_crystal.description 'ALL VALUES SAME AS 2GOZ' _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 301 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;THE ENZYME AND SUBSTRATE WERE MIXED IN EQUIMOLAR AMOUNTS IN A SOLUTION CONTAINING 50 MM MES PH 5.5, 1.5 MM EDTA. THE COMPLEX WAS FORMED BY INCUBATING THE MIXTURE AT 95C FOR 2 MIN., THEN AT 65C FOR 2 MIN., AND FINALLY AT 27C FOR 5 MIN. 1 MM MGCL2 WAS INCLUDED IN THE MIXTURE BEFORE THE FINAL INCUBATION STEP. A 10 MG/ML CONCENTRATION OF RNA WAS USED FOR THE CRYSTALLIZATION EXPERIMENTS. THE RESERVOIR SOLUTION CONTAINED 0.5M (NH4)2SO4, 100 MM MES PH 6.5, AND 35% PEG 3350. AFTER MIXING THE RESERVOIR SOLUTION, THE SALT AND PEG PHASES WERE ALLOWED TO SEPARATE, AND ONLY THE SALT PHASE WAS USED FOR THE DROPS. THE CRYSTALS GREW IN HANGING DROPS OF 2 MICROLITERS AFTER 12 MONTHS OF INCUBATION AT 28C. THE CRYSTALS WERE WASHED IN THE SALT PHASE OF THE RESERVOIR SOLUTION PRIOR TO CRYO-FREEZING. ; # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 _diffrn.pdbx_serial_crystal_experiment ? # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2006-02-27 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.919 1.0 2 0.920 1.0 3 0.9266 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL9-1' _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL9-1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.919, 0.920, 0.9266' # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 3ZD5 _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 55.73 _reflns.d_resolution_high 2.20 _reflns.number_obs 9712 _reflns.number_all ? _reflns.percent_possible_obs 99.2 _reflns.pdbx_Rmerge_I_obs 0.04 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 16.90 _reflns.B_iso_Wilson_estimate 43.18 _reflns.pdbx_redundancy 4.000 _reflns.pdbx_CC_half ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_Rrim_I_all ? # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 2.20 _reflns_shell.d_res_low 2.32 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.22 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.90 _reflns_shell.pdbx_redundancy 4.10 _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_CC_half ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_Rrim_I_all ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3ZD5 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 9615 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.50 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.220 _refine.ls_d_res_high 2.200 _refine.ls_percent_reflns_obs 99.13 _refine.ls_R_factor_obs 0.1805 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1768 _refine.ls_R_factor_R_free 0.2117 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.7 _refine.ls_number_reflns_R_free 935 _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 ? _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 ? _refine.details ;TLS MODEL BASED ON OUTPUT FROM TLS MOTION DETERMINATION SERVER. TO REPLACE 2GOZ COORDINATES (DATA REMAIN THE SAME). CORRECTED ANTI TO SYN BASE CONFORMATION OF C8 IN CHAIN A. IMPROVED TLS AND WATER MODELS ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _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 0.27 _refine.pdbx_overall_phase_error 25.51 _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 1346 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 34 _refine_hist.number_atoms_total 1380 _refine_hist.d_res_high 2.200 _refine_hist.d_res_low 20.220 # 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 0.005 ? ? 1503 'X-RAY DIFFRACTION' ? f_angle_d 0.937 ? ? 2337 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 15.306 ? ? 744 'X-RAY DIFFRACTION' ? f_chiral_restr 0.039 ? ? 309 'X-RAY DIFFRACTION' ? f_plane_restr 0.006 ? ? 63 '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' . 2.2004 2.3162 1246 0.2441 100.00 0.3060 . . 141 . . . . 'X-RAY DIFFRACTION' . 2.3162 2.4611 1217 0.2366 100.00 0.2735 . . 144 . . . . 'X-RAY DIFFRACTION' . 2.4611 2.6507 1255 0.2468 100.00 0.3087 . . 124 . . . . 'X-RAY DIFFRACTION' . 2.6507 2.9168 1247 0.2530 100.00 0.3115 . . 116 . . . . 'X-RAY DIFFRACTION' . 2.9168 3.3372 1254 0.1929 99.00 0.2504 . . 135 . . . . 'X-RAY DIFFRACTION' . 3.3372 4.1983 1239 0.1470 99.00 0.1994 . . 137 . . . . 'X-RAY DIFFRACTION' . 4.1983 20.2209 1222 0.1273 97.00 0.1330 . . 