data_2ESJ # _entry.id 2ESJ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2ESJ pdb_00002esj 10.2210/pdb2esj/pdb NDB DR0022 ? ? RCSB RCSB035039 ? ? WWPDB D_1000035039 ? ? # 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 2005-12-20 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 # _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' entity 6 4 'Structure model' pdbx_entity_nonpoly 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.name' 2 4 'Structure model' '_chem_comp.pdbx_synonyms' 3 4 'Structure model' '_database_2.pdbx_DOI' 4 4 'Structure model' '_database_2.pdbx_database_accession' 5 4 'Structure model' '_entity.pdbx_description' 6 4 'Structure model' '_pdbx_entity_nonpoly.name' 7 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 8 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 9 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2ESJ _pdbx_database_status.recvd_initial_deposition_date 2005-10-26 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1J7T 'Complex between natural paromomycin and 16S Rrna A Site' unspecified PDB 2BEE 'Crystal structure of the Complex Between Paromomycin derivative JS4 and the 16S-Rrna A Site' unspecified PDB 2BE0 'Complex Between Paromomycin Derivative JS5-39 and the 16S-Rrna A-Site' unspecified PDB 2ESI 'Crystal structure of the complex between Kanamycin A and the 16S-Rrna A Site' unspecified # _audit_author.name 'Westhof, E.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title ;Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 33 _citation.page_first 5677 _citation.page_last 5690 _citation.year 2005 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16214802 _citation.pdbx_database_id_DOI 10.1093/nar/gki862 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Francois, B.' 1 ? primary 'Russel, R.J.M.' 2 ? primary 'Murray, J.B.' 3 ? primary 'Aboul-ela, F.' 4 ? primary 'Masquida, B.' 5 ? primary 'Vicens, Q.' 6 ? primary 'Westhof, E.' 7 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'" 7048.259 2 ? ? ? 'bacterial A-Site' 2 non-polymer syn ;(2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R ,5S,6R)-3-AMINO-5-HYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-4-HYDROXY-2-(HYDROXYMET HYL)-TETRAHYDROFURAN-3-YLOXY)-4-HYDROXY-TETRAHYDRO-2H-PYRAN-3-YLOXY)-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-3,4,5-TRIOL ; 761.770 2 ? ? ? ? 3 water nat water 18.015 90 ? ? ? ? # _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 CGCGUCACACCGGUGAAGUCGC _entity_poly.pdbx_seq_one_letter_code_can CGCGUCACACCGGUGAAGUCGC _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 ;(2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R ,5S,6R)-3-AMINO-5-HYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-4-HYDROXY-2-(HYDROXYMET HYL)-TETRAHYDROFURAN-3-YLOXY)-4-HYDROXY-TETRAHYDRO-2H-PYRAN-3-YLOXY)-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-3,4,5-TRIOL ; LIV 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 G n 1 3 C n 1 4 G n 1 5 U n 1 6 C n 1 7 A n 1 8 C n 1 9 A n 1 10 C n 1 11 C n 1 12 G n 1 13 G n 1 14 U n 1 15 G n 1 16 A n 1 17 A n 1 18 G n 1 19 U n 1 20 C n 1 21 G n 1 22 C n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 LIV non-polymer . ;(2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R ,5S,6R)-3-AMINO-5-HYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-4-HYDROXY-2-(HYDROXYMET HYL)-TETRAHYDROFURAN-3-YLOXY)-4-HYDROXY-TETRAHYDRO-2H-PYRAN-3-YLOXY)-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-3,4,5-TRIOL ; ;LIVIDOMYCIN A; O-2-AMINO-2,3-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL-(1,4)-O-[BETA-D-MANNOPYRANOSYL-(1,4)-O-2,6-DIAMINO-2,6-DIDEOXY-BETA-L-IDOPY RANOSYL-(1,3)-BETA-D-RIBOFURANOSYL-(1,5)-2-DEOXY-D-STREPTAMINE ; 'C29 H55 N5 O18' 761.770 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 C 1 1 ? ? ? A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 U 5 5 5 U U A . n A 1 6 C 6 6 6 C C 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 A 9 9 9 A A A . n A 1 10 C 10 10 10 C C A . n A 1 11 C 11 11 11 C C A . n A 1 12 G 12 12 12 G G A . n A 1 13 G 13 13 13 G G A . n A 1 14 U 14 14 14 U U A . n A 1 15 G 15 15 15 G G A . n A 1 16 A 16 16 16 A A A . n A 1 17 A 17 17 17 A A A . n A 1 18 G 18 18 18 G G A . n A 1 19 U 19 19 19 U U A . n A 1 20 C 20 20 20 C C A . n A 1 21 G 21 21 21 G G A . n A 1 22 C 22 22 22 C C A . n B 1 1 C 1 24 ? ? ? B . n B 1 2 G 2 25 25 G G B . n B 1 3 C 3 26 26 C C B . n B 1 4 G 4 27 27 G G B . n B 1 5 U 5 28 28 U U B . n B 1 6 C 6 29 29 C C B . n B 1 7 A 7 30 30 A A B . n B 1 8 C 8 31 31 C C B . n B 1 9 A 9 32 32 A A B . n B 1 10 C 10 33 33 C C B . n B 1 11 C 11 34 34 C C B . n B 1 12 G 12 35 35 G G B . n B 1 13 G 13 36 36 G G B . n B 1 14 U 14 37 37 U U B . n B 1 15 G 15 38 38 G G B . n B 1 16 A 16 39 39 A A B . n B 1 17 A 17 40 40 A A B . n B 1 18 G 18 41 41 G G B . n B 1 19 U 19 42 42 U U B . n B 1 20 C 20 43 43 C C B . n B 1 21 G 21 44 44 G G B . n B 1 22 C 22 45 45 C C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 LIV 1 50 50 LIV LIV A . D 2 LIV 1 51 51 LIV LIV B . E 3 HOH 1 101 101 HOH HOH A . E 3 HOH 2 107 107 HOH HOH A . E 3 HOH 3 108 108 HOH HOH A . E 3 HOH 4 112 112 HOH HOH A . E 3 HOH 5 117 117 HOH HOH A . E 3 HOH 6 125 125 HOH HOH A . E 3 HOH 7 126 126 HOH HOH A . E 3 HOH 8 132 132 HOH HOH A . E 3 HOH 9 135 135 HOH HOH A . E 3 HOH 10 136 136 HOH HOH A . E 3 HOH 11 138 138 HOH HOH A . E 3 HOH 12 140 140 HOH HOH A . E 3 HOH 13 141 141 HOH HOH A . E 3 HOH 14 147 147 HOH HOH A . E 3 HOH 15 148 148 HOH HOH A . E 3 HOH 16 149 149 HOH HOH A . E 3 HOH 17 152 152 HOH HOH A . E 3 HOH 18 153 153 HOH HOH A . E 3 HOH 19 154 154 HOH HOH A . E 3 HOH 20 156 156 HOH HOH A . E 3 HOH 21 160 160 HOH HOH A . E 3 HOH 22 163 163 HOH HOH A . E 3 HOH 23 165 165 HOH HOH A . E 3 HOH 24 166 166 HOH HOH A . E 3 HOH 25 169 169 HOH HOH A . E 3 HOH 26 175 175 HOH HOH A . E 3 HOH 27 176 176 HOH HOH A . E 3 HOH 28 177 177 HOH HOH A . E 3 HOH 29 179 179 HOH HOH A . E 3 HOH 30 180 180 HOH HOH A . E 3 HOH 31 182 182 HOH HOH A . E 3 HOH 32 183 183 HOH HOH A . E 3 HOH 33 187 187 HOH HOH A . F 3 HOH 1 100 100 HOH HOH B . F 3 HOH 2 102 102 HOH HOH B . F 3 HOH 3 103 103 HOH HOH B . F 3 HOH 4 104 104 HOH HOH B . F 3 HOH 5 105 105 HOH HOH B . F 3 HOH 6 106 106 HOH HOH B . F 3 HOH 7 109 109 HOH HOH B . F 3 HOH 8 110 110 HOH HOH B . F 3 HOH 9 111 111 HOH HOH B . F 3 HOH 10 113 113 HOH HOH B . F 3 HOH 11 114 114 HOH HOH B . F 3 HOH 12 115 115 HOH HOH B . F 3 HOH 13 116 116 HOH HOH B . F 3 HOH 14 118 118 HOH HOH B . F 3 HOH 15 119 119 HOH HOH B . F 3 HOH 16 120 120 HOH HOH B . F 3 HOH 17 121 121 HOH HOH B . F 3 HOH 18 122 122 HOH HOH B . F 3 HOH 19 123 123 HOH HOH B . F 3 HOH 20 124 124 HOH HOH B . F 3 HOH 21 127 127 HOH HOH B . F 3 HOH 22 128 128 HOH HOH B . F 3 HOH 23 129 129 HOH HOH B . F 3 HOH 24 130 130 HOH HOH B . F 3 HOH 25 131 131 HOH HOH B . F 3 HOH 26 133 133 HOH HOH B . F 3 HOH 27 134 134 HOH HOH B . F 3 HOH 28 137 137 HOH HOH B . F 3 HOH 29 139 139 HOH HOH B . F 3 HOH 30 142 142 HOH HOH B . F 3 HOH 31 143 143 HOH HOH B . F 3 HOH 32 144 144 HOH HOH B . F 3 HOH 33 145 145 HOH HOH B . F 3 HOH 34 146 146 HOH HOH B . F 3 HOH 35 150 150 HOH HOH B . F 3 HOH 36 151 151 HOH HOH B . F 3 HOH 37 155 155 HOH HOH B . F 3 HOH 38 157 157 HOH HOH B . F 3 HOH 39 158 158 HOH HOH B . F 3 HOH 40 159 159 HOH HOH B . F 3 HOH 41 161 161 HOH HOH B . F 3 HOH 42 162 162 HOH HOH B . F 3 HOH 43 164 164 HOH HOH B . F 3 HOH 44 167 167 HOH HOH B . F 3 HOH 45 168 168 HOH HOH B . F 3 HOH 46 170 170 HOH HOH B . F 3 HOH 47 171 171 HOH HOH B . F 3 HOH 48 172 172 HOH HOH B . F 3 HOH 49 173 173 HOH HOH B . F 3 HOH 50 174 174 HOH HOH B . F 3 HOH 51 178 178 HOH HOH B . F 3 HOH 52 181 181 HOH HOH B . F 3 HOH 53 184 184 HOH HOH B . F 3 HOH 54 185 185 HOH HOH B . F 3 HOH 55 186 186 HOH HOH B . F 3 HOH 56 188 188 HOH HOH B . F 3 HOH 57 189 189 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 SCALEPACK 'data scaling' . ? 