data_397D # _entry.id 397D # _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 397D pdb_0000397d 10.2210/pdb397d/pdb RCSB URX075 ? ? WWPDB D_1000178861 ? ? # 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 1998-09-11 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-21 # _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' # 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_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_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.ptnr1_label_atom_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.value' 18 4 'Structure model' '_struct_conn.pdbx_dist_value' 19 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 20 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 25 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 26 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 27 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 31 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 32 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 33 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 34 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 397D _pdbx_database_status.recvd_initial_deposition_date 1998-04-30 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _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_ _audit_author.name _audit_author.pdbx_ordinal 'Ippolito, J.A.' 1 'Steitz, T.A.' 2 # _citation.id primary _citation.title ;A 1.3-A resolution crystal structure of the HIV-1 trans-activation response region RNA stem reveals a metal ion-dependent bulge conformation. ; _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 95 _citation.page_first 9819 _citation.page_last 9824 _citation.year 1998 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9707559 _citation.pdbx_database_id_DOI 10.1073/pnas.95.17.9819 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ippolito, J.A.' 1 ? primary 'Steitz, T.A.' 2 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;RNA (5'-R(*GP*GP*CP*CP*AP*GP*AP*UP*CP*UP*GP*AP*GP*CP*G)-3') ; 4846.954 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*GP*CP*UP*CP*UP*CP*UP*GP*GP*CP*CP*C)-3') ; 3740.248 1 ? ? ? ? 3 non-polymer syn 'CALCIUM ION' 40.078 4 ? ? ? ? 4 water nat water 18.015 178 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no GGCCAGAUCUGAGCG GGCCAGAUCUGAGCG A ? 2 polyribonucleotide no no GCUCUCUGGCCC GCUCUCUGGCCC B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'CALCIUM ION' CA 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 G n 1 3 C n 1 4 C n 1 5 A n 1 6 G n 1 7 A n 1 8 U n 1 9 C n 1 10 U n 1 11 G n 1 12 A n 1 13 G n 1 14 C n 1 15 G n 2 1 G n 2 2 C n 2 3 U n 2 4 C n 2 5 U n 2 6 C n 2 7 U n 2 8 G n 2 9 G n 2 10 C n 2 11 C n 2 12 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 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 G 1 16 16 G G A . n A 1 2 G 2 17 17 G G A . n A 1 3 C 3 18 18 C C A . n A 1 4 C 4 19 19 C C A . n A 1 5 A 5 20 20 A A A . n A 1 6 G 6 21 21 G G A . n A 1 7 A 7 22 22 A A A . n A 1 8 U 8 23 23 U U A . n A 1 9 C 9 24 24 C C A . n A 1 10 U 10 25 25 U U A . n A 1 11 G 11 26 26 G G A . n A 1 12 A 12 27 27 A A A . n A 1 13 G 13 28 28 G G A . n A 1 14 C 14 29 29 C C A . n A 1 15 G 15 30 30 G G A . n B 2 1 G 1 36 36 G G B . n B 2 2 C 2 37 37 C C B . n B 2 3 U 3 38 38 U U B . n B 2 4 C 4 39 39 C C B . n B 2 5 U 5 40 40 U U B . n B 2 6 C 6 41 41 C C B . n B 2 7 U 7 42 42 U U B . n B 2 8 G 8 43 43 G G B . n B 2 9 G 9 44 44 G G B . n B 2 10 C 10 45 45 C C B . n B 2 11 C 11 46 46 C C B . n B 2 12 C 12 47 47 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 3 CA 1 48 48 CA CA A . D 3 CA 1 49 49 CA CA A . E 3 CA 1 51 51 CA CA A . F 3 CA 1 50 50 CA CA A . G 4 HOH 1 52 52 HOH HOH A . G 4 HOH 2 53 53 HOH HOH A . G 4 HOH 3 54 54 HOH HOH A . G 4 HOH 4 55 55 HOH HOH A . G 4 HOH 5 56 56 HOH HOH A . G 4 HOH 6 57 57 HOH HOH A . G 4 HOH 7 58 58 HOH HOH A . G 4 HOH 8 59 59 HOH HOH A . G 4 HOH 9 60 60 HOH HOH A . G 4 HOH 10 61 61 HOH HOH A . G 4 HOH 11 62 62 HOH HOH A . G 4 HOH 12 63 63 HOH HOH A . G 4 HOH 13 64 64 HOH HOH A . G 4 HOH 14 65 65 HOH HOH A . G 4 HOH 15 66 66 HOH HOH A . G 4 HOH 16 67 67 HOH HOH A . G 4 HOH 17 68 68 HOH HOH A . G 4 HOH 18 69 69 HOH HOH A . G 4 HOH 19 70 70 HOH HOH A . G 4 HOH 20 71 71 HOH HOH