data_2G5K # _entry.id 2G5K # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.388 _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 2G5K pdb_00002g5k 10.2210/pdb2g5k/pdb NDB DR0030 ? ? RCSB RCSB036715 ? ? WWPDB D_1000036715 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2006-06-20 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-03-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_chem_comp.pdbx_synonyms' 2 4 'Structure model' '_database_2.pdbx_DOI' 3 4 'Structure model' '_database_2.pdbx_database_accession' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.value' 11 4 'Structure model' '_struct_conn.pdbx_dist_value' 12 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 13 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 14 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 15 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 16 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 17 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 18 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 19 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 20 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 21 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 22 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 23 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 24 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 25 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 26 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 2G5K _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2006-02-23 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2FQN _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kondo, J.' 1 'Francois, B.' 2 'Urzhumtsev, A.' 3 'Westhof, E.' 4 # _citation.id primary _citation.title 'Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site Complexed with Apramycin' _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_volume 45 _citation.page_first 3310 _citation.page_last 3314 _citation.year 2006 _citation.journal_id_ASTM ACIEAY _citation.country GE _citation.journal_id_ISSN 0570-0833 _citation.journal_id_CSD 0179 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16596680 _citation.pdbx_database_id_DOI 10.1002/anie.200600354 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Francois, B.' 2 ? primary 'Urzhumtsev, A.' 3 ? primary 'Westhof, E.' 4 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3'" 7355.409 2 ? ? ? ? 2 non-polymer syn APRAMYCIN 539.577 2 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 4 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 2 ? ? ? ? 5 water nat water 18.015 27 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code UUGCGUCGCUCCGGAAAAGUCGC _entity_poly.pdbx_seq_one_letter_code_can UUGCGUCGCUCCGGAAAAGUCGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 APRAMYCIN AM2 3 'MAGNESIUM ION' MG 4 'COBALT HEXAMMINE(III)' NCO 5 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 U n 1 3 G n 1 4 C n 1 5 G n 1 6 U n 1 7 C n 1 8 G n 1 9 C n 1 10 U n 1 11 C n 1 12 C n 1 13 G n 1 14 G n 1 15 A n 1 16 A n 1 17 A n 1 18 A n 1 19 G n 1 20 U n 1 21 C n 1 22 G n 1 23 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Chemically synthesized' # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 AM2 non-polymer . APRAMYCIN ;NEBRAMYCIN II; 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE ; 'C21 H41 N5 O11' 539.577 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 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 U 1 1 ? ? ? A . n A 1 2 U 2 2 2 U URI A . n A 1 3 G 3 3 3 G GUA A . n A 1 4 C 4 4 4 C CYT A . n A 1 5 G 5 5 5 G GUA A . n A 1 6 U 6 6 6 U URI A . n A 1 7 C 7 7 7 C CYT A . n A 1 8 G 8 8 8 G GUA A . n A 1 9 C 9 9 9 C CYT A . n A 1 10 U 10 10 10 U URI A . n A 1 11 C 11 11 11 C CYT A . n A 1 12 C 12 12 12 C CYT A . n A 1 13 G 13 13 13 G GUA A . n A 1 14 G 14 14 14 G GUA A . n A 1 15 A 15 15 15 A ADE A . n A 1 16 A 16 16 16 A ADE A . n A 1 17 A 17 17 17 A ADE A . n A 1 18 A 18 18 18 A ADE A . n A 1 19 G 19 19 19 G GUA A . n A 1 20 U 20 20 20 U URI A . n A 1 21 C 21 21 21 C CYT A . n A 1 22 G 22 22 22 G GUA A . n A 1 23 C 23 23 23 C CYT A . n B 1 1 U 1 24 ? ? ? B . n B 1 2 U 2 25 25 U URI B . n B 1 3 G 3 26 26 G GUA B . n B 1 4 C 4 27 27 C CYT B . n B 1 5 G 5 28 28 G GUA B . n B 1 6 U 6 29 29 U URI B . n B 1 7 C 7 30 30 C CYT