2 AMoRE phasing . ? 3 CNS refinement 1.1 ? 4 HKL-2000 'data reduction' . ? 5 # _cell.entry_id 2ESJ _cell.length_a 33.660 _cell.length_b 44.561 _cell.length_c 95.580 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ESJ _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 2ESJ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.54 _exptl_crystal.density_percent_sol 51.62 _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.temp 310 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.4 _exptl_crystal_grow.pdbx_details 'MPD, NACL, MGSO4, GLYCEROL, NA CACODYLATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K' _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 MPD ? ? ? 1 2 1 NACL ? ? ? 1 3 1 MGSO4 ? ? ? 1 4 1 GLYCEROL ? ? ? 1 5 1 'NA CACODYLATE' ? ? ? 1 6 1 H2O ? ? ? 1 7 2 MPD ? ? ? 1 8 2 NACL ? ? ? 1 9 2 MGSO4 ? ? ? 1 10 2 'NA CACODYLATE' ? ? ? 1 11 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.936 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.936 # _reflns.entry_id 2ESJ _reflns.observed_criterion_sigma_I 5 _reflns.observed_criterion_sigma_F 5 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.1 _reflns.number_obs 7759 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 2ESJ _refine.ls_number_reflns_obs 6628 _refine.ls_number_reflns_all 7759 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 30.0 _refine.ls_d_res_high 2.2 _refine.ls_percent_reflns_obs 85.4 _refine.ls_R_factor_obs 0.228 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.228 _refine.ls_R_factor_R_free 0.275 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 728 _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 ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _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.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_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_analyze.entry_id 2ESJ _refine_analyze.Luzzati_coordinate_error_obs 0.34 _refine_analyze.Luzzati_sigma_a_obs 0.30 _refine_analyze.Luzzati_d_res_low_obs 3.0 _refine_analyze.Luzzati_coordinate_error_free 0.40 _refine_analyze.Luzzati_sigma_a_free 0.23 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 898 _refine_hist.pdbx_number_atoms_ligand 104 _refine_hist.number_atoms_solvent 90 _refine_hist.number_atoms_total 1092 _refine_hist.d_res_high 2.2 _refine_hist.d_res_low 30.0 # 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 c_bond_d 0.0079 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d 1.309 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 12.812 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 2.00 ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 2ESJ _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 2ESJ _struct.title 'Complex between Lividomycin A and the 16S-Rrna A Site' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2ESJ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA-AMINOGLYCOSIDE INTERACTIONS, A SITE, UOU PAIRS, AA BULGES, 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 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2ESJ _struct_ref.pdbx_db_accession 2ESJ _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 2ESJ A 1 ? 22 ? 2ESJ 1 ? 22 ? 