A . G 4 HOH 21 72 72 HOH HOH A . G 4 HOH 22 73 73 HOH HOH A . G 4 HOH 23 74 74 HOH HOH A . G 4 HOH 24 76 76 HOH HOH A . G 4 HOH 25 77 77 HOH HOH A . G 4 HOH 26 81 81 HOH HOH A . G 4 HOH 27 82 82 HOH HOH A . G 4 HOH 28 83 83 HOH HOH A . G 4 HOH 29 84 84 HOH HOH A . G 4 HOH 30 85 85 HOH HOH A . G 4 HOH 31 86 86 HOH HOH A . G 4 HOH 32 91 91 HOH HOH A . G 4 HOH 33 92 92 HOH HOH A . G 4 HOH 34 93 93 HOH HOH A . G 4 HOH 35 94 94 HOH HOH A . G 4 HOH 36 96 96 HOH HOH A . G 4 HOH 37 97 97 HOH HOH A . G 4 HOH 38 98 98 HOH HOH A . G 4 HOH 39 99 99 HOH HOH A . G 4 HOH 40 100 100 HOH HOH A . G 4 HOH 41 101 101 HOH HOH A . G 4 HOH 42 104 104 HOH HOH A . G 4 HOH 43 105 105 HOH HOH A . G 4 HOH 44 106 106 HOH HOH A . G 4 HOH 45 107 107 HOH HOH A . G 4 HOH 46 110 110 HOH HOH A . G 4 HOH 47 111 111 HOH HOH A . G 4 HOH 48 112 112 HOH HOH A . G 4 HOH 49 113 113 HOH HOH A . G 4 HOH 50 115 115 HOH HOH A . G 4 HOH 51 116 116 HOH HOH A . G 4 HOH 52 122 122 HOH HOH A . G 4 HOH 53 123 123 HOH HOH A . G 4 HOH 54 124 124 HOH HOH A . G 4 HOH 55 127 127 HOH HOH A . G 4 HOH 56 128 128 HOH HOH A . G 4 HOH 57 129 129 HOH HOH A . G 4 HOH 58 131 131 HOH HOH A . G 4 HOH 59 135 135 HOH HOH A . G 4 HOH 60 136 136 HOH HOH A . G 4 HOH 61 140 140 HOH HOH A . G 4 HOH 62 141 141 HOH HOH A . G 4 HOH 63 142 142 HOH HOH A . G 4 HOH 64 144 144 HOH HOH A . G 4 HOH 65 145 145 HOH HOH A . G 4 HOH 66 148 148 HOH HOH A . G 4 HOH 67 149 149 HOH HOH A . G 4 HOH 68 153 153 HOH HOH A . G 4 HOH 69 154 154 HOH HOH A . G 4 HOH 70 155 155 HOH HOH A . G 4 HOH 71 156 156 HOH HOH A . G 4 HOH 72 157 157 HOH HOH A . G 4 HOH 73 158 158 HOH HOH A . G 4 HOH 74 159 159 HOH HOH A . G 4 HOH 75 164 164 HOH HOH A . G 4 HOH 76 165 165 HOH HOH A . G 4 HOH 77 166 166 HOH HOH A . G 4 HOH 78 167 167 HOH HOH A . G 4 HOH 79 168 168 HOH HOH A . G 4 HOH 80 169 169 HOH HOH A . G 4 HOH 81 170 170 HOH HOH A . G 4 HOH 82 172 172 HOH HOH A . G 4 HOH 83 173 173 HOH HOH A . G 4 HOH 84 176 176 HOH HOH A . G 4 HOH 85 178 178 HOH HOH A . G 4 HOH 86 179 179 HOH HOH A . G 4 HOH 87 181 181 HOH HOH A . G 4 HOH 88 182 182 HOH HOH A . G 4 HOH 89 183 183 HOH HOH A . G 4 HOH 90 189 189 HOH HOH A . G 4 HOH 91 193 193 HOH HOH A . G 4 HOH 92 195 195 HOH HOH A . G 4 HOH 93 196 196 HOH HOH A . G 4 HOH 94 201 201 HOH HOH A . G 4 HOH 95 203 203 HOH HOH A . G 4 HOH 96 205 205 HOH HOH A . G 4 HOH 97 206 206 HOH HOH A . G 4 HOH 98 207 207 HOH HOH A . G 4 HOH 99 208 208 HOH HOH A . G 4 HOH 100 209 209 HOH HOH A . G 4 HOH 101 210 210 HOH HOH A . G 4 HOH 102 214 214 HOH HOH A . G 4 HOH 103 215 215 HOH HOH A . G 4 HOH 104 216 216 HOH HOH A . G 4 HOH 105 217 217 HOH HOH A . G 4 HOH 106 218 218 HOH HOH A . G 4 HOH 107 223 223 HOH HOH A . G 4 HOH 108 224 224 HOH HOH A . G 4 HOH 109 225 225 HOH HOH A . G 4 HOH 110 226 226 HOH HOH A . H 4 HOH 1 75 75 HOH HOH B . H 4 HOH 2 78 78 HOH HOH B . H 4 HOH 3 79 79 HOH HOH B . H 4 HOH 4 80 80 HOH HOH B . H 4 HOH 5 87 87 HOH HOH B . H 4 HOH 6 88 88 HOH HOH B . H 4 HOH 7 89 89 HOH HOH B . H 4 HOH 8 90 90 HOH HOH B . H 4 HOH 9 95 95 HOH HOH B . H 4 HOH 10 102 102 HOH HOH B . H 4 HOH 11 103 103 HOH HOH B . H 4 HOH 12 108 108 HOH HOH B . H 4 HOH 13 109 109 HOH HOH B . H 4 HOH 14 114 114 HOH HOH B . H 4 HOH 15 117 117 HOH HOH B . H 4 HOH 16 118 118 HOH HOH B . H 4 HOH 17 119 119 HOH HOH B . H 4 HOH 18 120 120 HOH HOH B . H 4 HOH 19 121 121 HOH HOH B . H 4 HOH 20 125 125 HOH HOH B . H 4 HOH 21 126 126 HOH HOH B . H 4 HOH 22 130 130 HOH HOH B . H 4 HOH 23 132 132 HOH HOH B . H 4 HOH 24 133 133 HOH HOH B . H 4 HOH 25 134 134 HOH HOH B . H 4 HOH 26 137 137 HOH HOH B . H 4 HOH 27 138 138 HOH HOH B . H 4 HOH 28 139 139 HOH HOH B . H 4 HOH 29 143 143 HOH HOH B . H 4 HOH 30 146 146 HOH HOH B . H 4 HOH 31 147 147 HOH HOH B . H 4 HOH 32 150 150 HOH HOH B . H 4 HOH 33 151 151 HOH HOH B . H 4 HOH 34 152 152 HOH HOH B . H 4 HOH 35 160 160 HOH HOH B . H 4 HOH 36 161 161 HOH HOH B . H 4 HOH 37 162 162 HOH HOH B . H 4 HOH 38 163 163 HOH HOH B . H 4 HOH 39 171 171 HOH HOH B . H 4 HOH 40 174 174 HOH HOH B . H 4 HOH 41 175 175 HOH HOH B . H 4 HOH 42 177 177 HOH HOH B . H 4 HOH 43 180 180 HOH HOH B . H 4 HOH 44 184 184 HOH HOH B . H 4 HOH 45 185 185 HOH HOH B . H 4 HOH 46 186 186 HOH HOH B . H 4 HOH 47 187 187 HOH HOH B . H 4 HOH 48 188 188 HOH HOH B . H 4 HOH 49 190 190 HOH HOH B . H 4 HOH 