B . n B 1 8 G 8 31 31 G GUA B . n B 1 9 C 9 32 32 C CYT B . n B 1 10 U 10 33 33 U URI B . n B 1 11 C 11 34 34 C CYT B . n B 1 12 C 12 35 35 C CYT B . n B 1 13 G 13 36 36 G GUA B . n B 1 14 G 14 37 37 G GUA B . n B 1 15 A 15 38 38 A ADE B . n B 1 16 A 16 39 39 A ADE B . n B 1 17 A 17 40 40 A ADE B . n B 1 18 A 18 41 41 A ADE B . n B 1 19 G 19 42 42 G GUA B . n B 1 20 U 20 43 43 U URI B . n B 1 21 C 21 44 44 C CYT B . n B 1 22 G 22 45 45 G GUA B . n B 1 23 C 23 46 46 C CYT B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 AM2 1 102 102 AM2 AM2 A . D 3 MG 1 301 301 MG MO6 A . E 4 NCO 1 202 202 NCO NCO A . F 2 AM2 1 101 101 AM2 AM2 B . G 3 MG 1 302 302 MG MO6 B . H 4 NCO 1 201 201 NCO NCO B . I 5 HOH 1 401 401 HOH HOH A . I 5 HOH 2 402 402 HOH HOH A . I 5 HOH 3 405 405 HOH HOH A . I 5 HOH 4 406 406 HOH HOH A . I 5 HOH 5 408 408 HOH HOH A . I 5 HOH 6 409 409 HOH HOH A . I 5 HOH 7 411 411 HOH HOH A . I 5 HOH 8 413 413 HOH HOH A . I 5 HOH 9 415 415 HOH HOH A . I 5 HOH 10 416 301 HOH MO6 A . I 5 HOH 11 417 301 HOH MO6 A . I 5 HOH 12 419 301 HOH MO6 A . I 5 HOH 13 420 301 HOH MO6 A . I 5 HOH 14 421 301 HOH MO6 A . I 5 HOH 15 424 302 HOH MO6 A . J 5 HOH 1 403 403 HOH HOH B . J 5 HOH 2 404 404 HOH HOH B . J 5 HOH 3 407 407 HOH HOH B . J 5 HOH 4 410 410 HOH HOH B . J 5 HOH 5 412 412 HOH HOH B . J 5 HOH 6 414 414 HOH HOH B . J 5 HOH 7 418 301 HOH MO6 B . J 5 HOH 8 422 302 HOH MO6 B . J 5 HOH 9 423 302 HOH MO6 B . J 5 HOH 10 425 302 HOH MO6 B . J 5 HOH 11 426 302 HOH MO6 B . J 5 HOH 12 427 302 HOH MO6 B . # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal d*TREK 8.0SSI 'Feb 4 2003' package 'Pflugrath, J.W.' jwp@RigakuMSC.com 'data processing' http://www.msc.com/protein/dtrek.html ? ? 1 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns.csb.yale.edu/v1.1/ Fortran_77 ? 2 PDB_EXTRACT 1.701 'Nov. 1, 2005' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 3 CrystalClear '(MSC/RIGAKU)' ? ? ? ? 'data reduction' ? ? ? 4 CrystalClear '(MSC/RIGAKU)' ? ? ? ? 'data scaling' ? ? ? 5 AMoRE . ? ? ? ? phasing ? ? ? 6 # _cell.length_a 33.123 _cell.length_b 33.123 _cell.length_c 116.421 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.entry_id 2G5K _cell.pdbx_unique_axis ? _cell.Z_PDB 6 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.space_group_name_H-M 'P 31' _symmetry.entry_id 2G5K _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 144 _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.entry_id 2G5K _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.51 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 50.93 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 6.4 _exptl_crystal_grow.temp 300 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details ;50mM sodium cacodylate, 10mM hexammine cobalt chloride, 150mM potassium chloride, 1%(v/v) 2-methyl-2,4-pentanediol, 5%(v/v) glycerol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'sodium cacodylate' ? ? ? 1 2 1 'hexammine cobalt chloride' ? ? ? 1 3 1 'potassium chloride' ? ? ? 1 4 1 2-methyl-2,4-pentanediol ? ? ? 1 5 1 glycerol ? ? ? 1 6 1 H2O ? ? ? 1 7 2 'sodium cacodylate' ? ? ? 1 8 2 'hexammine cobalt chloride' ? ? ? 1 9 2 'potassium chloride' ? ? ? 1 10 2 glycerol ? ? ? 1 11 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2003-05-18 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator Diamond _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9793 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID14-4' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9793 _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID14-4 # _reflns.entry_id 2G5K _reflns.d_resolution_high 2.800 _reflns.d_resolution_low 27.850 _reflns.number_obs 3533 _reflns.pdbx_scaling_rejects 151 _reflns.pdbx_Rmerge_I_obs 0.056 _reflns.pdbx_netI_over_sigmaI 16.800 _reflns.pdbx_chi_squared 0.970 _reflns.pdbx_redundancy 5.590 _reflns.percent_possible_obs 100.000 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 2.80 2.90 ? 1993 346 0.397 2.1 ? 0.350 5.76 100.00 ? ? ? 1 2.90 3.02 ? 2190 380 0.309 2.7 ? 0.420 5.76 100.00 ? ? ? 2 3.02 3.15 ? 1872 326 0.151 5.1 ? 0.530 5.74 100.00 ? ? ? 3 3.15 3.32 ? 2121 367 0.131 7.5 ? 0.670 5.78 100.00 ? ? ? 4 3.32 3.53 ? 1918 334 0.103 10.1 ? 0.820 5.74 100.00 ? ? ? 5 3.53 3.80 ? 2092 364 0.087 13.4 ? 0.930 5.73 100.00 ? ? ? 6 3.80 4.18 ? 2024 361 0.063 21.1 ? 