1 22 2 1 2ESJ B 1 ? 22 ? 2ESJ 24 ? 45 ? 24 45 # _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 # _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 hydrog1 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 22 N3 ? ? A G 2 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 22 O2 ? ? A G 2 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 22 N4 ? ? A G 2 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 21 N1 ? ? A C 3 B G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 21 O6 ? ? A C 3 B G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 21 N2 ? ? A C 3 B G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 20 N3 ? ? A G 4 B C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 20 O2 ? ? A G 4 B C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 20 N4 ? ? A G 4 B C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 5 O4 ? ? ? 1_555 B U 19 N3 ? ? A U 5 B U 42 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog11 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 18 N1 ? ? A C 6 B G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 18 O6 ? ? A C 6 B G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 18 N2 ? ? A C 6 B G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 15 N1 ? ? A C 8 B G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 15 O6 ? ? A C 8 B G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 15 N2 ? ? A C 8 B G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 14 N3 ? ? A A 9 B U 37 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog18 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 10 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 10 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 10 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 11 B G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 11 B G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 11 B G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 12 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 12 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 12 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 13 B C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 13 B C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 13 B C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 14 N3 ? ? ? 1_555 B A 9 N1 ? ? A U 14 B A 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 14 O4 ? ? ? 1_555 B A 9 N6 ? ? A U 14 B A 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 15 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 15 B C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 15 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 15 B C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 15 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 15 B C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 18 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 18 B C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 18 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 18 B C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 18 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 18 B C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A U 19 N3 ? ? ? 