50 191 191 HOH HOH B . H 4 HOH 51 192 192 HOH HOH B . H 4 HOH 52 194 194 HOH HOH B . H 4 HOH 53 197 197 HOH HOH B . H 4 HOH 54 198 198 HOH HOH B . H 4 HOH 55 199 199 HOH HOH B . H 4 HOH 56 200 200 HOH HOH B . H 4 HOH 57 202 202 HOH HOH B . H 4 HOH 58 204 204 HOH HOH B . H 4 HOH 59 211 211 HOH HOH B . H 4 HOH 60 212 212 HOH HOH B . H 4 HOH 61 213 213 HOH HOH B . H 4 HOH 62 219 219 HOH HOH B . H 4 HOH 63 220 220 HOH HOH B . H 4 HOH 64 221 221 HOH HOH B . H 4 HOH 65 222 222 HOH HOH B . H 4 HOH 66 227 227 HOH HOH B . H 4 HOH 67 228 228 HOH HOH B . H 4 HOH 68 229 229 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXL-97 refinement . ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 # _cell.entry_id 397D _cell.length_a 27.100 _cell.length_b 27.100 _cell.length_c 31.600 _cell.angle_alpha 69.20 _cell.angle_beta 77.50 _cell.angle_gamma 63.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 397D _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _exptl.entry_id 397D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.25 _exptl_crystal.density_percent_sol 45.24 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 292.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.00 _exptl_crystal_grow.pdbx_details 'pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 292.00K' _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 WATER ? ? ? 1 2 1 MGCL2 ? ? ? 1 3 1 NA-CACODYLATE ? ? ? 1 4 1 NH4CL ? ? ? 1 5 1 CACL2 ? ? ? 1 6 2 WATER ? ? ? 1 7 2 NH4CL ? ? ? 1 8 2 CACL2 ? ? ? 1 9 2 'PRECIPITATING BUFFER' ? ? ? 1 10 3 'ETHYLENE GLYCOL' ? ? ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100.00 ? 1 2 ? ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'PRINCETON 2K' 1997-05-01 ? 2 'IMAGE PLATE' 'RIGAKU RAXIS IV' ? ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 ? ? ? x-ray 2 2 ? ? ? x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 . 1.0 2 . 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'CHESS BEAMLINE A1' CHESS A1 ? ? 2 'ROTATING ANODE' 'RIGAKU RU300' ? ? ? ? # _reflns.entry_id 397D _reflns.observed_criterion_sigma_I -3.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.000 _reflns.d_resolution_high 1.300 _reflns.number_obs 17465 _reflns.number_all ? _reflns.percent_possible_obs 95.000 _reflns.pdbx_Rmerge_I_obs 0.0600000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 4.800 _reflns.pdbx_diffrn_id 1,2 _reflns.pdbx_ordinal 1 # _refine.entry_id 397D _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 17465 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF 20.000 _refine.pdbx_data_cutoff_low_absF 15734.0 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.000 _refine.ls_d_res_high 1.300 _refine.ls_percent_reflns_obs 85.000 _refine.ls_R_factor_obs 0.1260000 _refine.ls_R_factor_all 0.1310000 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.1770000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 0.099 _refine.ls_number_reflns_R_free 1731 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _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_ls_cross_valid_method 'R FREE' _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _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.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 567 _refine_hist.pdbx_number_atoms_ligand 4 _refine_hist.number_atoms_solvent 178 _refine_hist.number_atoms_total 749 _refine_hist.d_res_high 1.300 _refine_hist.d_res_low 20.000 # 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 s_bond_d 0.009 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.025 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes ? ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr ? ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 397D _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 397D _struct.title ;A 1.3 A RESOLUTION CRYSTAL STRUCTURE OF THE HIV-1 TRANS-ACTIVATION RESPONSE REGION RNA STEM REVEALS A METAL ION-DEPENDENT BULGE CONFORMATION ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 397D _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'DOUBLE HELIX, OVERHANGING BASES, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 4 ? H N N 4 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 397D 397D ? ? ? 2 2 PDB 397D 397D ? ? ? # 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 397D A 1 ? 