1.170 5.56 100.00 ? ? ? 7 4.18 4.78 ? 1942 354 0.054 28.5 ? 1.340 5.43 100.00 ? ? ? 8 4.78 6.01 ? 1849 337 0.043 38.3 ? 1.610 5.37 100.00 ? ? ? 9 6.01 27.85 ? 1886 364 0.038 45.5 ? 2.080 5.01 100.00 ? ? ? 10 # _refine.ls_d_res_high 2.800 _refine.ls_d_res_low 10.000 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 100.000 _refine.ls_number_reflns_obs 3437 _refine.ls_R_factor_R_work 0.258 _refine.ls_R_factor_R_free 0.27 _refine.ls_percent_reflns_R_free 10.100 _refine.ls_number_reflns_R_free 347 _refine.B_iso_mean 93.873 _refine.solvent_model_param_bsol 75.808 _refine.aniso_B[1][1] 7.932 _refine.aniso_B[2][2] 7.932 _refine.aniso_B[3][3] -15.865 _refine.aniso_B[1][2] -1.148 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.overall_FOM_work_R_set 0.722 _refine.entry_id 2G5K _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ;G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996). ; _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 938 _refine_hist.pdbx_number_atoms_ligand 102 _refine_hist.number_atoms_solvent 15 _refine_hist.number_atoms_total 1055 _refine_hist.d_res_high 2.800 _refine_hist.d_res_low 10.000 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.005 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 0.9 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.5 ? ? ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id 2.800 2.920 8 . 389 . 0.553 0.578 . 34 . . 423 . 'X-RAY DIFFRACTION' 2.920 3.070 8 . 378 . 0.426 0.51 . 49 . . 427 . 'X-RAY DIFFRACTION' 3.070 3.260 8 . 387 . 0.155 0.284 . 49 . . 436 . 'X-RAY DIFFRACTION' 3.260 3.500 8 . 369 . 0.258 0.302 . 54 . . 423 . 'X-RAY DIFFRACTION' 3.500 3.840 8 . 399 . 0.282 0.256 . 41 . . 440 . 'X-RAY DIFFRACTION' 3.840 4.350 8 . 386 . 0.258 0.308 . 38 . . 424 . 'X-RAY DIFFRACTION' 4.350 5.340 8 . 390 . 0.234 0.19 . 46 . . 436 . 'X-RAY DIFFRACTION' 5.340 10.000 8 . 392 . 0.239 0.273 . 36 . . 428 . 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 dna-rna_rep.param dna-rna.top 'X-RAY DIFFRACTION' 2 am2_xplor.param am2_xplor.top 'X-RAY DIFFRACTION' 3 nco_xplor.param nco_xplor.top 'X-RAY DIFFRACTION' 4 mo6_xplor.param mo6_xplor.top 'X-RAY DIFFRACTION' 5 water_rep.param water.top 'X-RAY DIFFRACTION' # _struct.entry_id 2G5K _struct.title 'Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with Apramycin' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2G5K _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'aminoglycoside, antibiotics, apramycin, ribosome, decoding site, Homo sapiens, cytoplasm, 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 1 ? C N N 2 ? D N N 3 ? E N N 4 ? F N N 2 ? G N N 3 ? H N N 4 ? I N N 5 ? J N N 5 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2G5K _struct_ref.pdbx_db_accession 2G5K _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2G5K A 1 ? 23 ? 2G5K 1 ? 23 ? 1 23 2 1 2G5K B 1 ? 23 ? 2G5K 24 ? 46 ? 24 46 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J # _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 ? ? D MG . MG ? ? ? 1_555 I HOH . O ? ? A MG 301 A HOH 416 1_555 ? ? ? ? ? ? ? 2.074 ? ? metalc2 metalc ? ? D MG . MG ? ? ? 1_555 I HOH . O ? ? A MG 301 A HOH 417 1_555 ? ? ? ? ? ? ? 2.016 ? ? metalc3 metalc ? ? D MG . MG ? ? ? 1_555 I HOH . O ? ? A MG 301 A HOH 419 1_555 ? ? ? ? ? ? ? 2.068 ? ? metalc4 metalc ? ? D MG . MG ? ? ? 1_555 I HOH . O ? ? A MG 301 A HOH 420 1_555 ? ? ? ? ? ? ? 2.128 ? ? metalc5 metalc ? ? D MG . MG ? ? ? 1_555 I HOH . O ? ? A MG 301 A HOH 421 1_555 ? ? ? ? ? ? ? 2.120 ? ? metalc6 metalc ? ? D MG . MG ? ? ? 1_555 J HOH . O ? ? A MG 301 B HOH 418 1_555 ? ? ? ? ? ? ? 2.095 ? ? metalc7 metalc ? ? I HOH . O ? ? ? 1_555 G MG . MG ? ? A HOH 424 B MG 302 1_555 ? ? ? ? ? ? ? 2.098 ? ? metalc8 metalc ? ? G MG . MG ? ? ? 1_555 J HOH . O ? ? B MG 302 B HOH 422 1_555 ? ? ? ? ? ? ? 2.076 ? ? metalc9 metalc ? ? G MG . MG ? ? ? 1_555 J HOH . O ? ? B MG 302 B HOH 423 1_555 ? ? ? ? ? ? ? 2.015 ? ? metalc10 metalc ? ? G MG . MG ? ? ? 1_555 J HOH . O ? ? B MG 302 B HOH 425 1_555 ? ? ? ? ? ? ? 2.069 ? ? metalc11 metalc ? ? G MG . MG ? ? ? 1_555 J HOH . O ? ? B MG 302 B HOH 426 1_555 ? ? ? ? ? ? ? 2.127 ? ? metalc12 metalc ? ? G MG . MG ? ? ? 1_555 J HOH . O ? ? B MG 302 B HOH 427 1_555 ? ? ? ? ? ? ? 