1_555 B U 5 O4 ? ? A U 19 B U 28 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog39 hydrog ? ? A C 20 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 20 B G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 20 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 20 B G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 20 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 20 B G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 21 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 21 B C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 21 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 21 B C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 21 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 21 B C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 22 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 22 B G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 22 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 22 B G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 22 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 22 B G 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A LIV 50 ? 12 'BINDING SITE FOR RESIDUE LIV A 50' AC2 Software B LIV 51 ? 22 'BINDING SITE FOR RESIDUE LIV B 51' 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 12 U A 14 ? U A 14 . ? 1_555 ? 2 AC1 12 G A 15 ? G A 15 . ? 1_555 ? 3 AC1 12 A A 17 ? A A 17 . ? 1_555 ? 4 AC1 12 G A 18 ? G A 18 . ? 1_555 ? 5 AC1 12 U A 19 ? U A 19 . ? 1_555 ? 6 AC1 12 HOH E . ? HOH A 101 . ? 1_555 ? 7 AC1 12 HOH E . ? HOH A 117 . ? 1_555 ? 8 AC1 12 C B 3 ? C B 26 . ? 1_555 ? 9 AC1 12 G B 4 ? G B 27 . ? 1_555 ? 10 AC1 12 C B 6 ? C B 29 . ? 1_555 ? 11 AC1 12 A B 7 ? A B 30 . ? 1_555 ? 12 AC1 12 HOH F . ? HOH B 100 . ? 1_555 ? 13 AC2 22 C A 3 ? C A 3 . ? 1_555 ? 14 AC2 22 G A 4 ? G A 4 . ? 1_555 ? 15 AC2 22 U A 5 ? U A 5 . ? 1_555 ? 16 AC2 22 C A 6 ? C A 6 . ? 1_555 ? 17 AC2 22 A A 7 ? A A 7 . ? 1_555 ? 18 AC2 22 C A 20 ? C A 20 . ? 1_565 ? 19 AC2 22 U B 14 ? U B 37 . ? 1_555 ? 20 AC2 22 G B 15 ? G B 38 . ? 1_555 ? 21 AC2 22 A B 16 ? A B 39 . ? 1_555 ? 22 AC2 22 A B 17 ? A B 40 . ? 1_555 ? 23 AC2 22 G B 18 ? G B 41 . ? 1_555 ? 24 AC2 22 U B 19 ? U B 42 . ? 1_555 ? 25 AC2 22 HOH F . ? HOH B 105 . ? 1_555 ? 26 AC2 22 HOH F . ? HOH B 113 . ? 1_555 ? 27 AC2 22 HOH F . ? HOH B 124 . ? 1_555 ? 28 AC2 22 HOH F . ? HOH B 128 . ? 1_555 ? 29 AC2 22 HOH F . ? HOH B 129 . ? 1_555 ? 30 AC2 22 HOH F . ? HOH B 130 . ? 1_555 ? 31 AC2 22 HOH F . ? HOH B 137 . ? 1_555 ? 32 AC2 22 HOH F . ? HOH B 143 . ? 1_555 ? 33 AC2 22 HOH F . ? HOH B 170 . ? 1_555 ? 34 AC2 22 HOH F . ? HOH B 189 . ? 1_555 ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "C5'" _pdbx_validate_rmsd_angle.auth_asym_id_1 B _pdbx_validate_rmsd_angle.auth_comp_id_1 C _pdbx_validate_rmsd_angle.auth_seq_id_1 29 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C4'" _pdbx_validate_rmsd_angle.auth_asym_id_2 B _pdbx_validate_rmsd_angle.auth_comp_id_2 C _pdbx_validate_rmsd_angle.auth_seq_id_2 29 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 "C3'" _pdbx_validate_rmsd_angle.auth_asym_id_3 B _pdbx_validate_rmsd_angle.auth_comp_id_3 C _pdbx_validate_rmsd_angle.auth_seq_id_3 29 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 106.25 _pdbx_validate_rmsd_angle.angle_target_value 115.20 _pdbx_validate_rmsd_angle.angle_deviation -8.95 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.40 _pdbx_validate_rmsd_angle.linker_flag N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id A _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 40 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.057 _pdbx_validate_planes.type 'SIDE CHAIN' # _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 C 1 ? A C 1 2 1 Y 1 B C 24 ? B C 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 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 LIV C11 C N S 114 LIV O11 O N N 115 LIV C21 C N R 116 LIV N21 N N N 117 LIV C31 C N N 118 LIV C41 C N S 119 LIV O41 O N N 120 LIV C51 C N R 121 LIV O51 O N N 122 LIV C61 C N N 123 LIV O61 O N N 124 LIV C12 C N R 125 LIV N12 N N N 126 LIV C62 C N S 127 LIV O62 O N N 128 LIV C52 C N R 129 LIV O52 O N N 130 LIV