15 ? 397D 16 ? 30 ? 16 30 2 2 397D B 1 ? 12 ? 397D 36 ? 47 ? 36 47 # _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 # _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 # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A U 8 OP1 ? ? ? 1_555 C CA . CA ? ? A U 23 A CA 48 1_555 ? ? ? ? ? ? ? 2.278 ? ? metalc2 metalc ? ? A C 9 OP2 ? ? ? 1_555 C CA . CA ? ? A C 24 A CA 48 1_555 ? ? ? ? ? ? ? 2.316 ? ? metalc3 metalc ? ? A G 11 OP2 ? ? ? 1_555 C CA . CA ? ? A G 26 A CA 48 1_555 ? ? ? ? ? ? ? 2.318 ? ? metalc4 metalc ? ? A G 11 OP1 ? ? ? 1_555 D CA . CA ? ? A G 26 A CA 49 1_555 ? ? ? ? ? ? ? 2.356 ? ? metalc5 metalc ? ? A A 12 OP1 ? ? ? 1_555 F CA . CA ? ? A A 27 A CA 50 1_555 ? ? ? ? ? ? ? 2.317 ? ? metalc6 metalc ? ? C CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 48 A HOH 52 1_555 ? ? ? ? ? ? ? 2.419 ? ? metalc7 metalc ? ? C CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 48 A HOH 53 1_555 ? ? ? ? ? ? ? 2.373 ? ? metalc8 metalc ? ? C CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 48 A HOH 54 1_555 ? ? ? ? ? ? ? 2.363 ? ? metalc9 metalc ? ? D CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 49 A HOH 55 1_555 ? ? ? ? ? ? ? 2.416 ? ? metalc10 metalc ? ? D CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 49 A HOH 56 1_555 ? ? ? ? ? ? ? 2.406 ? ? metalc11 metalc ? ? D CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 49 A HOH 58 1_555 ? ? ? ? ? ? ? 2.361 ? ? metalc12 metalc ? ? D CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 49 A HOH 59 1_555 ? ? ? ? ? ? ? 2.478 ? ? metalc13 metalc ? ? D CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 49 A HOH 60 1_555 ? ? ? ? ? ? ? 2.463 ? ? metalc14 metalc ? ? D CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 49 A HOH 136 1_555 ? ? ? ? ? ? ? 2.328 ? ? metalc15 metalc ? ? F CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 50 A HOH 61 1_555 ? ? ? ? ? ? ? 2.342 ? ? metalc16 metalc ? ? F CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 50 A HOH 62 1_555 ? ? ? ? ? ? ? 2.368 ? ? metalc17 metalc ? ? F CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 50 A HOH 63 1_555 ? ? ? ? ? ? ? 2.439 ? ? metalc18 metalc ? ? F CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 50 A HOH 64 1_555 ? ? ? ? ? ? ? 2.376 ? ? metalc19 metalc ? ? F CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 50 A HOH 65 1_555 ? ? ? ? ? ? ? 2.488 ? ? metalc20 metalc ? ? F CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 50 A HOH 66 1_555 ? ? ? ? ? ? ? 2.438 ? ? metalc21 metalc ? ? E CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 51 A HOH 67 1_555 ? ? ? ? ? ? ? 2.417 ? ? metalc22 metalc ? ? E CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 51 A HOH 68 1_555 ? ? ? ? ? ? ? 2.414 ? ? metalc23 metalc ? ? E CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 51 A HOH 69 1_555 ? ? ? ? ? ? ? 2.419 ? ? metalc24 metalc ? ? E CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 51 A HOH 70 1_555 ? ? ? ? ? ? ? 2.510 ? ? metalc25 metalc ? ? E CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 51 A HOH 71 1_555 ? ? ? ? ? ? ? 2.473 ? ? metalc26 metalc ? ? E CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 51 A HOH 189 1_555 ? ? ? ? ? ? ? 2.473 ? ? metalc27 metalc ? ? E CA . CA ? ? ? 1_555 G HOH . O ? ? A CA 51 A HOH 210 1_555 ? ? ? ? ? ? ? 2.174 ? ? metalc28 metalc ? ? E CA . CA ? ? ? 1_555 H HOH . O ? ? A CA 51 B HOH 162 1_555 ? ? ? ? ? ? ? 2.659 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 16 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 16 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 16 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 17 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 17 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 17 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 9 N1 ? ? A C 18 B G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 9 O6 ? ? A C 18 B G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 9 N2 ? ? A C 18 B G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 8 N1 ? ? A C 19 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 8 O6 ? ? A C 19 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 8 N2 ? ? A C 19 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N1 ? ? ? 