138 . . . . # _database_PDB_matrix.entry_id 3ZD5 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 3ZD5 _struct.title 'THE 2.2 A STRUCTURE OF A FULL-LENGTH CATALYTICALLY ACTIVE HAMMERHEAD RIBOZYME' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3ZD5 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'CATALYTIC RNA, IN-LINE ATTACK, HAMMERHEAD RNA, STEM-LOOP INTERACTION, URIDINE TURN, A-FORM HELIX, 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 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 3ZD5 1 ? ? 3ZD5 ? 2 PDB 3ZD5 2 ? ? 3ZD5 ? # 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 3ZD5 A 1 ? 43 ? 3ZD5 1 ? 43 ? 1 43 2 2 3ZD5 B 1 ? 20 ? 3ZD5 1 ? 20 ? 1 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # 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)' 4570 ? 1 MORE -2.0 ? 1 'SSA (A^2)' 9950 ? # _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 # _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 GDP 1 "O3'" ? ? ? 1_555 A G 2 P ? ? A GDP 1 A G 2 1_555 ? ? ? ? ? ? ? 1.590 ? ? covale2 covale both ? B U 5 "O3'" ? ? ? 1_555 B OMC 6 P ? ? B U 5 B OMC 6 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale3 covale both ? B OMC 6 "O3'" ? ? ? 1_555 B C 7 P ? ? B OMC 6 B C 7 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale4 covale both ? B G 10 "O3'" ? ? ? 1_555 B 5BU 11 P ? ? B G 10 B 5BU 11 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale5 covale both ? B 5BU 11 "O3'" ? ? ? 1_555 B A 12 P ? ? B 5BU 11 B A 12 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale6 covale both ? B A 17 "O3'" ? ? ? 1_555 B 5BU 18 P ? ? B A 17 B 5BU 18 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale7 covale both ? B 5BU 18 "O3'" ? ? ? 1_555 B C 19 P ? ? B 5BU 18 B C 19 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale8 covale both ? B C 19 "O3'" ? ? ? 1_555 B DC 20 P ? ? B C 19 B DC 20 1_555 ? ? ? ? ? ? ? 1.612 ? ? hydrog1 hydrog ? ? A GDP 1 N1 ? ? ? 1_555 B DC 20 N3 ? ? A GDP 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A GDP 1 N2 ? ? ? 1_555 B DC 20 O2 ? ? A GDP 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A GDP 1 O6 ? ? ? 1_555 B DC 20 N4 ? ? A GDP 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 19 N3 ? ? A G 2 B C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 19 O2 ? ? A G 2 B C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 19 N4 ? ? A G 2 B C 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B 5BU 18 N3 ? ? A A 3 B 5BU 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B 5BU 18 O4 ? ? A A 3 B 5BU 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A U 4 O4 ? ? ? 1_555 B C 15 N4 ? ? A U 4 B C 15 1_555 ? ? ? ? ? ? 'U-C MISPAIR' ? ? ? hydrog10 hydrog ? ? A U 4 O2 ? ? ? 1_555 B A 17 N6 ? ? A U 4 B A 17 1_555 ? ? ? ? ? ? 'U-A PAIR' ? ? ? hydrog11 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 14 N3 ? ? A G 5 B C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 14 O2 ? ? A G 5 B C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 14 N4 ? ? A G 5 B C 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 6 N3 ? ? ? 1_555 A A 28 N7 ? ? A U 6 A A 28 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog15 hydrog ? ? A U 6 O2 ? ? ? 1_555 A A 28 N6 ? ? A U 6 A A 28 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog16 hydrog ? ? A C 8 N4 ? ? ? 1_555 A C 26 O2 ? ? A C 8 A C 26 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog17 hydrog ? ? A C 8 O2 ? ? ? 1_555 A C 26 N4 ? ? A C 8 A C 26 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog18 hydrog ? ? A U 9 N3 ? ? ? 1_555 B A 12 N1 ? ? A U 9 B A 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 9 O4 ? ? ? 1_555 B A 12 N6 ? ? A U 9 B A 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A A 10 N1 ? ? ? 1_555 B 5BU 11 N3 ? ? A A 10 B 5BU 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A A 10 N6 ? ? ? 1_555 B 5BU 11 O4 ? ? A A 10 B 5BU 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 11 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 11 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 11 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 12 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 12 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 12 B G 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A A 13 N1 ? ? ? 1_555 B U 8 N3 ? ? A A 13 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A A 13 N6 ? ? ? 1_555 B U 8 O4 ? ? A A 13 B U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 14 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 14 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 14 B C 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 15 N3 ? ? ? 1_555 A G 20 N1 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 15 N4 ? ? ? 1_555 A G 20 O6 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 15 O2 ? ? ? 