2.118 ? ? hydrog1 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 23 N3 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 23 O2 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 23 N4 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 22 N1 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 22 O6 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 22 N2 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 21 N3 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 6 N3 ? ? ? 1_555 B U 20 O4 ? ? A U 6 B U 43 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog11 hydrog ? ? A U 6 O2 ? ? ? 1_555 B U 20 N3 ? ? A U 6 B U 43 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog12 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 9 N4 ? ? ? 1_555 B A 17 N3 ? ? A C 9 B A 40 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog16 hydrog ? ? A U 10 N3 ? ? ? 1_555 B A 15 N1 ? ? A U 10 B A 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 10 O4 ? ? ? 1_555 B A 15 N6 ? ? A U 10 B A 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 14 N1 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 14 O6 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 14 N2 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 15 N1 ? ? ? 1_555 B U 10 N3 ? ? A A 15 B U 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 15 N6 ? ? ? 1_555 B U 10 O4 ? ? A A 15 B U 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A A 17 N3 ? ? ? 1_555 B C 9 N4 ? ? A A 17 B C 32 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog33 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A U 20 N3 ? ? ? 1_555 B U 6 O2 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog37 hydrog ? ? A U 20 O4 ? ? ? 1_555 B U 6 N3 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog38 hydrog ? ? A C 21 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 21 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 22 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 22 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 22 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 23 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 23 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 23 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? I HOH . ? A HOH 416 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? I HOH . ? A HOH 417 ? 1_555 179.8 ? 2 O ? I HOH . ? A HOH 416 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? I HOH . ? A HOH 419 ? 1_555 90.0 ? 3 O ? I HOH . ? A HOH 417 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? I HOH . ? A HOH 419 ? 1_555 89.9 ? 4 O ? I HOH . ? A HOH 416 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? I HOH . ? A HOH 420 ? 1_555 90.0 ? 5 O ? I HOH . ? A HOH 417 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? I HOH . ? A HOH 420 ? 1_555 89.9 ? 6 O ? I HOH . ? A HOH 419 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? I HOH . ? A HOH 420 ? 1_555 90.2 ? 7 O ? I HOH . ? A HOH 416 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? I HOH . ? A HOH 421 ? 1_555 89.8 ? 8 O ? I HOH . ? A HOH 417 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? I HOH . ? A HOH 421 ? 1_555 90.3 ? 9 O ? I HOH . ? A HOH 419 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? I HOH . ? A HOH 421 ? 1_555 89.9 ? 10 O ? I HOH . ? A HOH 420 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? I HOH . ? A HOH 421 ? 1_555 179.8 ? 11 O ? I HOH . ? A HOH 416 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? J HOH . ? B HOH 418 ? 1_555 90.1 ? 12 O ? I HOH . ? A HOH 417 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? J HOH . ? B HOH 418 ? 1_555 90.0 ? 13 O ? I HOH . ? A HOH 419 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? J HOH . ? B HOH 418 ? 1_555 179.8 ? 14 O ? I HOH . ? A HOH 420 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? J HOH . ? B HOH 418 ? 1_555 89.9 ? 15 O ? I HOH . ? A HOH 421 ? 1_555 MG ? D MG . ? A MG 301 ? 1_555 O ? J HOH . ? B HOH 418 ? 1_555 90.0 ? 16 O ? I HOH . ? A HOH 424 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 422 ? 1_555 90.0 ? 17 O ? I HOH . ? A HOH 424 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 423 ? 1_555 90.0 ? 18 O ? J HOH . ? B HOH 422 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 423 ? 1_555 179.9 ? 19 O ? I HOH . ? A HOH 424 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 425 ? 1_555 179.8 ? 20 O ? J HOH . ? B HOH 422 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 425 ? 