1_555 B U 7 N3 ? ? A A 20 B U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A A 5 N6 ? ? ? 1_555 B U 7 O4 ? ? A A 20 B U 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 21 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 21 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 21 B C 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 7 N1 ? ? ? 1_555 B U 5 N3 ? ? A A 22 B U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A A 7 N6 ? ? ? 1_555 B U 5 O4 ? ? A A 22 B U 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 11 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 26 B C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 11 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 26 B C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 11 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 26 B C 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A A 12 N1 ? ? ? 1_555 B U 3 N3 ? ? A A 27 B U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A A 12 N6 ? ? ? 1_555 B U 3 O4 ? ? A A 27 B U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 28 B C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 28 B C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 28 B C 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 14 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 29 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 14 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 29 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 14 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 29 B G 36 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 OP1 ? A U 8 ? A U 23 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 OP2 ? A C 9 ? A C 24 ? 1_555 89.3 ? 2 OP1 ? A U 8 ? A U 23 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 OP2 ? A G 11 ? A G 26 ? 1_555 94.0 ? 3 OP2 ? A C 9 ? A C 24 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 OP2 ? A G 11 ? A G 26 ? 1_555 107.3 ? 4 OP1 ? A U 8 ? A U 23 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 O ? G HOH . ? A HOH 52 ? 1_555 177.1 ? 5 OP2 ? A C 9 ? A C 24 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 O ? G HOH . ? A HOH 52 ? 1_555 89.7 ? 6 OP2 ? A G 11 ? A G 26 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 O ? G HOH . ? A HOH 52 ? 1_555 83.7 ? 7 OP1 ? A U 8 ? A U 23 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 O ? G HOH . ? A HOH 53 ? 1_555 93.3 ? 8 OP2 ? A C 9 ? A C 24 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 O ? G HOH . ? A HOH 53 ? 1_555 84.1 ? 9 OP2 ? A G 11 ? A G 26 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 O ? G HOH . ? A HOH 53 ? 1_555 166.5 ? 10 O ? G HOH . ? A HOH 52 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 O ? G HOH . ? A HOH 53 ? 1_555 89.3 ? 11 OP1 ? A U 8 ? A U 23 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 O ? G HOH . ? A HOH 54 ? 1_555 92.6 ? 12 OP2 ? A C 9 ? A C 24 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 O ? G HOH . ? A HOH 54 ? 1_555 170.0 ? 13 OP2 ? A G 11 ? A G 26 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 O ? G HOH . ? A HOH 54 ? 1_555 82.4 ? 14 O ? G HOH . ? A HOH 52 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 O ? G HOH . ? A HOH 54 ? 1_555 88.8 ? 15 O ? G HOH . ? A HOH 53 ? 1_555 CA ? C CA . ? A CA 48 ? 1_555 O ? G HOH . ? A HOH 54 ? 1_555 86.0 ? 16 OP1 ? A G 11 ? A G 26 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 55 ? 1_555 72.7 ? 17 OP1 ? A G 11 ? A G 26 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 56 ? 1_555 139.4 ? 18 O ? G HOH . ? A HOH 55 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 56 ? 1_555 69.3 ? 19 OP1 ? A G 11 ? A G 26 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 58 ? 1_555 84.6 ? 20 O ? G HOH . ? A HOH 55 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 58 ? 1_555 99.7 ? 21 O ? G HOH . ? A HOH 56 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 58 ? 1_555 88.0 ? 22 OP1 ? A G 11 ? A G 26 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 59 ? 1_555 86.7 ? 23 O ? G HOH . ? A HOH 55 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 59 ? 1_555 157.0 ? 24 O ? G HOH . ? A HOH 56 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 59 ? 1_555 133.0 ? 