1_555 A G 20 N2 ? ? A C 15 A G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 17 N2 ? ? ? 1_555 A A 38 N1 ? ? A G 17 A A 38 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog37 hydrog ? ? A A 21 N6 ? ? ? 1_555 A G 36 N3 ? ? A A 21 A G 36 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog38 hydrog ? ? A A 21 N7 ? ? ? 1_555 A G 36 N2 ? ? A A 21 A G 36 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog39 hydrog ? ? A G 22 N1 ? ? ? 1_555 A C 35 N3 ? ? A G 22 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 22 N2 ? ? ? 1_555 A C 35 O2 ? ? A G 22 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 22 O6 ? ? ? 1_555 A C 35 N4 ? ? A G 22 A C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A U 23 N3 ? ? ? 1_555 A A 34 N1 ? ? A U 23 A A 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A U 23 O4 ? ? ? 1_555 A A 34 N6 ? ? A U 23 A A 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 24 N3 ? ? ? 1_555 A G 33 N1 ? ? A C 24 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 24 N4 ? ? ? 1_555 A G 33 O6 ? ? A C 24 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 24 O2 ? ? ? 1_555 A G 33 N2 ? ? A C 24 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 25 N3 ? ? ? 1_555 A G 32 N1 ? ? A C 25 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 25 N4 ? ? ? 1_555 A G 32 O6 ? ? A C 25 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A C 25 O2 ? ? ? 1_555 A G 32 N2 ? ? A C 25 A G 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A A 28 N3 ? ? ? 1_555 A U 30 N3 ? ? A A 28 A U 30 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog51 hydrog ? ? A A 31 N6 ? ? ? 1_555 B U 13 O2 ? ? A A 31 B U 13 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog52 hydrog ? ? A A 31 N7 ? ? ? 1_555 B U 13 N3 ? ? A A 31 B U 13 1_555 ? ? ? ? ? ? 'REVERSED HOOGSTEEN' ? ? ? hydrog53 hydrog ? ? A A 37 N6 ? ? ? 1_555 B OMC 6 O2 ? ? A A 37 B OMC 6 1_555 ? ? ? ? ? ? 'A-OMC MISPAIR' ? ? ? hydrog54 hydrog ? ? A A 38 N6 ? ? ? 1_555 B OMC 6 O2 ? ? A A 38 B OMC 6 1_555 ? ? ? ? ? ? 'A-OMC MISPAIR' ? ? ? hydrog55 hydrog ? ? A A 39 N1 ? ? ? 1_555 B U 5 N3 ? ? A A 39 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A A 39 N6 ? ? ? 1_555 B U 5 O4 ? ? A A 39 B U 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A C 40 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 40 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A C 40 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 40 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A C 40 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 40 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A G 41 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 41 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A G 41 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 41 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A G 41 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 41 B C 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A C 42 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 42 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? A C 42 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 42 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? A C 42 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 42 B G 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A C 43 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 43 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A C 43 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 43 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A C 43 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 43 B G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_angle.auth_asym_id_1 B _pdbx_validate_rmsd_angle.auth_comp_id_1 DC _pdbx_validate_rmsd_angle.auth_seq_id_1 20 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_2 B _pdbx_validate_rmsd_angle.auth_comp_id_2 DC _pdbx_validate_rmsd_angle.auth_seq_id_2 20 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N1 _pdbx_validate_rmsd_angle.auth_asym_id_3 B _pdbx_validate_rmsd_angle.auth_comp_id_3 DC _pdbx_validate_rmsd_angle.auth_seq_id_3 20 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 110.23 _pdbx_validate_rmsd_angle.angle_target_value 108.30 _pdbx_validate_rmsd_angle.angle_deviation 1.93 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.30 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A GDP 1 A GDP 1 ? G "GUANOSINE-5'-DIPHOSPHATE" 2 B OMC 6 B OMC 6 ? C "O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE" 