C42 C N R 131 LIV C32 C N S 132 LIV N32 N N N 133 LIV C22 C N N 134 LIV C13 C N S 135 LIV C23 C N R 136 LIV O23 O N N 137 LIV C33 C N S 138 LIV C43 C N R 139 LIV O43 O N N 140 LIV C53 C N N 141 LIV O53 O N N 142 LIV C44 C N S 143 LIV O44 O N N 144 LIV C34 C N R 145 LIV O34 O N N 146 LIV C24 C N R 147 LIV N24 N N N 148 LIV C14 C N R 149 LIV O33 O N N 150 LIV C54 C N S 151 LIV O54 O N N 152 LIV C64 C N N 153 LIV N64 N N N 154 LIV C15 C N R 155 LIV C25 C N S 156 LIV C35 C N S 157 LIV C45 C N S 158 LIV C55 C N R 159 LIV C65 C N N 160 LIV O25 O N N 161 LIV O35 O N N 162 LIV O45 O N N 163 LIV O55 O N N 164 LIV O65 O N N 165 LIV H11 H N N 166 LIV H21 H N N 167 LIV H211 H N N 168 LIV H212 H N N 169 LIV H311 H N N 170 LIV H312 H N N 171 LIV H41 H N N 172 LIV H3 H N N 173 LIV H51 H N N 174 LIV H611 H N N 175 LIV H612 H N N 176 LIV H61 H N N 177 LIV H12 H N N 178 LIV H121 H N N 179 LIV H122 H N N 180 LIV H62 H N N 181 LIV H2 H N N 182 LIV H52 H N N 183 LIV H42 H N N 184 LIV H32 H N N 185 LIV H321 H N N 186 LIV H322 H N N 187 LIV H221 H N N 188 LIV H222 H N N 189 LIV H13 H N N 190 LIV H23 H N N 191 LIV H1 H N N 192 LIV H33 H N N 193 LIV H43 H N N 194 LIV H531 H N N 195 LIV H532 H N N 196 LIV H53 H N N 197 LIV H44 H N N 198 LIV H34 H N N 199 LIV H4 H N N 200 LIV H24 H N N 201 LIV H241 H N N 202 LIV H242 H N N 203 LIV H14 H N N 204 LIV H54 H N N 205 LIV H11A H N N 206 LIV H12A H N N 207 LIV H641 H N N 208 LIV H642 H N N 209 LIV H15 H N N 210 LIV H25 H N N 211 LIV H35 H N N 212 LIV H45 H N N 213 LIV H55 H N N 214 LIV H651 H N N 215 LIV H652 H N N 216 LIV H7 H N N 217 LIV H6 H N N 218 LIV H5 H N N 219 LIV H65 H N N 220 U OP3 O N N 221 U P P N N 222 U OP1 O N N 223 U OP2 O N N 224 U "O5'" O N N 225 U "C5'" C N N 226 U "C4'" C N R 227 U "O4'" O N N 228 U "C3'" C N S 229 U "O3'" O N N 230 U "C2'" C N R 231 U "O2'" O N N 232 U "C1'" C N R 233 U N1 N N N 234 U C2 C N N 235 U O2 O N N 236 U N3 N N N 237 U C4 C N N 238 U O4 O N N 239 U C5 C N N 240 U C6 C N N 241 U HOP3 H N N 242 U HOP2 H N N 243 U "H5'" H N N 244 U "H5''" H N N 245 U "H4'" H N N 246 U "H3'" H N N 247 U "HO3'" H N N 248 U "H2'" H N N 249 U "HO2'" H N N 250 U "H1'" H N N 251 U H3 H N N 252 U H5 H N N 253 U H6 H N N 254 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 LIV C11 O11 sing N N 118 LIV C11 C21 sing N N 119 LIV C11 O51 sing N N 120 LIV C11 H11 sing N N 121 LIV O11 C42 sing N N 122 LIV C21 N21 sing N N 123 LIV C21 C31 sing N N 124 LIV C21 H21 sing N N 125 LIV N21 H211 sing N N 126 LIV N21 H212 sing N N 127 LIV C31 C41 sing N N 128 LIV C31 H311 sing N N 129 LIV C31 H312 sing N N 130 LIV C41 O41 sing N N 131 LIV C41 C51 sing N N 132 LIV C41 H41 sing N N 133 LIV O41 H3 sing N N 134 LIV C51 O51 sing N N 135 LIV C51 C61 sing N N 136 LIV C51 H51 sing N N 137 LIV C61 O61 sing N N 138 LIV C61 H611 sing N N 139 LIV C61 H612 sing N N 140 LIV O61 H61 sing N N 141 LIV C12 N12 sing N N 142 LIV C12 C62 sing N N 143 LIV C12 C22 sing N N 144 LIV C12 H12 sing N N 145 LIV N12 H121 sing N N 146 LIV N12 H122 sing N N 147 LIV C62 O62 sing N N 148 LIV C62 C52 sing N N 149 LIV C62 H62 sing N N 150 LIV O62 H2 sing N N 151 LIV C52 O52 sing N N 152 LIV C52 C42 sing N N 153 LIV C52 H52 sing N N 154 LIV O52 C13 sing N N 155 LIV C42 C32 sing N N 156 LIV C42 H42 sing N N 157 LIV C32 N32 sing N N 158 LIV C32 C22 sing N N 159 LIV C32 H32 sing N N 160 LIV N32 H321 sing N N 161 LIV N32 H322 sing N N 162 LIV C22 H221 sing N N 163 LIV C22 H222 sing N N 164 LIV C13 C23 sing N N 165 LIV C13 O43 sing N N 166 LIV C13 H13 sing N N 167 LIV C23 O23 sing N N 168 LIV C23 C33 sing N N 169 LIV C23 H23 sing N N 170 LIV O23 H1 sing N N 171 LIV C33 C43 sing N N 172 LIV C33 O33 sing N N 173 LIV C33 H33 sing N N 174 LIV