25 O ? G HOH . ? A HOH 58 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 59 ? 1_555 88.2 ? 26 OP1 ? A G 11 ? A G 26 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 60 ? 1_555 150.9 ? 27 O ? G HOH . ? A HOH 55 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 60 ? 1_555 135.3 ? 28 O ? G HOH . ? A HOH 56 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 60 ? 1_555 69.5 ? 29 O ? G HOH . ? A HOH 58 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 60 ? 1_555 95.5 ? 30 O ? G HOH . ? A HOH 59 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 60 ? 1_555 64.3 ? 31 OP1 ? A G 11 ? A G 26 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 136 ? 1_555 97.1 ? 32 O ? G HOH . ? A HOH 55 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 136 ? 1_555 83.2 ? 33 O ? G HOH . ? A HOH 56 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 136 ? 1_555 92.3 ? 34 O ? G HOH . ? A HOH 58 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 136 ? 1_555 177.0 ? 35 O ? G HOH . ? A HOH 59 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 136 ? 1_555 89.4 ? 36 O ? G HOH . ? A HOH 60 ? 1_555 CA ? D CA . ? A CA 49 ? 1_555 O ? G HOH . ? A HOH 136 ? 1_555 81.8 ? 37 OP1 ? A A 12 ? A A 27 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 61 ? 1_555 165.0 ? 38 OP1 ? A A 12 ? A A 27 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 62 ? 1_555 101.2 ? 39 O ? G HOH . ? A HOH 61 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 62 ? 1_555 88.9 ? 40 OP1 ? A A 12 ? A A 27 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 63 ? 1_555 87.1 ? 41 O ? G HOH . ? A HOH 61 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 63 ? 1_555 84.2 ? 42 O ? G HOH . ? A HOH 62 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 63 ? 1_555 78.3 ? 43 OP1 ? A A 12 ? A A 27 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 64 ? 1_555 90.3 ? 44 O ? G HOH . ? A HOH 61 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 64 ? 1_555 75.6 ? 45 O ? G HOH . ? A HOH 62 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 64 ? 1_555 149.1 ? 46 O ? G HOH . ? A HOH 63 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 64 ? 1_555 73.7 ? 47 OP1 ? A A 12 ? A A 27 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 65 ? 1_555 113.5 ? 48 O ? G HOH . ? A HOH 61 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 65 ? 1_555 79.6 ? 49 O ? G HOH . ? A HOH 62 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 65 ? 1_555 75.4 ? 50 O ? G HOH . ? A HOH 63 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 65 ? 1_555 149.2 ? 51 O ? G HOH . ? A HOH 64 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 65 ? 1_555 126.1 ? 52 OP1 ? A A 12 ? A A 27 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 66 ? 1_555 76.1 ? 53 O ? G HOH . ? A HOH 61 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 66 ? 1_555 104.9 ? 54 O ? G HOH . ? A HOH 62 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 66 ? 1_555 133.4 ? 55 O ? G HOH . ? A HOH 63 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 66 ? 1_555 146.0 ? 56 O ? G HOH . ? A HOH 64 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 66 ? 1_555 77.1 ? 57 O ? G HOH . ? A HOH 65 ? 1_555 CA ? F CA . ? A CA 50 ? 1_555 O ? G HOH . ? A HOH 66 ? 1_555 64.3 ? 58 O ? G HOH . ? A HOH 67 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 68 ? 1_555 66.0 ? 59 O ? G HOH . ? A HOH 67 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 69 ? 1_555 93.5 ? 60 O ? G HOH . ? A HOH 68 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 69 ? 1_555 73.5 ? 61 O ? G HOH . ? A HOH 67 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 70 ? 1_555 79.4 ? 62 O ? G HOH . ? A HOH 68 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 70 ? 1_555 128.6 ? 63 O ? G HOH . ? A HOH 69 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 70 ? 1_555 71.9 ? 64 O ? G HOH . ? A HOH 67 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 71 ? 1_555 144.9 ? 65 O ? G HOH . ? A HOH 68 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 71 ? 1_555 148.5 ? 66 O ? G HOH . ? A HOH 69 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 71 ? 1_555 102.6 ? 67 O ? G HOH . ? A HOH 70 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 71 ? 1_555 76.4 ? 