3 B 5BU 11 B 5BU 11 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 4 B 5BU 18 B 5BU 18 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined -9.4762 18.8698 11.7237 0.5529 0.4116 0.3284 -0.0185 -0.0203 -0.0640 4.2525 5.9746 8.1616 3.7274 -1.4449 -4.3063 -0.0481 -0.2587 -0.2765 -0.2380 0.5956 0.1284 1.4790 -0.2624 -0.6610 'X-RAY DIFFRACTION' 2 ? refined -11.2335 7.2618 -8.4889 0.3748 0.3427 0.4996 -0.0208 0.0732 -0.0166 0.1185 3.4935 0.0587 2.1936 0.8110 2.0312 -0.0296 0.0249 -0.1988 -0.5860 0.1500 -0.8705 -0.2272 0.1963 -0.1333 'X-RAY DIFFRACTION' 3 ? refined -18.2368 10.2441 -21.6235 0.6297 0.6993 0.5237 -0.1779 0.0322 0.0433 1.1610 0.8835 1.4751 -1.4915 0.2145 0.8948 -0.2676 0.3754 0.4036 0.1056 0.2926 -0.2755 -0.4368 0.7151 -0.0777 'X-RAY DIFFRACTION' 4 ? refined -18.2041 15.7910 0.2597 0.4701 0.6644 0.6720 -0.1401 0.0522 -0.0378 4.3930 1.2620 5.5628 -1.4466 -1.0017 0.6210 -0.6095 -1.4966 -0.0746 0.9010 -0.4580 0.0125 -0.1193 -1.0944 0.6970 'X-RAY DIFFRACTION' 5 ? refined -22.8821 13.9208 -9.7629 0.3956 0.6957 0.4378 0.0378 -0.1072 -0.0582 7.7184 2.0765 3.2916 -1.8808 2.4962 0.5637 0.2971 0.1801 -0.6982 0.1852 0.0797 0.5144 -0.9466 -0.6731 -0.1671 'X-RAY DIFFRACTION' 6 ? refined -23.8178 17.1293 -25.1717 0.9536 0.5902 0.5295 -0.0010 -0.1477 0.0682 3.7046 3.6976 2.5770 1.1976 1.2242 -2.0981 -0.7316 -0.3674 0.4529 -0.0315 0.2016 -0.2399 -1.7445 -0.7544 0.5146 'X-RAY DIFFRACTION' 7 ? refined -31.7080 7.8629 -33.0374 0.5127 0.4467 0.3924 -0.0212 0.0421 0.0750 1.9145 2.3512 2.0369 -1.2449 0.7325 0.1903 -0.2403 0.2234 -0.0918 -0.3927 0.1205 0.0220 -0.0439 0.5354 0.0781 'X-RAY DIFFRACTION' 8 ? refined -30.5658 12.8975 -25.8106 0.6174 0.4516 0.3581 -0.0624 -0.0321 0.0405 0.5070 0.8180 1.2216 -1.0476 0.3118 -0.6756 -0.3777 0.1473 0.2175 -0.0535 0.1307 -0.1940 -0.6890 0.0862 0.0967 'X-RAY DIFFRACTION' 9 ? refined -14.9224 2.3326 -3.8181 0.4262 0.3767 0.5244 -0.0580 -0.0383 0.0474 -0.1116 3.0746 0.6162 -0.3328 0.0103 -0.2820 0.0456 -0.1905 0.4418 0.5737 -0.4214 -0.4682 0.0470 -0.0405 0.3955 'X-RAY DIFFRACTION' 10 ? refined -0.2282 22.1563 9.4133 0.4093 0.3500 0.4702 -0.0295 -0.0215 0.0490 2.0548 1.7338 3.9355 -0.7013 -1.3473 1.4534 -0.0634 0.0029 -0.5053 0.0372 -0.0266 -0.1175 0.8374 -0.0763 -0.0151 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 1:4)' 'X-RAY DIFFRACTION' 2 2 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 5:14)' 'X-RAY DIFFRACTION' 3 3 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 15:25)' 'X-RAY DIFFRACTION' 4 4 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 26:30)' 'X-RAY DIFFRACTION' 5 5 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 31:34)' 'X-RAY DIFFRACTION' 6 6 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 35:38)' 'X-RAY DIFFRACTION' 7 7 ? ? ? ? ? ? ? ? ? '(CHAIN A AND RESID 39:43)' 'X-RAY DIFFRACTION' 8 8 ? ? ? ? ? ? ? ? ? '(CHAIN B AND RESID 1:7)' 'X-RAY DIFFRACTION' 9 9 ? ? ? ? ? ? ? ? ? '(CHAIN B AND RESID 8:15)' 'X-RAY DIFFRACTION' 10 10 ? ? ? ? ? ? ? ? ? '(CHAIN B AND RESID 16:20)' # _pdbx_entry_details.entry_id 3ZD5 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ;O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE (OMC): CLEAVAGE SITE SUBSTRATE ANALOGUE INHIBITOR GUANOSINE-5'-DIPHOSPHATE (GDP): 5 PRIME END OF TRANSCRIBED SEQUENCE. 5-BROMO-URIDINE-5'-MONOPHOSPHATE (5BU): USED FOR MAD PHASING ; _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? # 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 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 A OP3 O N N 35 A P P N N 36 A OP1 O N N 37 A OP2 O N N 38 A "O5'" O N N 39 A "C5'" C N N 40 A "C4'" C N R 41 A "O4'" O N N 42 A "C3'" C N S 43 A "O3'" O N N 44 A "C2'" C N R 45 A "O2'" O N N 46 A "C1'" C N R 47 A N9 N Y N 48 A C8 C Y N 49 A N7 N Y N 50 A C5 C Y N 51 A C6 C Y N 52 A N6 N N N 53 A N1 N Y N 54 A C2 C Y N 55 A N3 N Y N 56 A C4 C Y N 57 A HOP3 H N N 58 A HOP2 H N N 59 A "H5'" H N N 60 A "H5''" H N N 61 A "H4'" H N N 62 A "H3'" H N N 63 A "HO3'" H N N 64 A "H2'" H N N 65 A "HO2'" H N N 66 A "H1'" H N N 67 A H8 H N N 68 A H61 H N N 69 A H62 H N N 70 A H2 H N N 71 C OP3 O N N 72 C P P N N 73 C OP1 O N N 74 C OP2 O N N 75 C "O5'" O N N 76 C "C5'" C N N 77 C "C4'" C N R 78 C "O4'" O N N 79 C "C3'" C N S 80 C "O3'" O N N 81 C "C2'" C N R 82 C "O2'" O N N 83 C "C1'" C N R 84 C N1 N N N 85 C C2 C N N 86 C O2 O N N 87 C N3 N N N 88 C C4 C N N 89 C N4 N N N 90 C C5 C N N 91 C C6 C N N 92 C HOP3 H N N 93 C HOP2 H N N 94 C "H5'" H N N 95 C "H5''" H N N 96 C "H4'" H N N 97 C "H3'" H N N 98 C "HO3'" H N N 99 