ID code: '1NK7' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 8 C1' G B 21 beta 4 9 7 30 C1' C B 22 beta 26 31 29 49 C1' A B 23 beta 45 50 48 70 C1' T B 24 beta 66 71 69 90 C1' C B 25 beta 86 91 89 109 C1' A B 26 beta 105 110 108 130 C1' T B 27 beta 126 131 129 150 C1' G B 28 beta 146 151 149 172 C1' C B 29 beta 168 173 171 189 C1' G C 6 beta 185 190 188 211 C1' C C 7 beta 207 212 210 230 C1' A C 8 beta 226 231 229 251 C1' T C 9 beta 247 252 250 271 C1' G C 10 beta 267 272 270 293 C1' A C 11 beta 289 294 292 314 C1' T C 12 beta 310 315 313 334 C1' G C 13 beta 330 335 333 356 C1' C C 14 beta 352 357 355 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 21 8 5 29 C2' C B 22 30 27 48 C2' A B 23 49 46 69 C2' T B 24 70 67 89 C2' C B 25 90 87 108 C2' A B 26 109 106 129 C2' T B 27 130 127 149 C2' G B 28 150 147 171 C2' C B 29 172 169 188 C2' G C 6 189 186 210 C2' C C 7 211 208 229 C2' A C 8 230 227 250 C2' T C 9 251 248 270 C2' G C 10 271 268 292 C2' A C 11 293 290 313 C2' T C 12 314 311 333 C2' G C 13 334 331 355 C2' C C 14 356 353 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 21 OK 3 6 7 27 C3' C B 22 OK 25 28 29 46 C3' A B 23 OK 44 47 48 67 C3' T B 24 OK 65 68 69 87 C3' C B 25 OK 85 88 89 106 C3' A B 26 OK 104 107 108 127 C3' T B 27 OK 125 128 129 147 C3' G B 28 OK 145 148 149 169 C3' C B 29 OK 167 170 171 186 C3' G C 6 OK 184 187 188 208 C3' C C 7 OK 206 209 210 227 C3' A C 8 OK 225 228 229 248 C3' T C 9 OK 246 249 250 268 C3' G C 10 OK 266 269 270 290 C3' A C 11 OK 288 291 292 311 C3' T C 12 OK 309 312 313 331 C3' G C 13 OK 329 332 333 353 C3' C C 14 OK 351 354 355 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 21 OK 5 2 4 25 C4' C B 22 OK 27 24 26 44 C4' A B 23 OK 46 43 45 65 C4' T B 24 OK 67 64 66 85 C4' C B 25 OK 87 84 86 104 C4' A B 26 OK 106 103 105 125 C4' T B 27 OK 127 124 126 145 C4' G B 28 OK 147 144 146 167 C4' C B 29 OK 169 166 168 184 C4' G C 6 OK 186 183 185 206 C4' C C 7 OK 208 205 207 225 C4' A C 8 OK 227 224 226 246 C4' T C 9 OK 248 245 247 266 C4' G C 10 OK 268 265 267 288 C4' A C 11 OK 290 287 289 309 C4' T C 12 OK 311 308 310 329 C4' G C 13 OK 331 328 330 351 C4' C C 14 OK 353 350 352 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 21 1 3 24 C5' C B 22 23 25 43 C5' A B 23 42 44 64 C5' T B 24 63 65 84 C5' C B 25 83 85 103 C5' A B 26 102 104 124 C5' T B 27 123 125 144 C5' G B 28 143 145 166 C5' C B 29 165 167 183 C5' G C 6 182 184 205 C5' C C 7 204 206 224 C5' A C 8 223 225 245 C5' T C 9 244 246 265 C5' G C 10 264 266 287 C5' A C 11 286 288 308 C5' T C 12 307 309 328 C5' G C 13 327 329 350 C5' C C 14 349 351 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C B 22 distorted distorted 6 21 22 23 39 P A B 23 distorted distorted 28 40 41 42 60 P T B 24 distorted distorted 47 61 62 63 80 P C B 25 distorted distorted 68 81 82 83 99 P A B 26 distorted distorted 88 100 101 102 120 P T B 27 distorted distorted 107 121 122 123 140 P G B 28 distorted distorted 128 141 142 143 162 P C B 29 distorted distorted 148 163 164 165 201 P C C 7 distorted distorted 187 202 203 204 220 P A C 8 distorted distorted 209 221 222 223 241 P T C 9 distorted distorted 228 242 243 244 261 P G C 10 distorted distorted 249 262 263 264 283 P A C 11 distorted distorted 269 284 285 286 304 P T C 12 distorted distorted 291 305 306 307 324 P G C 13 distorted distorted 312 325 326 327 346 P C C 14 distorted distorted 332 347 348 349 ---------------------------------------------------------------------------------