68 O ? G HOH . ? A HOH 67 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 189 ? 1_555 81.5 ? 69 O ? G HOH . ? A HOH 68 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 189 ? 1_555 132.9 ? 70 O ? G HOH . ? A HOH 69 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 189 ? 1_555 144.6 ? 71 O ? G HOH . ? A HOH 70 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 189 ? 1_555 72.7 ? 72 O ? G HOH . ? A HOH 71 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 189 ? 1_555 67.3 ? 73 O ? G HOH . ? A HOH 67 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 210 ? 1_555 97.2 ? 74 O ? G HOH . ? A HOH 68 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 210 ? 1_555 88.2 ? 75 O ? G HOH . ? A HOH 69 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 210 ? 1_555 152.8 ? 76 O ? G HOH . ? A HOH 70 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 210 ? 1_555 134.6 ? 77 O ? G HOH . ? A HOH 71 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 210 ? 1_555 82.5 ? 78 O ? G HOH . ? A HOH 189 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? G HOH . ? A HOH 210 ? 1_555 62.2 ? 79 O ? G HOH . ? A HOH 67 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? H HOH . ? B HOH 162 ? 1_555 146.4 ? 80 O ? G HOH . ? A HOH 68 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? H HOH . ? B HOH 162 ? 1_555 81.5 ? 81 O ? G HOH . ? A HOH 69 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? H HOH . ? B HOH 162 ? 1_555 84.9 ? 82 O ? G HOH . ? A HOH 70 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? H HOH . ? B HOH 162 ? 1_555 130.8 ? 83 O ? G HOH . ? A HOH 71 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? H HOH . ? B HOH 162 ? 1_555 67.0 ? 84 O ? G HOH . ? A HOH 189 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? H HOH . ? B HOH 162 ? 1_555 118.0 ? 85 O ? G HOH . ? A HOH 210 ? 1_555 CA ? E CA . ? A CA 51 ? 1_555 O ? H HOH . ? B HOH 162 ? 1_555 72.4 ? # 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 CA 48 ? 6 'BINDING SITE FOR RESIDUE CA A 48' AC2 Software A CA 49 ? 7 'BINDING SITE FOR RESIDUE CA A 49' AC3 Software A CA 51 ? 8 'BINDING SITE FOR RESIDUE CA A 51' AC4 Software A CA 50 ? 7 'BINDING SITE FOR RESIDUE CA A 50' # 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 6 U A 8 ? U A 23 . ? 1_555 ? 2 AC1 6 C A 9 ? C A 24 . ? 1_555 ? 3 AC1 6 G A 11 ? G A 26 . ? 1_555 ? 4 AC1 6 HOH G . ? HOH A 52 . ? 1_555 ? 5 AC1 6 HOH G . ? HOH A 53 . ? 1_555 ? 6 AC1 6 HOH G . ? HOH A 54 . ? 1_555 ? 7 AC2 7 G A 11 ? G A 26 . ? 1_555 ? 8 AC2 7 HOH G . ? HOH A 55 . ? 1_555 ? 9 AC2 7 HOH G . ? HOH A 56 . ? 1_555 ? 10 AC2 7 HOH G . ? HOH A 58 . ? 1_555 ? 11 AC2 7 HOH G . ? HOH A 59 . ? 1_555 ? 12 AC2 7 HOH G . ? HOH A 60 . ? 1_555 ? 13 AC2 7 HOH G . ? HOH A 136 . ? 1_555 ? 14 AC3 8 HOH G . ? HOH A 67 . ? 1_555 ? 15 AC3 8 HOH G . ? HOH A 68 . ? 1_555 ? 16 AC3 8 HOH G . ? HOH A 69 . ? 1_555 ? 17 AC3 8 HOH G . ? HOH A 70 . ? 1_555 ? 18 AC3 8 HOH G . ? HOH A 71 . ? 1_555 ? 19 AC3 8 HOH G . ? HOH A 189 . ? 1_555 ? 20 AC3 8 HOH G . ? HOH A 210 . ? 1_555 ? 21 AC3 8 HOH H . ? HOH B 162 . ? 1_555 ? 22 AC4 7 A A 12 ? A A 27 . ? 1_555 ? 23 AC4 7 HOH G . ? HOH A 61 . ? 1_555 ? 24 AC4 7 HOH G . ? HOH A 62 . ? 1_555 ? 25 AC4 7 HOH G . ? HOH A 63 . ? 1_555 ? 26 AC4 7 HOH G . ? HOH A 64 . ? 1_555 ? 27 AC4 7 HOH G . ? HOH A 65 . ? 1_555 ? 28 AC4 7 HOH G . ? HOH A 66 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C3'" A G 21 ? ? "C2'" A G 21 ? ? "C1'" A G 21 ? ? 96.87 101.30 -4.43 0.70 N 2 1 N9 A G 30 ? ? "C1'" A G 30 ? ? "C2'" A G 30 ? ? 104.40 112.00 -7.60 1.10 N 3 1 "O4'" A G 30 ? ? "C1'" A G 30 ? ? N9 A G 30 ? ? 123.41 108.50 14.91 0.70 N 4 1 N3 B C 37 ? ? C4 B C 37 ? ? C5 B C 37 ? ? 119.40 121.90 -2.50 0.40 N # 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 CA CA CA N N 73 G OP3 O N N 74 G P P N N 75 G OP1 O N N 76 G OP2 O N N 77 G "O5'" O N N 78 G "C5'" C N N 79 G "C4'" C N R 80 G "O4'" O N N 81 G "C3'" C N S 82 G "O3'" O N N 83 G "C2'" C N R 84 G "O2'" O N N 85 G "C1'" C N R 86 G N9 N Y N 87 G C8 C Y N 88 G N7 N Y N 89 G C5 C Y N 90 G C6 C N N 91 G O6 O N N 92 G N1 N N N 93 G C2 C N N 94 G N2 N N N 95 G N3 N N N 96 G C4 C Y N 97 G HOP3 H N N 98 G HOP2 H N N 99 G "H5'" H N N 100 G "H5''" H N N 101 G "H4'" H N N 102 G "H3'" H N N 103 G "HO3'" H N N 104 G "H2'" H N N 105 G "HO2'" H N N 106 G "H1'" H N N 