C "H2'" H N N 100 C "HO2'" H N N 101 C "H1'" H N N 102 C H41 H N N 103 C H42 H N N 104 C H5 H N N 105 C H6 H N N 106 DC OP3 O N N 107 DC P P N N 108 DC OP1 O N N 109 DC OP2 O N N 110 DC "O5'" O N N 111 DC "C5'" C N N 112 DC "C4'" C N R 113 DC "O4'" O N N 114 DC "C3'" C N S 115 DC "O3'" O N N 116 DC "C2'" C N N 117 DC "C1'" C N R 118 DC N1 N N N 119 DC C2 C N N 120 DC O2 O N N 121 DC N3 N N N 122 DC C4 C N N 123 DC N4 N N N 124 DC C5 C N N 125 DC C6 C N N 126 DC HOP3 H N N 127 DC HOP2 H N N 128 DC "H5'" H N N 129 DC "H5''" H N N 130 DC "H4'" H N N 131 DC "H3'" H N N 132 DC "HO3'" H N N 133 DC "H2'" H N N 134 DC "H2''" H N N 135 DC "H1'" H N N 136 DC H41 H N N 137 DC H42 H N N 138 DC H5 H N N 139 DC H6 H N N 140 G OP3 O N N 141 G P P N N 142 G OP1 O N N 143 G OP2 O N N 144 G "O5'" O N N 145 G "C5'" C N N 146 G "C4'" C N R 147 G "O4'" O N N 148 G "C3'" C N S 149 G "O3'" O N N 150 G "C2'" C N R 151 G "O2'" O N N 152 G "C1'" C N R 153 G N9 N Y N 154 G C8 C Y N 155 G N7 N Y N 156 G C5 C Y N 157 G C6 C N N 158 G O6 O N N 159 G N1 N N N 160 G C2 C N N 161 G N2 N N N 162 G N3 N N N 163 G C4 C Y N 164 G HOP3 H N N 165 G HOP2 H N N 166 G "H5'" H N N 167 G "H5''" H N N 168 G "H4'" H N N 169 G "H3'" H N N 170 G "HO3'" H N N 171 G "H2'" H N N 172 G "HO2'" H N N 173 G "H1'" H N N 174 G H8 H N N 175 G H1 H N N 176 G H21 H N N 177 G H22 H N N 178 GDP PB P N N 179 GDP O1B O N N 180 GDP O2B O N N 181 GDP O3B O N N 182 GDP O3A O N N 183 GDP PA P N N 184 GDP O1A O N N 185 GDP O2A O N N 186 GDP "O5'" O N N 187 GDP "C5'" C N N 188 GDP "C4'" C N R 189 GDP "O4'" O N N 190 GDP "C3'" C N S 191 GDP "O3'" O N N 192 GDP "C2'" C N R 193 GDP "O2'" O N N 194 GDP "C1'" C N R 195 GDP N9 N Y N 196 GDP C8 C Y N 197 GDP N7 N Y N 198 GDP C5 C Y N 199 GDP C6 C N N 200 GDP O6 O N N 201 GDP N1 N N N 202 GDP C2 C N N 203 GDP N2 N N N 204 GDP N3 N N N 205 GDP C4 C Y N 206 GDP HOB2 H N N 207 GDP HOB3 H N N 208 GDP HOA2 H N N 209 GDP "H5'" H N N 210 GDP "H5''" H N N 211 GDP "H4'" H N N 212 GDP "H3'" H N N 213 GDP "HO3'" H N N 214 GDP "H2'" H N N 215 GDP "HO2'" H N N 216 GDP "H1'" H N N 217 GDP H8 H N N 218 GDP HN1 H N N 219 GDP HN21 H N N 220 GDP HN22 H N N 221 HOH O O N N 222 HOH H1 H N N 223 HOH H2 H N N 224 OMC N1 N N N 225 OMC C2 C N N 226 OMC N3 N N N 227 OMC C4 C N N 228 OMC C5 C N N 229 OMC C6 C N N 230 OMC O2 O N N 231 OMC N4 N N N 232 OMC "C1'" C N R 233 OMC "C2'" C N R 234 OMC "O2'" O N N 235 OMC CM2 C N N 236 OMC "C3'" C N R 237 OMC "C4'" C N R 238 OMC "O4'" O N N 239 OMC "O3'" O N N 240 OMC "C5'" C N N 241 OMC "O5'" O N N 242 OMC P P N N 243 OMC OP1 O N N 244 OMC OP2 O N N 245 OMC OP3 O N N 246 OMC H5 H N N 247 OMC H6 H N N 248 OMC HN41 H N N 249 OMC HN42 H N N 250 OMC "H1'" H N N 251 OMC "H2'" H N N 252 OMC HM21 H N N 253 OMC HM22 H N N 254 OMC HM23 H N N 255 OMC "H3'" H N N 256 OMC "H4'" H N N 257 OMC "HO3'" H N N 258 OMC "H5'" H N N 259 OMC "H5''" H N N 260 OMC HOP2 H N N 261 OMC HOP3 H N N 262 U OP3 O N N 263 U P P N N 264 U OP1 O N N 265 U OP2 O N N 266 U "O5'" O N N 267 U "C5'" C N N 268 U "C4'" C N R 269 U "O4'" O N N 270 U "C3'" C N S 271 U "O3'" O N N 272 U "C2'" C N R 273 U "O2'" O N N 274 U "C1'" C N R 275 U N1 N N N 276 U C2 C N N 277 U O2 O N N 278 U N3 N N N 279 U C4 C N N 280 U O4 O N N 281 U C5 C N N 282 U C6 C N N 283 U HOP3 H N N 284 U HOP2 H N N 285 U "H5'" H N N 286 U "H5''" H N N 287 U "H4'" H N N 288 U "H3'" H N N 289 U "HO3'" H N N 290 U "H2'" H N N 291 U "HO2'" H N N 292 U "H1'" H N N 293 U H3 H N N 294 U H5 H N N 295 U H6 H N N 296 # 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 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 A OP3 P sing N N 36 A OP3 HOP3 sing N N 37 A P OP1 doub N N 38 A P OP2 sing N N 39 A P "O5'" sing N N 40 A OP2 HOP2 sing N N 41 A "O5'" "C5'" sing N N 42 A "C5'" "C4'" sing N N 43 A "C5'" "H5'" sing N N 44 A "C5'" "H5''" sing N N 45 A "C4'" "O4'" sing N N 46 A "C4'" "C3'" sing N N 47 A "C4'" "H4'" sing N N 48 A "O4'" "C1'" sing N N 49 A "C3'" "O3'" sing N N 50 A "C3'" "C2'" sing N N 51 A "C3'" "H3'" sing N N 52 A "O3'" "HO3'" sing N N 53 A "C2'" "O2'" sing N N 54 A "C2'" "C1'" sing N N 55 A "C2'" "H2'" sing N N 56 A "O2'" "HO2'" sing N N 57 A "C1'" N9 sing N N 58 A "C1'" "H1'" sing N N 59 A N9 C8 sing Y N 60 A N9 C4 sing Y N 61 A C8 N7 doub Y N 62 A C8 H8 sing N N 63 A N7 C5 sing Y N 64 A C5 C6 sing Y N 65 A C5 C4 doub Y N 66 A C6 N6 sing N N 67 A C6 N1 doub Y N 68 A N6 H61 sing N N 69 A N6 H62 sing N N 70 A N1 C2 sing Y N 71 A C2 N3 doub Y N 72 A C2 H2 sing N N 73 A N3 C4 sing Y N 74 C OP3 P sing N N 75 C OP3 HOP3 sing N N 76 C