1_555 90.1 ? 21 O ? J HOH . ? B HOH 423 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 425 ? 1_555 89.9 ? 22 O ? I HOH . ? A HOH 424 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 426 ? 1_555 89.8 ? 23 O ? J HOH . ? B HOH 422 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 426 ? 1_555 90.1 ? 24 O ? J HOH . ? B HOH 423 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 426 ? 1_555 89.8 ? 25 O ? J HOH . ? B HOH 425 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 426 ? 1_555 90.3 ? 26 O ? I HOH . ? A HOH 424 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 427 ? 1_555 90.1 ? 27 O ? J HOH . ? B HOH 422 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 427 ? 1_555 89.8 ? 28 O ? J HOH . ? B HOH 423 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 427 ? 1_555 90.3 ? 29 O ? J HOH . ? B HOH 425 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 427 ? 1_555 89.8 ? 30 O ? J HOH . ? B HOH 426 ? 1_555 MG ? G MG . ? B MG 302 ? 1_555 O ? J HOH . ? B HOH 427 ? 1_555 179.9 ? # 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 B AM2 101 ? 11 'BINDING SITE FOR RESIDUE AM2 B 101' AC2 Software A AM2 102 ? 11 'BINDING SITE FOR RESIDUE AM2 A 102' AC3 Software A MG 301 ? 6 'BINDING SITE FOR RESIDUE MG A 301' AC4 Software B MG 302 ? 6 'BINDING SITE FOR RESIDUE MG B 302' AC5 Software B NCO 201 ? 2 'BINDING SITE FOR RESIDUE NCO B 201' AC6 Software A NCO 202 ? 2 'BINDING SITE FOR RESIDUE NCO A 202' 1 ? ? ? ? ? ? ? # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 11 A A 15 ? A A 15 . ? 1_555 ? 2 AC1 11 A A 17 ? A A 17 . ? 1_555 ? 3 AC1 11 A A 18 ? A A 18 . ? 1_555 ? 4 AC1 11 G A 19 ? G A 19 . ? 1_555 ? 5 AC1 11 HOH I . ? HOH A 415 . ? 1_555 ? 6 AC1 11 C B 4 ? C B 27 . ? 1_555 ? 7 AC1 11 G B 5 ? G B 28 . ? 1_555 ? 8 AC1 11 U B 6 ? U B 29 . ? 1_555 ? 9 AC1 11 C B 7 ? C B 30 . ? 1_555 ? 10 AC1 11 G B 8 ? G B 31 . ? 1_555 ? 11 AC1 11 HOH J . ? HOH B 407 . ? 1_555 ? 12 AC2 11 C A 4 ? C A 4 . ? 1_555 ? 13 AC2 11 G A 5 ? G A 5 . ? 1_555 ? 14 AC2 11 U A 6 ? U A 6 . ? 1_555 ? 15 AC2 11 C A 7 ? C A 7 . ? 1_555 ? 16 AC2 11 G A 8 ? G A 8 . ? 1_555 ? 17 AC2 11 HOH I . ? HOH A 405 . ? 1_555 ? 18 AC2 11 A B 15 ? A B 38 . ? 1_555 ? 19 AC2 11 A B 17 ? A B 40 . ? 1_555 ? 20 AC2 11 A B 18 ? A B 41 . ? 1_555 ? 21 AC2 11 G B 19 ? G B 42 . ? 1_555 ? 22 AC2 11 HOH J . ? HOH B 414 . ? 1_555 ? 23 AC3 6 HOH I . ? HOH A 416 . ? 1_555 ? 24 AC3 6 HOH I . ? HOH A 417 . ? 1_555 ? 25 AC3 6 HOH I . ? HOH A 419 . ? 1_555 ? 26 AC3 6 HOH I . ? HOH A 420 . ? 1_555 ? 27 AC3 6 HOH I . ? HOH A 421 . ? 1_555 ? 28 AC3 6 HOH J . ? HOH B 418 . ? 1_555 ? 29 AC4 6 HOH I . ? HOH A 424 . ? 1_555 ? 30 AC4 6 HOH J . ? HOH B 422 . ? 1_555 ? 31 AC4 6 HOH J . ? HOH B 423 . ? 1_555 ? 32 AC4 6 HOH J . ? HOH B 425 . ? 1_555 ? 33 AC4 6 HOH J . ? HOH B 426 . ? 1_555 ? 34 AC4 6 HOH J . ? HOH B 427 . ? 1_555 ? 35 AC5 2 G B 13 ? G B 36 . ? 1_555 ? 36 AC5 2 G B 14 ? G B 37 . ? 1_555 ? 37 AC6 2 G A 13 ? G A 13 . ? 1_555 ? 38 AC6 2 G A 14 ? G A 14 . ? 1_555 ? # _struct_site_keywords.site_id 1 _struct_site_keywords.text bis-intercalation # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A U 1 ? A U 1 2 1 Y 1 B U 24 ? B U 1 # 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 AM2 CA1 C N S 38 AM2 CA2 C N R 39 AM2 CA3 C N N 40 AM2 CA4 C N S 41 AM2 CA5 C N R 42 AM2 CA6 C N R 43 AM2 CA7 C N S 44 AM2 CA8 C N R 45 AM2 CA9 C N N 46 AM2 OA4 O N N 47 AM2 OA5 O N N 48 AM2 NA2 N N N 49 AM2 NA7 N N N 50 AM2 OA6 O N N 51 AM2 OA8 O N N 52 AM2 OA1 O N N 53 AM2 CB1 C N R 54 AM2 CB2 C N R 55 AM2 CB3 C N S 56 AM2 CB4 C N S 57 AM2 CB5 C N S 58 AM2 CB6 C N N 59 AM2 OB1 O N N 60 AM2 NB4 N N N 61 AM2 OB2 O N N 62 AM2 OB3 O N N 63 AM2 OB6 O N N 64 AM2 CC1 C N R 65 AM2 CC2 C N R 66 AM2 CC3 C N S 67 AM2 CC4 C N R 68 AM2 CC5 C N N 69 AM2 CC6 C N S 70 AM2 NC4 N N N 71 AM2 NC6 N N N 72 AM2 OC2 O N N 73 AM2 OC3 O N N 74 AM2 HA1 H N N 75 AM2 HA2 H N N 76 AM2 HA31 H N N 77 AM2 HA32 H N N 78 AM2 HA4 H N N 79 AM2 HA5 H N N 80 AM2 HA6 H N N 81 AM2 HA7 H N N 82 AM2 HA8 H N N 83 AM2 HA91 H N N 84 AM2 HA92 H N N 85 AM2 HA93 H N N 86 AM2 HA21 H N N 87 AM2 HA22 H N N 88 AM2 H2 H N N 89 AM2 H1 H N N 90 AM2 HB1 H N N 91 AM2 HB2 H N N 92 AM2 HB3 H N N 93 AM2 HB4 H N N 94 AM2 HB5 H N N 95 AM2 HB61 H N N 96 AM2 HB62 H N N 97 AM2 HB41 H N N 98 AM2 HB42 H N N 99 AM2 H5 H N N 100 AM2 H6 H N N 101 