107 G H8 H N N 108 G H1 H N N 109 G H21 H N N 110 G H22 H N N 111 HOH O O N N 112 HOH H1 H N N 113 HOH H2 H N N 114 U OP3 O N N 115 U P P N N 116 U OP1 O N N 117 U OP2 O N N 118 U "O5'" O N N 119 U "C5'" C N N 120 U "C4'" C N R 121 U "O4'" O N N 122 U "C3'" C N S 123 U "O3'" O N N 124 U "C2'" C N R 125 U "O2'" O N N 126 U "C1'" C N R 127 U N1 N N N 128 U C2 C N N 129 U O2 O N N 130 U N3 N N N 131 U C4 C N N 132 U O4 O N N 133 U C5 C N N 134 U C6 C N N 135 U HOP3 H N N 136 U HOP2 H N N 137 U "H5'" H N N 138 U "H5''" H N N 139 U "H4'" H N N 140 U "H3'" H N N 141 U "HO3'" H N N 142 U "H2'" H N N 143 U "HO2'" H N N 144 U "H1'" H N N 145 U H3 H N N 146 U H5 H N N 147 U H6 H N N 148 # 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 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 397D 'double helix' 397D 'a-form double helix' 397D 'bulge 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 1 1_555 B C 11 1_555 -0.313 -0.160 -0.112 -8.186 -15.194 1.719 1 A_G16:C46_B A 16 ? B 46 ? 19 1 1 A G 2 1_555 B C 10 1_555 -0.299 -0.142 -0.280 -15.749 -14.052 -4.600 2 A_G17:C45_B A 17 ? B 45 ? 19 1 1 A C 3 1_555 B G 9 1_555 0.262 -0.116 0.203 -3.701 -7.444 2.023 3 A_C18:G44_B A 18 ? B 44 ? 19 1 1 A C 4 1_555 B G 8 1_555 0.187 -0.136 0.016 2.187 -8.849 -0.781 4 A_C19:G43_B A 19 ? B 43 ? 19 1 1 A A 5 1_555 B U 7 1_555 0.153 -0.078 0.114 0.895 -9.999 2.180 5 A_A20:U42_B A 20 ? B 42 ? 20 1 1 A G 6 1_555 B C 6 1_555 -0.239 -0.107 0.042 -6.202 -16.935 1.599 6 A_G21:C41_B A 21 ? B 41 ? 19 1 1 A A 7 1_555 B U 5 1_555 0.045 -0.060 0.008 -2.095 -11.198 0.212 7 A_A22:U40_B A 22 ? B 40 ? 20 1 1 A G 11 1_555 B C 4 1_555 -0.216 -0.166 0.104 -1.060 -13.544 -0.791 8 A_G26:C39_B A 26 ? B 39 ? 19 1 1 A A 12 1_555 B U 3 1_555 0.024 -0.094 -0.067 -3.199 -10.734 -0.726 9 A_A27:U38_B A 27 ? B 38 ? 20 1 1 A G 13 1_555 B C 2 1_555 -0.033 -0.105 -0.090 -7.158 -16.715 -0.327 10 A_G28:C37_B A 28 ? B 37 ? 19 1 1 A C 14 1_555 B G 1 1_555 0.048 -0.144 0.410 -9.146 -9.290 -2.897 11 A_C29:G36_B A 29 ? B 36 ? 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 1 1_555 B C 11 1_555 A G 2 1_555 B C 10 1_555 -0.749 -1.962 3.446 0.827 8.436 32.960 -4.675 1.411 2.853 14.570 -1.429 34.003 1 AA_G16G17:C45C46_BB A 16 ? B 46 ? A 17 ? B 45 ? 1 A G 2 1_555 B C 10 1_555 A C 3 1_555 B G 9 1_555 0.948 -1.063 2.985 -2.039 7.891 31.466 -3.098 -2.005 2.584 14.252 3.682 32.478 2 AA_G17C18:G44C45_BB A 17 ? B 45 ? A 18 ? B 44 ? 1 A C 3 1_555 B G 9 1_555 A C 4 1_555 B G 8 1_555 -0.013 -1.951 3.079 3.164 4.182 28.872 -4.663 0.639 2.758 8.300 -6.280 29.335 3 AA_C18C19:G43G44_BB A 18 ? B 44 ? A 19 ? B 43 ? 1 A C 4 1_555 B G 8 1_555 A A 5 1_555 B U 7 1_555 0.154 -1.588 3.222 0.093 6.031 30.045 -4.124 -0.275 2.857 11.487 -0.178 30.631 4 AA_C19A20:U42G43_BB A 19 ? B 43 ? A 20 ? B 42 ? 1 A A 5 1_555 B U 7 1_555 A G 6 1_555 B C 6 1_555 0.263 -1.683 3.371 1.932 7.067 30.493 -4.416 -0.132 2.927 13.198 -3.608 31.341 5 AA_A20G21:C41U42_BB A 20 ? B 42 ? A 21 ? B 41 ? 1 A G 6 1_555 B C 6 1_555 A A 7 1_555 B U 5 1_555 -0.465 -1.205 3.108 0.568 4.860 35.781 -2.581 0.824 2.917 7.864 -0.919 36.103 6 AA_G21A22:U40C41_BB A 21 ? B 41 ? A 22 ? B 40 ? 1 A A 7 1_555 B U 5 1_555 A G 11 1_555 B C 4 1_555 1.363 -2.130 3.161 2.711 9.145 21.675 -7.820 -2.547 2.240 22.940 -6.800 23.658 7 AA_A22G26:C39U40_BB A 22 ? B 40 ? A 26 ? B 39 ? 1 A G 11 1_555 B C 4 1_555 A A 12 1_555 B U 3 1_555 -0.738 -1.176 3.235 -0.895 4.722 37.671 -2.392 1.024 3.087 7.277 1.379 37.965 8 AA_G26A27:U38C39_BB A 26 ? B 39 ? A 27 ? B 38 ? 1 A A 12 1_555 B U 3 1_555 A G 13 1_555 B C 2 1_555 0.631 -1.710 3.317 3.012 10.200 29.495 -4.977 -0.634 2.644 19.263 -5.688 31.314 9 AA_A27G28:C37U38_BB A 27 ? B 38 ? A 28 ? B 37 ? 1 A G 13 1_555 B C 2 1_555 A C 14 1_555 B G 1 1_555 0.319 -2.012 3.280 -0.154 2.337 34.995 -3.683 -0.552 3.142 3.880 0.256 35.071 10 AA_G28C29:G36C37_BB A 28 ? B 37 ? A 29 ? B 36 ? # _atom_sites.entry_id 397D _atom_sites.fract_transf_matrix[1][1] 0.036900 _atom_sites.fract_transf_matrix[1][2] -0.018802 _atom_sites.fract_transf_matrix[1][3] -0.002752 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.041414 _atom_sites.fract_transf_matrix[2][3] -0.012799 _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] 0.033926 _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 CA N O P # loop_