ID code: '1NJZ' 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 20 beta 4 9 7 30 C1' C B 21 beta 26 31 29 49 C1' G B 22 beta 45 50 48 71 C1' A B 23 beta 67 72 70 92 C1' T B 24 beta 88 93 91 112 C1' C B 25 beta 108 113 111 131 C1' A B 26 beta 127 132 130 152 C1' G B 27 beta 148 153 151 174 C1' C B 28 beta 170 175 173 193 C1' C B 29 beta 189 194 192 213 C1' T C 6 beta 209 214 212 233 C1' G C 7 beta 229 234 232 255 C1' C C 8 beta 251 256 254 274 C1' T C 9 beta 270 275 273 294 C1' G C 10 beta 290 295 293 316 C1' A C 11 beta 312 317 315 337 C1' T C 12 beta 333 338 336 357 C1' C C 13 beta 353 358 356 376 C1' G C 14 beta 372 377 375 398 C1' C C 15 beta 394 399 397 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 20 8 5 29 C2' C B 21 30 27 48 C2' G B 22 49 46 70 C2' A B 23 71 68 91 C2' T B 24 92 89 111 C2' C B 25 112 109 130 C2' A B 26 131 128 151 C2' G B 27 152 149 173 C2' C B 28 174 171 192 C2' C B 29 193 190 212 C2' T C 6 213 210 232 C2' G C 7 233 230 254 C2' C C 8 255 252 273 C2' T C 9 274 271 293 C2' G C 10 294 291 315 C2' A C 11 316 313 336 C2' T C 12 337 334 356 C2' C C 13 357 354 375 C2' G C 14 376 373 397 C2' C C 15 398 395 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 20 OK 3 6 7 27 C3' C B 21 OK 25 28 29 46 C3' G B 22 OK 44 47 48 68 C3' A B 23 OK 66 69 70 89 C3' T B 24 OK 87 90 91 109 C3' C B 25 OK 107 110 111 128 C3' A B 26 OK 126 129 130 149 C3' G B 27 OK 147 150 151 171 C3' C B 28 OK 169 172 173 190 C3' C B 29 OK 188 191 192 210 C3' T C 6 OK 208 211 212 230 C3' G C 7 OK 228 231 232 252 C3' C C 8 OK 250 253 254 271 C3' T C 9 OK 269 272 273 291 C3' G C 10 OK 289 292 293 313 C3' A C 11 OK 311 314 315 334 C3' T C 12 OK 332 335 336 354 C3' C C 13 OK 352 355 356 373 C3' G C 14 OK 371 374 375 395 C3' C C 15 OK 393 396 397 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 20 OK 5 2 4 25 C4' C B 21 OK 27 24 26 44 C4' G B 22 OK 46 43 45 66 C4' A B 23 OK 68 65 67 87 C4' T B 24 OK 89 86 88 107 C4' C B 25 OK 109 106 108 126 C4' A B 26 OK 128 125 127 147 C4' G B 27 OK 149 146 148 169 C4' C B 28 OK 171 168 170 188 C4' C B 29 OK 190 187 189 208 C4' T C 6 OK 210 207 209 228 C4' G C 7 OK 230 227 229 250 C4' C C 8 OK 252 249 251 269 C4' T C 9 OK 271 268 270 289 C4' G C 10 OK 291 288 290 311 C4' A C 11 OK 313 310 312 332 C4' T C 12 OK 334 331 333 352 C4' C C 13 OK 354 351 353 371 C4' G C 14 OK 373 370 372 393 C4' C C 15 OK 395 392 394 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 20 1 3 24 C5' C B 21 23 25 43 C5' G B 22 42 44 65 C5' A B 23 64 66 86 C5' T B 24 85 87 106 C5' C B 25 105 107 125 C5' A B 26 124 126 146 C5' G B 27 145 147 168 C5' C B 28 167 169 187 C5' C B 29 186 188 207 C5' T C 6 206 208 227 C5' G C 7 226 228 249 C5' C C 8 248 250 268 C5' T C 9 267 269 288 C5' G C 10 287 289 310 C5' A C 11 309 311 331 C5' T C 12 330 332 351 C5' C C 13 350 352 370 C5' G C 14 369 371 392 C5' C C 15 391 393 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C B 21 distorted distorted 6 21 22 23 39 P G B 22 distorted distorted 28 40 41 42 61 P A B 23 distorted distorted 47 62 63 64 82 P T B 24 distorted distorted 69 83 84 85 102 P C B 25 distorted distorted 90 103 104 105 121 P A B 26 distorted distorted 110 122 123 124 142 P G B 27 distorted distorted 129 143 144 145 164 P C B 28 distorted distorted 150 165 166 167 183 P C B 29 distorted distorted 172 184 185 186 203 P T C 6 OK OK 204 205 206 223 P G C 7 distorted distorted 211 224 225 226 245 P C C 8 distorted distorted 231 246 247 248 264 P T C 9 distorted distorted 253 265 266 267 284 P G C 10 distorted distorted 272 285 286 287 306 P A C 11 distorted distorted 292 307 308 309 327 P T C 12 distorted distorted 314 328 329 330 347 P C C 13 distorted distorted 335 348 349 350 366 P G C 14 distorted distorted 355 367 368 369 388 P C C 15 distorted distorted 374 389 390 391 ---------------------------------------------------------------------------------