AM2 HB6 H N N 102 AM2 HC1 H N N 103 AM2 HC2 H N N 104 AM2 HC3 H N N 105 AM2 HC4 H N N 106 AM2 HC51 H N N 107 AM2 HC52 H N N 108 AM2 HC6 H N N 109 AM2 HC41 H N N 110 AM2 HC42 H N N 111 AM2 HC61 H N N 112 AM2 HC62 H N N 113 AM2 H3 H N N 114 AM2 H4 H N N 115 C OP3 O N N 116 C P P N N 117 C OP1 O N N 118 C OP2 O N N 119 C "O5'" O N N 120 C "C5'" C N N 121 C "C4'" C N R 122 C "O4'" O N N 123 C "C3'" C N S 124 C "O3'" O N N 125 C "C2'" C N R 126 C "O2'" O N N 127 C "C1'" C N R 128 C N1 N N N 129 C C2 C N N 130 C O2 O N N 131 C N3 N N N 132 C C4 C N N 133 C N4 N N N 134 C C5 C N N 135 C C6 C N N 136 C HOP3 H N N 137 C HOP2 H N N 138 C "H5'" H N N 139 C "H5''" H N N 140 C "H4'" H N N 141 C "H3'" H N N 142 C "HO3'" H N N 143 C "H2'" H N N 144 C "HO2'" H N N 145 C "H1'" H N N 146 C H41 H N N 147 C H42 H N N 148 C H5 H N N 149 C H6 H N N 150 G OP3 O N N 151 G P P N N 152 G OP1 O N N 153 G OP2 O N N 154 G "O5'" O N N 155 G "C5'" C N N 156 G "C4'" C N R 157 G "O4'" O N N 158 G "C3'" C N S 159 G "O3'" O N N 160 G "C2'" C N R 161 G "O2'" O N N 162 G "C1'" C N R 163 G N9 N Y N 164 G C8 C Y N 165 G N7 N Y N 166 G C5 C Y N 167 G C6 C N N 168 G O6 O N N 169 G N1 N N N 170 G C2 C N N 171 G N2 N N N 172 G N3 N N N 173 G C4 C Y N 174 G HOP3 H N N 175 G HOP2 H N N 176 G "H5'" H N N 177 G "H5''" H N N 178 G "H4'" H N N 179 G "H3'" H N N 180 G "HO3'" H N N 181 G "H2'" H N N 182 G "HO2'" H N N 183 G "H1'" H N N 184 G H8 H N N 185 G H1 H N N 186 G H21 H N N 187 G H22 H N N 188 HOH O O N N 189 HOH H1 H N N 190 HOH H2 H N N 191 MG MG MG N N 192 NCO CO CO N N 193 NCO N1 N N N 194 NCO N2 N N N 195 NCO N3 N N N 196 NCO N4 N N N 197 NCO N5 N N N 198 NCO N6 N N N 199 NCO HN11 H N N 200 NCO HN12 H N N 201 NCO HN13 H N N 202 NCO HN21 H N N 203 NCO HN22 H N N 204 NCO HN23 H N N 205 NCO HN31 H N N 206 NCO HN32 H N N 207 NCO HN33 H N N 208 NCO HN41 H N N 209 NCO HN42 H N N 210 NCO HN43 H N N 211 NCO HN51 H N N 212 NCO HN52 H N N 213 NCO HN53 H N N 214 NCO HN61 H N N 215 NCO HN62 H N N 216 NCO HN63 H N N 217 U OP3 O N N 218 U P P N N 219 U OP1 O N N 220 U OP2 O N N 221 U "O5'" O N N 222 U "C5'" C N N 223 U "C4'" C N R 224 U "O4'" O N N 225 U "C3'" C N S 226 U "O3'" O N N 227 U "C2'" C N R 228 U "O2'" O N N 229 U "C1'" C N R 230 U N1 N N N 231 U C2 C N N 232 U O2 O N N 233 U N3 N N N 234 U C4 C N N 235 U O4 O N N 236 U C5 C N N 237 U C6 C N N 238 U HOP3 H N N 239 U HOP2 H N N 240 U "H5'" H N N 241 U "H5''" H N N 242 U "H4'" H N N 243 U "H3'" H N N 244 U "HO3'" H N N 245 U "H2'" H N N 246 U "HO2'" H N N 247 U "H1'" H N N 248 U H3 H N N 249 U H5 H N N 250 U H6 H N N 251 # 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 AM2 CA1 CA2 sing N N 40 AM2 CA1 OA4 sing N N 41 AM2 CA1 OA1 sing N N 42 AM2 CA1 HA1 sing N N 43 AM2 CA2 CA3 sing N N 44 AM2 CA2 NA2 sing N N 45 AM2 CA2 HA2 sing N N 46 AM2 CA3 CA4 sing N N 47 AM2 CA3 HA31 sing N N 48 AM2 CA3 HA32 sing N N 49 AM2 CA4 CA5 sing N N 50 AM2 CA4 OA5 sing N N 51 AM2 CA4 HA4 sing N N 52 AM2 CA5 CA6 sing N N 53 AM2 CA5 OA4 sing N N 54 AM2 CA5 HA5 sing N N 55 AM2 CA6 CA7 sing N N 56 AM2 CA6 OA6 sing N N 57 AM2 CA6 HA6 sing N N 58 AM2 CA7 CA8 sing N N 59 AM2 CA7 NA7 sing N N 60 AM2 CA7 HA7 sing N N 61 AM2 CA8 OA5 sing N N 62 AM2 CA8 OA8 sing N N 63 AM2 CA8 HA8 sing N N 64 AM2 CA9 NA7 sing N N 65 AM2 CA9 HA91 sing N N 66 AM2 CA9 HA92 sing N N 67 AM2 CA9 HA93 sing N N 68 AM2 NA2 HA21 sing N N 69 AM2 NA2 HA22 sing N N 70 AM2 NA7 H2 sing N N 71 AM2 OA6 H1 sing N N 72 AM2 OA8 CB1 sing N N 73 AM2 OA1 CC1 sing N N 74 AM2 CB1 CB2 sing N N 75 AM2 CB1 OB1 sing N N 76 AM2 CB1 HB1 sing N N 77 AM2 CB2 CB3 sing N N 78 AM2 CB2 OB2 sing N N 79 AM2 CB2 HB2 sing N N 80 AM2 CB3 CB4 sing N N 81 AM2 CB3 OB3 sing N N 82 AM2 CB3 HB3 sing N N 83 AM2 CB4 CB5 sing N N 84 AM2 CB4 NB4 sing N N 85 AM2 CB4 HB4 sing N N 86 AM2 CB5 CB6 sing N N 87 AM2 CB5 OB1 sing N N 88 AM2 CB5 HB5 sing N N 89 AM2 CB6 OB6 sing N N 90 AM2 CB6 HB61 sing N N 91 AM2 CB6 HB62 sing N N 92 AM2 NB4 HB41 sing N N 93 AM2 NB4 HB42 sing N N 94 AM2 OB2 H5 sing N N 95 AM2 OB3 H6 sing N N 96 AM2 OB6 HB6 sing N N 97 AM2 CC1 CC2 sing N N 98 AM2 CC1 CC6 sing N N 99 AM2 CC1 HC1 sing N N 100 AM2 CC2 CC3 sing N N 101 AM2 CC2 OC2 sing N N 102 AM2 CC2 HC2 sing N N 103 AM2 CC3 CC4 sing N N 104 AM2 CC3 OC3 sing N N 105 AM2 CC3 HC3 sing N N 106 AM2 CC4 CC5 sing N N 107 AM2 CC4 NC4 sing N N 108 AM2 CC4 HC4 sing N N 109 AM2 CC5 CC6 