P OP1 doub N N 77 C P OP2 sing N N 78 C P "O5'" sing N N 79 C OP2 HOP2 sing N N 80 C "O5'" "C5'" sing N N 81 C "C5'" "C4'" sing N N 82 C "C5'" "H5'" sing N N 83 C "C5'" "H5''" sing N N 84 C "C4'" "O4'" sing N N 85 C "C4'" "C3'" sing N N 86 C "C4'" "H4'" sing N N 87 C "O4'" "C1'" sing N N 88 C "C3'" "O3'" sing N N 89 C "C3'" "C2'" sing N N 90 C "C3'" "H3'" sing N N 91 C "O3'" "HO3'" sing N N 92 C "C2'" "O2'" sing N N 93 C "C2'" "C1'" sing N N 94 C "C2'" "H2'" sing N N 95 C "O2'" "HO2'" sing N N 96 C "C1'" N1 sing N N 97 C "C1'" "H1'" sing N N 98 C N1 C2 sing N N 99 C N1 C6 sing N N 100 C C2 O2 doub N N 101 C C2 N3 sing N N 102 C N3 C4 doub N N 103 C C4 N4 sing N N 104 C C4 C5 sing N N 105 C N4 H41 sing N N 106 C N4 H42 sing N N 107 C C5 C6 doub N N 108 C C5 H5 sing N N 109 C C6 H6 sing N N 110 DC OP3 P sing N N 111 DC OP3 HOP3 sing N N 112 DC P OP1 doub N N 113 DC P OP2 sing N N 114 DC P "O5'" sing N N 115 DC OP2 HOP2 sing N N 116 DC "O5'" "C5'" sing N N 117 DC "C5'" "C4'" sing N N 118 DC "C5'" "H5'" sing N N 119 DC "C5'" "H5''" sing N N 120 DC "C4'" "O4'" sing N N 121 DC "C4'" "C3'" sing N N 122 DC "C4'" "H4'" sing N N 123 DC "O4'" "C1'" sing N N 124 DC "C3'" "O3'" sing N N 125 DC "C3'" "C2'" sing N N 126 DC "C3'" "H3'" sing N N 127 DC "O3'" "HO3'" sing N N 128 DC "C2'" "C1'" sing N N 129 DC "C2'" "H2'" sing N N 130 DC "C2'" "H2''" sing N N 131 DC "C1'" N1 sing N N 132 DC "C1'" "H1'" sing N N 133 DC N1 C2 sing N N 134 DC N1 C6 sing N N 135 DC C2 O2 doub N N 136 DC C2 N3 sing N N 137 DC N3 C4 doub N N 138 DC C4 N4 sing N N 139 DC C4 C5 sing N N 140 DC N4 H41 sing N N 141 DC N4 H42 sing N N 142 DC C5 C6 doub N N 143 DC C5 H5 sing N N 144 DC C6 H6 sing N N 145 G OP3 P sing N N 146 G OP3 HOP3 sing N N 147 G P OP1 doub N N 148 G P OP2 sing N N 149 G P "O5'" sing N N 150 G OP2 HOP2 sing N N 151 G "O5'" "C5'" sing N N 152 G "C5'" "C4'" sing N N 153 G "C5'" "H5'" sing N N 154 G "C5'" "H5''" sing N N 155 G "C4'" "O4'" sing N N 156 G "C4'" "C3'" sing N N 157 G "C4'" "H4'" sing N N 158 G "O4'" "C1'" sing N N 159 G "C3'" "O3'" sing N N 160 G "C3'" "C2'" sing N N 161 G "C3'" "H3'" sing N N 162 G "O3'" "HO3'" sing N N 163 G "C2'" "O2'" sing N N 164 G "C2'" "C1'" sing N N 165 G "C2'" "H2'" sing N N 166 G "O2'" "HO2'" sing N N 167 G "C1'" N9 sing N N 168 G "C1'" "H1'" sing N N 169 G N9 C8 sing Y N 170 G N9 C4 sing Y N 171 G C8 N7 doub Y N 172 G C8 H8 sing N N 173 G N7 C5 sing Y N 174 G C5 C6 sing N N 175 G C5 C4 doub Y N 176 G C6 O6 doub N N 177 G C6 N1 sing N N 178 G N1 C2 sing N N 179 G N1 H1 sing N N 180 G C2 N2 sing N N 181 G C2 N3 doub N N 182 G N2 H21 sing N N 183 G N2 H22 sing N N 184 G N3 C4 sing N N 185 GDP PB O1B doub N N 186 GDP PB O2B sing N N 187 GDP PB O3B sing N N 188 GDP PB O3A sing N N 189 GDP O2B HOB2 sing N N 190 GDP O3B HOB3 sing N N 191 GDP O3A PA sing N N 192 GDP PA O1A doub N N 193 GDP PA O2A sing N N 194 GDP PA "O5'" sing N N 195 GDP O2A HOA2 sing N N 196 GDP "O5'" "C5'" sing N N 197 GDP "C5'" "C4'" sing N N 198 GDP "C5'" "H5'" sing N N 199 GDP "C5'" "H5''" sing N N 200 GDP "C4'" "O4'" sing N N 201 GDP "C4'" "C3'" sing N N 202 GDP "C4'" "H4'" sing N N 203 GDP "O4'" "C1'" sing N N 204 GDP "C3'" "O3'" sing N N 205 GDP "C3'" "C2'" sing N N 206 GDP "C3'" "H3'" sing N N 207 GDP "O3'" "HO3'" sing N N 208 GDP "C2'" "O2'" sing N N 209 GDP "C2'" "C1'" sing N N 210 GDP "C2'" "H2'" sing N N 211 GDP "O2'" "HO2'" sing N N 212 GDP "C1'" N9 sing N N 213 GDP "C1'" "H1'" sing N N 214 GDP N9 C8 sing Y N 215 GDP N9 C4 sing Y N 216 GDP C8 N7 doub Y N 217 GDP C8 H8 sing N N 218 GDP N7 C5 sing Y N 219 GDP C5 C6 sing N N 220 GDP C5 C4 doub Y N 221 GDP C6 O6 doub N N 222 GDP C6 N1 sing N N 223 GDP N1 C2 sing N N 224 GDP N1 HN1 sing N N 225 GDP C2 N2 sing N N 226 GDP C2 N3 doub N N 227 GDP N2 HN21 sing N N 228 GDP N2 HN22 sing N N 229 GDP N3 C4 sing N N 230 HOH O H1 sing N N 231 HOH O H2 sing N N 232 OMC N1 C2 sing N N 233 OMC N1 C6 sing N N 234 OMC N1 "C1'" sing N N 235 OMC C2 N3 sing N N 236 OMC C2 O2 doub N N 237 OMC N3 C4 doub N N 238 OMC C4 C5 sing N N 239 OMC C4 N4 sing N N 240 OMC C5 C6 doub N N 241 OMC C5 H5 sing N N 242 OMC C6 H6 sing N N 243 OMC N4 HN41 sing N N 244 OMC N4 HN42 sing N N 245 OMC "C1'" "C2'" sing N N 246 OMC "C1'" "O4'" sing N N 247 OMC "C1'" "H1'" sing N N 248 OMC "C2'" "O2'" sing N N 249 OMC "C2'" "C3'" sing N N 250 OMC "C2'" "H2'" sing N N 251 OMC "O2'" CM2 sing N N 252 OMC CM2 HM21 sing N N 253 OMC CM2 HM22 sing N N 254 OMC CM2 HM23 sing N N 255 OMC "C3'" "C4'" sing N N 256 OMC "C3'" "O3'" sing N N 257 OMC "C3'" "H3'" sing N N 258 OMC "C4'" "O4'" sing