C43 O43 sing N N 175 LIV C43 C53 sing N N 176 LIV C43 H43 sing N N 177 LIV C53 O53 sing N N 178 LIV C53 H531 sing N N 179 LIV C53 H532 sing N N 180 LIV O53 H53 sing N N 181 LIV C44 O44 sing N N 182 LIV C44 C34 sing N N 183 LIV C44 C54 sing N N 184 LIV C44 H44 sing N N 185 LIV O44 C15 sing N N 186 LIV C34 O34 sing N N 187 LIV C34 C24 sing N N 188 LIV C34 H34 sing N N 189 LIV O34 H4 sing N N 190 LIV C24 N24 sing N N 191 LIV C24 C14 sing N N 192 LIV C24 H24 sing N N 193 LIV N24 H241 sing N N 194 LIV N24 H242 sing N N 195 LIV C14 O33 sing N N 196 LIV C14 O54 sing N N 197 LIV C14 H14 sing N N 198 LIV C54 O54 sing N N 199 LIV C54 C64 sing N N 200 LIV C54 H54 sing N N 201 LIV C64 N64 sing N N 202 LIV C64 H11A sing N N 203 LIV C64 H12A sing N N 204 LIV N64 H641 sing N N 205 LIV N64 H642 sing N N 206 LIV C15 C25 sing N N 207 LIV C15 O55 sing N N 208 LIV C15 H15 sing N N 209 LIV C25 C35 sing N N 210 LIV C25 O25 sing N N 211 LIV C25 H25 sing N N 212 LIV C35 C45 sing N N 213 LIV C35 O35 sing N N 214 LIV C35 H35 sing N N 215 LIV C45 C55 sing N N 216 LIV C45 O45 sing N N 217 LIV C45 H45 sing N N 218 LIV C55 C65 sing N N 219 LIV C55 O55 sing N N 220 LIV C55 H55 sing N N 221 LIV C65 O65 sing N N 222 LIV C65 H651 sing N N 223 LIV C65 H652 sing N N 224 LIV O25 H7 sing N N 225 LIV O35 H6 sing N N 226 LIV O45 H5 sing N N 227 LIV O65 H65 sing N N 228 U OP3 P sing N N 229 U OP3 HOP3 sing N N 230 U P OP1 doub N N 231 U P OP2 sing N N 232 U P "O5'" sing N N 233 U OP2 HOP2 sing N N 234 U "O5'" "C5'" sing N N 235 U "C5'" "C4'" sing N N 236 U "C5'" "H5'" sing N N 237 U "C5'" "H5''" sing N N 238 U "C4'" "O4'" sing N N 239 U "C4'" "C3'" sing N N 240 U "C4'" "H4'" sing N N 241 U "O4'" "C1'" sing N N 242 U "C3'" "O3'" sing N N 243 U "C3'" "C2'" sing N N 244 U "C3'" "H3'" sing N N 245 U "O3'" "HO3'" sing N N 246 U "C2'" "O2'" sing N N 247 U "C2'" "C1'" sing N N 248 U "C2'" "H2'" sing N N 249 U "O2'" "HO2'" sing N N 250 U "C1'" N1 sing N N 251 U "C1'" "H1'" sing N N 252 U N1 C2 sing N N 253 U N1 C6 sing N N 254 U C2 O2 doub N N 255 U C2 N3 sing N N 256 U N3 C4 sing N N 257 U N3 H3 sing N N 258 U C4 O4 doub N N 259 U C4 C5 sing N N 260 U C5 C6 doub N N 261 U C5 H5 sing N N 262 U C6 H6 sing N N 263 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2ESJ 'double helix' 2ESJ 'a-form double helix' 2ESJ 'mismatched base pair' 2ESJ '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 2 1_555 B C 22 1_555 -0.810 -0.459 0.238 6.294 -7.248 1.734 1 A_G2:C45_B A 2 ? B 45 ? 19 1 1 A C 3 1_555 B G 21 1_555 -0.502 -0.377 0.024 0.500 -12.299 -2.616 2 A_C3:G44_B A 3 ? B 44 ? 19 1 1 A G 4 1_555 B C 20 1_555 -0.168 -0.178 -0.126 -2.913 -11.418 0.274 3 A_G4:C43_B A 4 ? B 43 ? 19 1 1 A U 5 1_555 B U 19 1_555 -2.294 -1.045 -0.684 8.509 -12.512 -26.249 4 A_U5:U42_B A 5 ? B 42 ? ? ? 1 A C 6 1_555 B G 18 1_555 0.320 -0.187 -0.288 3.710 -5.557 1.302 5 A_C6:G41_B A 6 ? B 41 ? 19 1 1 A C 8 1_555 B G 15 1_555 0.199 -0.152 0.164 5.875 -16.787 2.257 6 A_C8:G38_B A 8 ? B 38 ? 19 1 1 A A 9 1_555 B U 14 1_555 0.145 0.105 0.550 7.441 -16.173 12.370 7 A_A9:U37_B A 9 ? B 37 ? ? 1 1 A C 10 1_555 B G 13 1_555 0.485 -0.084 -0.073 16.058 -23.102 0.103 8 A_C10:G36_B A 10 ? B 36 ? 19 1 1 A C 11 1_555 B G 12 1_555 0.343 -0.144 0.285 -0.375 -12.007 -4.328 9 A_C11:G35_B A 11 ? B 35 ? 19 1 1 A G 12 1_555 B C 11 1_555 -0.036 -0.463 0.219 -0.921 -11.759 -4.715 10 A_G12:C34_B A 12 ? B 34 ? 19 1 1 A G 13 1_555 B C 10 1_555 -0.115 -0.093 0.086 -6.738 -19.421 2.260 11 A_G13:C33_B A 13 ? B 33 ? 19 1 1 A U 14 1_555 B A 9 1_555 0.357 -0.272 0.579 -4.486 -14.562 1.186 12 A_U14:A32_B A 14 ? B 32 ? 20 1 1 A G 15 1_555 B C 8 1_555 -0.318 -0.189 -0.170 -5.554 -17.199 1.836 13 A_G15:C31_B A 15 ? B 31 ? 