sing N N 110 AM2 CC5 HC51 sing N N 111 AM2 CC5 HC52 sing N N 112 AM2 CC6 NC6 sing N N 113 AM2 CC6 HC6 sing N N 114 AM2 NC4 HC41 sing N N 115 AM2 NC4 HC42 sing N N 116 AM2 NC6 HC61 sing N N 117 AM2 NC6 HC62 sing N N 118 AM2 OC2 H3 sing N N 119 AM2 OC3 H4 sing N N 120 C OP3 P sing N N 121 C OP3 HOP3 sing N N 122 C P OP1 doub N N 123 C P OP2 sing N N 124 C P "O5'" sing N N 125 C OP2 HOP2 sing N N 126 C "O5'" "C5'" sing N N 127 C "C5'" "C4'" sing N N 128 C "C5'" "H5'" sing N N 129 C "C5'" "H5''" sing N N 130 C "C4'" "O4'" sing N N 131 C "C4'" "C3'" sing N N 132 C "C4'" "H4'" sing N N 133 C "O4'" "C1'" sing N N 134 C "C3'" "O3'" sing N N 135 C "C3'" "C2'" sing N N 136 C "C3'" "H3'" sing N N 137 C "O3'" "HO3'" sing N N 138 C "C2'" "O2'" sing N N 139 C "C2'" "C1'" sing N N 140 C "C2'" "H2'" sing N N 141 C "O2'" "HO2'" sing N N 142 C "C1'" N1 sing N N 143 C "C1'" "H1'" sing N N 144 C N1 C2 sing N N 145 C N1 C6 sing N N 146 C C2 O2 doub N N 147 C C2 N3 sing N N 148 C N3 C4 doub N N 149 C C4 N4 sing N N 150 C C4 C5 sing N N 151 C N4 H41 sing N N 152 C N4 H42 sing N N 153 C C5 C6 doub N N 154 C C5 H5 sing N N 155 C C6 H6 sing N N 156 G OP3 P sing N N 157 G OP3 HOP3 sing N N 158 G P OP1 doub N N 159 G P OP2 sing N N 160 G P "O5'" sing N N 161 G OP2 HOP2 sing N N 162 G "O5'" "C5'" sing N N 163 G "C5'" "C4'" sing N N 164 G "C5'" "H5'" sing N N 165 G "C5'" "H5''" sing N N 166 G "C4'" "O4'" sing N N 167 G "C4'" "C3'" sing N N 168 G "C4'" "H4'" sing N N 169 G "O4'" "C1'" sing N N 170 G "C3'" "O3'" sing N N 171 G "C3'" "C2'" sing N N 172 G "C3'" "H3'" sing N N 173 G "O3'" "HO3'" sing N N 174 G "C2'" "O2'" sing N N 175 G "C2'" "C1'" sing N N 176 G "C2'" "H2'" sing N N 177 G "O2'" "HO2'" sing N N 178 G "C1'" N9 sing N N 179 G "C1'" "H1'" sing N N 180 G N9 C8 sing Y N 181 G N9 C4 sing Y N 182 G C8 N7 doub Y N 183 G C8 H8 sing N N 184 G N7 C5 sing Y N 185 G C5 C6 sing N N 186 G C5 C4 doub Y N 187 G C6 O6 doub N N 188 G C6 N1 sing N N 189 G N1 C2 sing N N 190 G N1 H1 sing N N 191 G C2 N2 sing N N 192 G C2 N3 doub N N 193 G N2 H21 sing N N 194 G N2 H22 sing N N 195 G N3 C4 sing N N 196 HOH O H1 sing N N 197 HOH O H2 sing N N 198 NCO CO N1 sing N N 199 NCO CO N2 sing N N 200 NCO CO N3 sing N N 201 NCO CO N4 sing N N 202 NCO CO N5 sing N N 203 NCO CO N6 sing N N 204 NCO N1 HN11 sing N N 205 NCO N1 HN12 sing N N 206 NCO N1 HN13 sing N N 207 NCO N2 HN21 sing N N 208 NCO N2 HN22 sing N N 209 NCO N2 HN23 sing N N 210 NCO N3 HN31 sing N N 211 NCO N3 HN32 sing N N 212 NCO N3 HN33 sing N N 213 NCO N4 HN41 sing N N 214 NCO N4 HN42 sing N N 215 NCO N4 HN43 sing N N 216 NCO N5 HN51 sing N N 217 NCO N5 HN52 sing N N 218 NCO N5 HN53 sing N N 219 NCO N6 HN61 sing N N 220 NCO N6 HN62 sing N N 221 NCO N6 HN63 sing N N 222 U OP3 P sing N N 223 U OP3 HOP3 sing N N 224 U P OP1 doub N N 225 U P OP2 sing N N 226 U P "O5'" sing N N 227 U OP2 HOP2 sing N N 228 U "O5'" "C5'" sing N N 229 U "C5'" "C4'" sing N N 230 U "C5'" "H5'" sing N N 231 U "C5'" "H5''" sing N N 232 U "C4'" "O4'" sing N N 233 U "C4'" "C3'" sing N N 234 U "C4'" "H4'" sing N N 235 U "O4'" "C1'" sing N N 236 U "C3'" "O3'" sing N N 237 U "C3'" "C2'" sing N N 238 U "C3'" "H3'" sing N N 239 U "O3'" "HO3'" sing N N 240 U "C2'" "O2'" sing N N 241 U "C2'" "C1'" sing N N 242 U "C2'" "H2'" sing N N 243 U "O2'" "HO2'" sing N N 244 U "C1'" N1 sing N N 245 U "C1'" "H1'" sing N N 246 U N1 C2 sing N N 247 U N1 C6 sing N N 248 U C2 O2 doub N N 249 U C2 N3 sing N N 250 U N3 C4 sing N N 251 U N3 H3 sing N N 252 U C4 O4 doub N N 253 U C4 C5 sing N N 254 U C5 C6 doub N N 255 U C5 H5 sing N N 256 U C6 H6 sing N N 257 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2G5K 'double helix' 2G5K 'a-form double helix' 2G5K 'mismatched base pair' 2G5K 'internal loop' # 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 G 3 1_555 B C 23 1_555 -0.836 -0.326 -0.017 -1.620 1.022 -0.237 1 A_G3:C46_B A 3 ? B 46 ? 19 1 1 A C 4 1_555 B G 22 1_555 0.033 -0.434 0.147 6.793 3.558 -3.952 2 A_C4:G45_B A 4 ? B 45 ? 19 1 1 A G 5 1_555 B C 21 1_555 0.295 -0.454 -0.046 -0.863 -12.505 -0.203 3 A_G5:C44_B A 5 ? B 44 ? 19 1 1 A U 6 1_555 B U 20 1_555 2.403 -2.011 0.526 -2.538 -13.533 4.193 4 A_U6:U43_B A 6 ? B 43 ? 16 1 1 A C 7 1_555 B G 19 1_555 0.412 -0.224 -0.075 3.991 -7.395 -14.088 5 A_C7:G42_B A 7 ? B 42 ? 19 1 1 A C 9 1_555 B A 17 1_555 -5.519 -0.757 0.499 20.159 -0.859 62.937 6 A_C9:A40_B A 9 ? B 40 ? ? 