N N 259 OMC "C4'" "C5'" sing N N 260 OMC "C4'" "H4'" sing N N 261 OMC "O3'" "HO3'" sing N N 262 OMC "C5'" "O5'" sing N N 263 OMC "C5'" "H5'" sing N N 264 OMC "C5'" "H5''" sing N N 265 OMC "O5'" P sing N N 266 OMC P OP1 doub N N 267 OMC P OP2 sing N N 268 OMC P OP3 sing N N 269 OMC OP2 HOP2 sing N N 270 OMC OP3 HOP3 sing N N 271 U OP3 P sing N N 272 U OP3 HOP3 sing N N 273 U P OP1 doub N N 274 U P OP2 sing N N 275 U P "O5'" sing N N 276 U OP2 HOP2 sing N N 277 U "O5'" "C5'" sing N N 278 U "C5'" "C4'" sing N N 279 U "C5'" "H5'" sing N N 280 U "C5'" "H5''" sing N N 281 U "C4'" "O4'" sing N N 282 U "C4'" "C3'" sing N N 283 U "C4'" "H4'" sing N N 284 U "O4'" "C1'" sing N N 285 U "C3'" "O3'" sing N N 286 U "C3'" "C2'" sing N N 287 U "C3'" "H3'" sing N N 288 U "O3'" "HO3'" sing N N 289 U "C2'" "O2'" sing N N 290 U "C2'" "C1'" sing N N 291 U "C2'" "H2'" sing N N 292 U "O2'" "HO2'" sing N N 293 U "C1'" N1 sing N N 294 U "C1'" "H1'" sing N N 295 U N1 C2 sing N N 296 U N1 C6 sing N N 297 U C2 O2 doub N N 298 U C2 N3 sing N N 299 U N3 C4 sing N N 300 U N3 H3 sing N N 301 U C4 O4 doub N N 302 U C4 C5 sing N N 303 U C5 C6 doub N N 304 U C5 H5 sing N N 305 U C6 H6 sing N N 306 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3ZD5 'double helix' 3ZD5 'a-form double helix' 3ZD5 'hairpin loop' 3ZD5 '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 GDP 1 1_555 B DC 20 1_555 -0.404 -0.076 -0.097 -5.307 -6.252 4.729 1 A_GDP1:DC20_B A 1 ? B 20 ? 19 1 1 A G 2 1_555 B C 19 1_555 -0.393 -0.272 -0.275 -10.724 -10.087 -2.186 2 A_G2:C19_B A 2 ? B 19 ? 19 1 1 A A 3 1_555 B 5BU 18 1_555 0.122 -0.053 0.016 -8.375 -11.721 0.272 3 A_A3:5BU18_B A 3 ? B 18 ? 20 1 1 A U 4 1_555 B C 15 1_555 -1.019 -0.109 -1.235 -9.687 -8.799 -35.853 4 A_U4:C15_B A 4 ? B 15 ? ? ? 1 A G 5 1_555 B C 14 1_555 -0.114 -0.240 0.352 3.578 -9.837 -2.710 5 A_G5:C14_B A 5 ? B 14 ? 19 1 1 A U 6 1_555 A A 28 1_555 4.043 -2.049 -0.097 -11.073 -5.619 -94.895 6 A_U6:A28_A A 6 ? A 28 ? 24 4 1 A A 31 1_555 B U 13 1_555 -4.142 -2.169 -0.102 -10.255 5.395 -96.684 7 A_A31:U13_B A 31 ? B 13 ? 24 4 1 A U 9 1_555 B A 12 1_555 -0.054 -0.086 0.414 5.918 -10.978 3.442 8 A_U9:A12_B A 9 ? B 12 ? 20 1 1 A A 10 1_555 B 5BU 11 1_555 0.172 -0.189 0.105 14.450 -16.858 6.286 9 A_A10:5BU11_B A 10 ? B 11 ? 20 1 1 A C 11 1_555 B G 10 1_555 0.242 -0.125 -0.246 14.167 -17.789 3.906 10 A_C11:G10_B A 11 ? B 10 ? 19 1 1 A C 12 1_555 B G 9 1_555 0.260 -0.128 -0.248 -1.765 -10.077 1.080 11 A_C12:G9_B A 12 ? B 9 ? 19 1 1 A A 13 1_555 B U 8 1_555 0.111 -0.198 0.088 -6.292 -11.503 2.780 12 A_A13:U8_B A 13 ? B 8 ? 20 1 1 A G 14 1_555 B C 7 1_555 0.104 -0.192 0.249 -0.419 -15.422 2.954 13 A_G14:C7_B A 14 ? B 7 ? 19 1 1 A C 15 1_555 A G 20 1_555 0.800 -0.222 0.107 13.903 -8.762 -0.696 14 A_C15:G20_A A 15 ? A 20 ? 19 1 1 A C 8 1_555 A C 26 1_555 -1.975 -1.748 -0.037 -9.087 -3.338 -178.626 15 A_C8:C26_A A 8 ? A 26 ? 15 2 1 A G 32 1_555 A C 25 1_555 -0.145 -0.050 0.174 -1.917 -8.816 -4.108 16 A_G32:C25_A A 32 ? A 25 ? 19 1 1 A G 33 1_555 A C 24 1_555 -0.894 -0.358 -0.049 -2.820 -9.295 5.634 17 A_G33:C24_A A 33 ? A 24 ? 19 1 1 A A 34 1_555 A U 23 1_555 0.363 -0.175 -0.240 -6.083 -15.885 0.313 18 A_A34:U23_A A 34 ? A 23 ? 20 1 1 A C 35 1_555 A G 22 1_555 0.657 -0.308 -0.215 1.699 -15.771 -0.424 19 A_C35:G22_A A 35 ? A 22 ? 19 1 1 A G 36 1_555 A A 21 1_555 6.593 -3.730 0.671 -9.342 -10.408 -0.980 20 A_G36:A21_A A 36 ? A 21 ? 11 9 1 A A 37 1_555 B OMC 6 1_555 -6.092 -2.416 -0.821 -20.177 -3.704 -53.045 21 A_A37:OMC6_B A 37 ? B 6 ? ? ? 1 A A 38 1_555 A G 17 1_555 -3.906 3.647 0.244 38.966 -42.908 83.527 22 A_A38:G17_A A 38 ? A 17 ? ? ? 1 A A 39 1_555 B U 5 1_555 0.180 -0.027 0.457 7.719 -8.196 1.810 23 A_A39:U5_B A 39 ? B 5 ? 20 1 1 A C 40 1_555 B G 4 1_555 0.320 -0.253 -0.268 13.872 -18.786 2.130 24 A_C40:G4_B A 40 ? B 4 ? 19 1 1 A G 41 1_555 B C 3 1_555 -0.252 -0.245 -0.038 -4.795 -18.048 0.333 25 A_G41:C3_B A 41 ? B 3 ? 19 1 1 A C 42 1_555 B G 2 1_555 0.322 -0.123 0.307 -11.834 -13.010 2.749 26 A_C42:G2_B A 42 ? B 2 ? 19 1 1 A C 43 1_555 B G 1 1_555 0.451 -0.198 0.144 4.915 -3.656 0.835 27 A_C43:G1_B A 43 ? B 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A GDP 1 1_555 B DC 20 1_555 A G 2 1_555 B C 19 1_555 -0.857 -2.102 3.500 -0.073 2.464 29.445 -4.668 1.664 3.319 4.838 0.143 29.546 1 AA_GDP1G2:C19DC20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A G 2 1_555 B C 19 1_555 A A 3 1_555 B 5BU 18 1_555 -0.180 -1.481 3.292 -1.156 4.593 34.745 -3.134 0.130 3.082 7.648 1.924 35.056 2 AA_G2A3:5BU18C19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A A 3 1_555 B 5BU 18 1_555 A U 4 1_555 B C 15 1_555 3.165 -1.160 4.348 -3.491 9.837 66.484 -1.540 -3.034 4.010 8.915 3.164 67.205 3 AA_A3U4:C155BU18_BB A 3 ? B 18 ? A 4 ? B 15 ? 