19 1 1 A G 18 1_555 B C 6 1_555 -0.089 -0.069 -0.015 -1.377 -3.390 1.263 14 A_G18:C29_B A 18 ? B 29 ? 19 1 1 A U 19 1_555 B U 5 1_555 2.141 -1.201 -0.115 -5.856 -7.744 -29.741 15 A_U19:U28_B A 19 ? B 28 ? ? ? 1 A C 20 1_555 B G 4 1_555 0.721 -0.211 0.016 -4.655 -7.187 0.830 16 A_C20:G27_B A 20 ? B 27 ? 19 1 1 A G 21 1_555 B C 3 1_555 0.261 -0.314 0.162 -2.830 -9.777 0.127 17 A_G21:C26_B A 21 ? B 26 ? 19 1 1 A C 22 1_555 B G 2 1_555 0.703 -0.292 0.091 -1.279 -11.931 1.191 18 A_C22:G25_B A 22 ? B 25 ? 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 2 1_555 B C 22 1_555 A C 3 1_555 B G 21 1_555 -0.652 -1.648 3.347 -2.263 4.636 33.244 -3.603 0.759 3.131 8.043 3.926 33.631 1 AA_G2C3:G44C45_BB A 2 ? B 45 ? A 3 ? B 44 ? 1 A C 3 1_555 B G 21 1_555 A G 4 1_555 B C 20 1_555 -0.156 -1.604 3.242 1.930 9.861 35.983 -3.716 0.481 2.712 15.591 -3.051 37.315 2 AA_C3G4:C43G44_BB A 3 ? B 44 ? A 4 ? B 43 ? 1 A G 4 1_555 B C 20 1_555 A U 5 1_555 B U 19 1_555 -0.761 -1.926 3.052 2.545 3.102 22.080 -5.960 2.784 2.656 8.014 -6.574 22.437 3 AA_G4U5:U42C43_BB A 4 ? B 43 ? A 5 ? B 42 ? 1 A U 5 1_555 B U 19 1_555 A C 6 1_555 B G 18 1_555 2.381 -2.395 3.450 -0.573 3.973 40.348 -3.907 -3.501 3.177 5.743 0.828 40.539 4 AA_U5C6:G41U42_BB A 5 ? B 42 ? A 6 ? B 41 ? 1 A C 8 1_555 B G 15 1_555 A A 9 1_555 B U 14 1_555 0.636 -1.744 2.863 -1.013 11.424 31.678 -4.475 -1.228 2.105 20.121 1.785 33.640 5 AA_C8A9:U37G38_BB A 8 ? B 38 ? A 9 ? B 37 ? 1 A A 9 1_555 B U 14 1_555 A C 10 1_555 B G 13 1_555 -0.804 -0.950 2.906 4.008 6.332 31.636 -2.637 2.031 2.555 11.416 -7.226 32.489 6 AA_A9C10:G36U37_BB A 9 ? B 37 ? A 10 ? B 36 ? 1 A C 10 1_555 B G 13 1_555 A C 11 1_555 B G 12 1_555 -0.402 -1.853 3.570 -4.734 7.667 35.124 -4.102 -0.046 3.136 12.452 7.690 36.226 7 AA_C10C11:G35G36_BB A 10 ? B 36 ? A 11 ? B 35 ? 1 A C 11 1_555 B G 12 1_555 A G 12 1_555 B C 11 1_555 -0.565 -2.263 3.142 -0.544 8.696 24.559 -7.042 1.129 2.234 19.670 1.230 26.036 8 AA_C11G12:C34G35_BB A 11 ? B 35 ? A 12 ? B 34 ? 1 A G 12 1_555 B C 11 1_555 A G 13 1_555 B C 10 1_555 -0.002 -1.402 3.305 -0.913 7.544 33.622 -3.500 -0.134 2.930 12.840 1.553 34.446 9 AA_G12G13:C33C34_BB A 12 ? B 34 ? A 13 ? B 33 ? 1 A G 13 1_555 B C 10 1_555 A U 14 1_555 B A 9 1_555 0.124 -1.100 3.153 -4.932 6.023 34.156 -2.675 -0.899 2.878 10.092 8.264 35.006 10 AA_G13U14:A32C33_BB A 13 ? B 33 ? A 14 ? B 32 ? 1 A U 14 1_555 B A 9 1_555 A G 15 1_555 B C 8 1_555 -0.188 -1.808 3.163 4.816 7.624 31.644 -4.370 1.074 2.612 13.638 -8.615 32.872 11 AA_U14G15:C31A32_BB A 14 ? B 32 ? A 15 ? B 31 ? 1 A G 15 1_555 B C 8 1_555 A G 18 1_555 B C 6 1_555 -1.370 -3.594 6.363 9.624 19.725 78.972 -3.672 1.498 5.338 15.241 -7.436 81.482 12 AA_G15G18:C29C31_BB A 15 ? B 31 ? A 18 ? B 29 ? 1 A G 18 1_555 B C 6 1_555 A U 19 1_555 B U 5 1_555 -2.185 -2.661 3.404 -1.330 1.003 39.832 -4.023 3.044 3.407 1.472 1.952 39.865 13 AA_G18U19:U28C29_BB A 18 ? B 29 ? A 19 ? B 28 ? 1 A U 19 1_555 B U 5 1_555 A C 20 1_555 B G 4 1_555 0.821 -2.227 3.136 0.357 4.553 26.105 -5.947 -1.706 2.726 9.982 -0.782 26.494 14 AA_U19C20:G27U28_BB A 19 ? B 28 ? A 20 ? B 27 ? 1 A C 20 1_555 B G 4 1_555 A G 21 1_555 B C 3 1_555 0.089 -1.723 3.027 -1.369 8.647 31.049 -4.422 -0.369 2.464 15.764 2.496 32.231 15 AA_C20G21:C26G27_BB A 20 ? B 27 ? A 21 ? B 26 ? 1 A G 21 1_555 B C 3 1_555 A C 22 1_555 B G 2 1_555 0.353 -1.590 3.265 4.172 3.251 35.495 -3.038 0.014 3.132 5.296 -6.796 35.874 16 AA_G21C22:G25C26_BB A 21 ? B 26 ? A 22 ? B 25 ? # _atom_sites.entry_id 2ESJ _atom_sites.fract_transf_matrix[1][1] 0.029709 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.022441 _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] 0.010462 _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 N O P # loop_