5 1 A U 10 1_555 B A 15 1_555 -0.531 -0.263 0.408 9.441 -1.921 -2.119 7 A_U10:A38_B A 10 ? B 38 ? 20 1 1 A C 11 1_555 B G 14 1_555 -0.767 -0.113 -0.194 19.314 -9.615 3.508 8 A_C11:G37_B A 11 ? B 37 ? 19 1 1 A C 12 1_555 B G 13 1_555 0.064 -0.161 0.028 1.926 -5.240 3.891 9 A_C12:G36_B A 12 ? B 36 ? 19 1 1 A G 13 1_555 B C 12 1_555 -0.062 -0.163 0.029 -1.876 -5.132 3.870 10 A_G13:C35_B A 13 ? B 35 ? 19 1 1 A G 14 1_555 B C 11 1_555 0.765 -0.111 -0.198 -19.529 -9.536 3.519 11 A_G14:C34_B A 14 ? B 34 ? 19 1 1 A A 15 1_555 B U 10 1_555 0.531 -0.265 0.408 -9.678 -1.848 -2.175 12 A_A15:U33_B A 15 ? B 33 ? 20 1 1 A A 17 1_555 B C 9 1_555 5.516 -0.754 0.504 -20.663 -0.786 62.912 13 A_A17:C32_B A 17 ? B 32 ? ? 5 1 A G 19 1_555 B C 7 1_555 -0.419 -0.217 -0.072 -4.069 -7.453 -14.032 14 A_G19:C30_B A 19 ? B 30 ? 19 1 1 A U 20 1_555 B U 6 1_555 -2.405 -2.001 0.510 2.349 -13.780 4.263 15 A_U20:U29_B A 20 ? B 29 ? 16 1 1 A C 21 1_555 B G 5 1_555 -0.299 -0.445 -0.043 0.878 -12.638 -0.160 16 A_C21:G28_B A 21 ? B 28 ? 19 1 1 A G 22 1_555 B C 4 1_555 -0.027 -0.422 0.121 -7.461 3.172 -3.976 17 A_G22:C27_B A 22 ? B 27 ? 19 1 1 A C 23 1_555 B G 3 1_555 0.837 -0.325 -0.049 1.877 1.051 -0.370 18 A_C23:G26_B A 23 ? B 26 ? 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 G 3 1_555 B C 23 1_555 A C 4 1_555 B G 22 1_555 -0.732 -1.990 3.138 -1.905 -1.856 36.597 -2.912 0.907 3.264 -2.952 3.029 36.691 1 AA_G3C4:G45C46_BB A 3 ? B 46 ? A 4 ? B 45 ? 1 A C 4 1_555 B G 22 1_555 A G 5 1_555 B C 21 1_555 -0.237 -1.798 3.424 0.384 6.082 31.037 -4.421 0.506 3.022 11.230 -0.709 31.615 2 AA_C4G5:C44G45_BB A 4 ? B 45 ? A 5 ? B 44 ? 1 A G 5 1_555 B C 21 1_555 A U 6 1_555 B U 20 1_555 0.538 -1.574 3.160 -2.950 6.410 40.248 -2.908 -1.070 2.842 9.229 4.248 40.836 3 AA_G5U6:U43C44_BB A 5 ? B 44 ? A 6 ? B 43 ? 1 A U 6 1_555 B U 20 1_555 A C 7 1_555 B G 19 1_555 -0.570 -1.923 2.917 8.628 4.025 26.578 -4.720 2.828 2.311 8.420 -18.048 28.203 4 AA_U6C7:G42U43_BB A 6 ? B 43 ? A 7 ? B 42 ? 1 A C 9 1_555 B A 17 1_555 A U 10 1_555 B A 15 1_555 -0.785 0.076 3.384 -0.976 0.478 73.226 0.048 0.626 3.394 0.401 0.818 73.233 5 AA_C9U10:A38A40_BB A 9 ? B 40 ? A 10 ? B 38 ? 1 A U 10 1_555 B A 15 1_555 A C 11 1_555 B G 14 1_555 -0.060 -2.085 2.818 -0.515 6.165 26.525 -5.651 0.025 2.284 13.210 1.104 27.224 6 AA_U10C11:G37A38_BB A 10 ? B 38 ? A 11 ? B 37 ? 1 A C 11 1_555 B G 14 1_555 A C 12 1_555 B G 13 1_555 -0.348 -2.080 3.597 -4.310 7.355 34.579 -4.521 -0.085 3.123 12.147 7.117 35.583 7 AA_C11C12:G36G37_BB A 11 ? B 37 ? A 12 ? B 36 ? 1 A C 12 1_555 B G 13 1_555 A G 13 1_555 B C 12 1_555 0.001 -1.495 3.192 -0.008 8.728 31.073 -4.113 -0.002 2.685 15.903 0.014 32.247 8 AA_C12G13:C35G36_BB A 12 ? B 36 ? A 13 ? B 35 ? 1 A G 13 1_555 B C 12 1_555 A G 14 1_555 B C 11 1_555 0.350 -2.082 3.603 4.299 7.454 34.568 -4.539 0.081 3.121 12.308 -7.099 35.591 9 AA_G13G14:C34C35_BB A 13 ? B 35 ? A 14 ? B 34 ? 1 A G 14 1_555 B C 11 1_555 A A 15 1_555 B U 10 1_555 0.055 -2.085 2.818 0.487 6.152 26.544 -5.645 -0.021 2.286 13.173 -1.044 27.239 10 AA_G14A15:U33C34_BB A 14 ? B 34 ? A 15 ? B 33 ? 1 A A 15 1_555 B U 10 1_555 A A 17 1_555 B C 9 1_555 0.783 0.073 3.389 0.881 0.415 73.236 0.047 -0.627 3.397 0.348 -0.738 73.242 11 AA_A15A17:C32U33_BB A 15 ? B 33 ? A 17 ? B 32 ? 1 A G 19 1_555 B C 7 1_555 A U 20 1_555 B U 6 1_555 0.562 -1.923 2.922 -8.546 4.177 26.570 -4.753 -2.798 2.310 8.741 17.881 28.192 12 AA_G19U20:U29C30_BB A 19 ? B 30 ? A 20 ? B 29 ? 1 A U 20 1_555 B U 6 1_555 A C 21 1_555 B G 5 1_555 -0.541 -1.571 3.158 2.702 6.275 40.215 -2.896 1.052 2.850 9.046 -3.896 40.768 13 AA_U20C21:G28U29_BB A 20 ? B 29 ? A 21 ? B 28 ? 1 A C 21 1_555 B G 5 1_555 A G 22 1_555 B C 4 1_555 0.233 -1.790 3.446 -0.071 6.112 31.079 -4.412 -0.440 3.047 11.270 0.130 31.660 14 AA_C21G22:C27G28_BB A 21 ? B 28 ? A 22 ? B 27 ? 1 A G 22 1_555 B C 4 1_555 A C 23 1_555 B G 3 1_555 0.735 -1.973 3.117 1.878 -1.982 36.544 -2.874 -0.917 3.248 -3.155 -2.990 36.643 15 AA_G22C23:G26C27_BB A 22 ? B 27 ? A 23 ? B 26 ? # _atom_sites.entry_id 2G5K _atom_sites.fract_transf_matrix[1][1] 0.030191 _atom_sites.fract_transf_matrix[1][2] 0.017430 _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] 0.034861 _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] 0.008590 _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 CO MG N O P # loop_