1 A U 4 1_555 B C 15 1_555 A G 5 1_555 B C 14 1_555 1.814 -1.628 2.964 -13.211 10.679 33.009 -3.621 -4.164 1.567 17.431 21.566 37.015 4 AA_U4G5:C14C15_BB A 4 ? B 15 ? A 5 ? B 14 ? 1 A G 5 1_555 B C 14 1_555 A U 6 1_555 A A 28 1_555 -2.740 -2.378 3.581 2.902 0.310 80.478 -1.848 2.202 3.490 0.240 -2.245 80.522 5 AA_G5U6:A28C14_AB A 5 ? B 14 ? A 6 ? A 28 ? 1 A U 6 1_555 A A 28 1_555 A A 31 1_555 B U 13 1_555 3.364 -3.713 4.923 42.602 -67.337 -154.286 2.167 1.886 4.157 34.275 21.685 -160.325 6 AA_U6A31:U13A28_BA A 6 ? A 28 ? A 31 ? B 13 ? 1 A A 31 1_555 B U 13 1_555 A U 9 1_555 B A 12 1_555 1.692 -1.233 3.013 -11.953 6.728 77.840 -1.132 -1.619 2.677 5.316 9.445 78.850 7 AA_A31U9:A12U13_BB A 31 ? B 13 ? A 9 ? B 12 ? 1 A U 9 1_555 B A 12 1_555 A A 10 1_555 B 5BU 11 1_555 -0.500 -1.302 2.804 -0.909 13.851 31.688 -3.871 0.733 2.083 23.979 1.574 34.524 8 AA_U9A10:5BU11A12_BB A 9 ? B 12 ? A 10 ? B 11 ? 1 A A 10 1_555 B 5BU 11 1_555 A C 11 1_555 B G 10 1_555 0.365 -1.414 3.168 0.975 5.411 34.373 -3.137 -0.471 2.927 9.084 -1.637 34.797 9 AA_A10C11:G105BU11_BB A 10 ? B 11 ? A 11 ? B 10 ? 1 A C 11 1_555 B G 10 1_555 A C 12 1_555 B G 9 1_555 -0.958 -2.167 3.629 -2.489 12.663 28.755 -6.337 1.307 2.544 24.028 4.723 31.463 10 AA_C11C12:G9G10_BB A 11 ? B 10 ? A 12 ? B 9 ? 1 A C 12 1_555 B G 9 1_555 A A 13 1_555 B U 8 1_555 0.150 -1.121 3.203 -0.208 17.150 35.024 -3.578 -0.248 2.417 26.616 0.323 38.879 11 AA_C12A13:U8G9_BB A 12 ? B 9 ? A 13 ? B 8 ? 1 A A 13 1_555 B U 8 1_555 A G 14 1_555 B C 7 1_555 0.883 -1.602 3.087 4.241 9.239 28.566 -4.726 -0.929 2.558 18.017 -8.271 30.286 12 AA_A13G14:C7U8_BB A 13 ? B 8 ? A 14 ? B 7 ? 1 A G 14 1_555 B C 7 1_555 A C 15 1_555 A G 20 1_555 -0.900 -0.672 2.951 3.422 14.265 28.107 -3.455 2.184 2.237 27.156 -6.514 31.636 13 AA_G14C15:G20C7_AB A 14 ? B 7 ? A 15 ? A 20 ? 1 A C 8 1_555 A C 26 1_555 A G 32 1_555 A C 25 1_555 -2.726 2.236 0.395 -154.318 -85.797 -129.224 -1.107 -1.383 -0.199 42.979 -77.304 -178.527 14 AA_C8G32:C25C26_AA A 8 ? A 26 ? A 32 ? A 25 ? 1 A G 32 1_555 A C 25 1_555 A G 33 1_555 A C 24 1_555 0.309 -2.124 3.206 1.678 4.130 28.093 -5.210 -0.268 2.883 8.440 -3.429 28.438 15 AA_G32G33:C24C25_AA A 32 ? A 25 ? A 33 ? A 24 ? 1 A G 33 1_555 A C 24 1_555 A A 34 1_555 A U 23 1_555 -0.621 -1.306 3.317 0.329 7.395 37.708 -2.886 0.984 3.012 11.308 -0.503 38.402 16 AA_G33A34:U23C24_AA A 33 ? A 24 ? A 34 ? A 23 ? 1 A A 34 1_555 A U 23 1_555 A C 35 1_555 A G 22 1_555 0.234 -1.483 3.008 2.324 7.214 31.259 -3.805 -0.059 2.620 13.147 -4.235 32.143 17 AA_A34C35:G22U23_AA A 34 ? A 23 ? A 35 ? A 22 ? 1 A C 35 1_555 A G 22 1_555 A G 36 1_555 A A 21 1_555 0.466 -0.846 3.679 1.314 9.753 59.173 -1.384 -0.394 3.522 9.803 -1.321 59.912 18 AA_C35G36:A21G22_AA A 35 ? A 22 ? A 36 ? A 21 ? 1 A G 36 1_555 A A 21 1_555 A A 37 1_555 B OMC 6 1_555 -0.224 -0.952 3.655 8.236 -0.158 19.316 -2.540 4.473 3.287 -0.446 -23.226 20.984 19 AA_G36A37:OMC6A21_BA A 36 ? A 21 ? A 37 ? B 6 ? 1 A A 37 1_555 B OMC 6 1_555 A A 38 1_555 A G 17 1_555 1.036 -4.228 1.907 -27.319 38.218 -17.578 0.808 -1.773 4.458 -57.459 -41.073 -49.984 20 AA_A37A38:G17OMC6_AB A 37 ? B 6 ? A 38 ? A 17 ? 1 A A 38 1_555 A G 17 1_555 A A 39 1_555 B U 5 1_555 0.920 2.712 3.378 -0.989 -21.922 86.183 2.388 -0.680 2.761 -15.827 0.714 88.399 21 AA_A38A39:U5G17_BA A 38 ? A 17 ? A 39 ? B 5 ? 1 A A 39 1_555 B U 5 1_555 A C 40 1_555 B G 4 1_555 -0.203 -1.032 3.102 4.746 11.379 32.283 -3.320 1.001 2.550 19.595 -8.173 34.499 22 AA_A39C40:G4U5_BB A 39 ? B 5 ? A 40 ? B 4 ? 1 A C 40 1_555 B G 4 1_555 A G 41 1_555 B C 3 1_555 -0.115 -1.583 3.625 -3.149 16.844 31.264 -5.045 -0.271 2.478 28.713 5.368 35.549 23 AA_C40G41:C3G4_BB A 40 ? B 4 ? A 41 ? B 3 ? 1 A G 41 1_555 B C 3 1_555 A C 42 1_555 B G 2 1_555 0.062 -1.332 3.314 -0.683 8.148 38.245 -2.946 -0.173 2.978 12.265 1.029 39.077 24 AA_G41C42:G2C3_BB A 41 ? B 3 ? A 42 ? B 2 ? 1 A C 42 1_555 B G 2 1_555 A C 43 1_555 B G 1 1_555 1.294 -2.232 2.777 6.381 4.915 24.374 -6.186 -1.413 2.536 11.256 -14.611 25.651 25 AA_C42C43:G1G2_BB A 42 ? B 2 ? A 43 ? B 1 ? # _atom_sites.entry_id 3ZD5 _atom_sites.fract_transf_matrix[1][1] 0.020046 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.008030 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.014449 _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] 0.017931 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol BR C N O P # loop_