ID code: '4MSR' 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' --------------------------------------------------------------------------------- 9 C1' C A 1 beta 4 10 7 29 C1' C A 2 beta 24 30 27 141 C1' C A 5 beta 136 142 139 161 C1' G A 6 beta 156 162 159 184 C1' C A 7 beta 179 185 182 204 C1' C A 8 beta 199 205 202 224 C1' G A 9 beta 219 225 222 247 C1' G A 10 beta 242 248 245 268 C1' C B 1 beta 263 269 266 288 C1' C B 2 beta 283 289 286 308 C1' G B 3 beta 303 309 306 331 C1' G B 4 beta 326 332 329 354 C1' C B 5 beta 349 355 352 374 C1' G B 6 beta 369 375 372 397 C1' C B 7 beta 392 398 395 457 C1' G B 9 beta 452 458 455 480 C1' G B 10 beta 475 481 478 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' C A 2 OK 29 25 28 139 C2' C A 5 OK 141 137 140 159 C2' G A 6 OK 161 157 160 182 C2' C A 7 OK 184 180 183 202 C2' C A 8 OK 204 200 203 222 C2' G A 9 OK 224 220 223 245 C2' G A 10 OK 247 243 246 266 C2' C B 1 OK 268 264 267 286 C2' C B 2 OK 288 284 287 306 C2' G B 3 OK 308 304 307 329 C2' G B 4 OK 331 327 330 352 C2' C B 5 OK 354 350 353 372 C2' G B 6 OK 374 370 373 395 C2' C B 7 OK 397 393 396 455 C2' G B 9 OK 457 453 456 478 C2' G B 10 OK 480 476 479 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' C A 2 OK 23 26 27 137 C3' C A 5 OK 135 138 139 157 C3' G A 6 OK 155 158 159 180 C3' C A 7 OK 178 181 182 200 C3' C A 8 OK 198 201 202 220 C3' G A 9 OK 218 221 222 243 C3' G A 10 OK 241 244 245 264 C3' C B 1 OK 262 265 266 284 C3' C B 2 OK 282 285 286 304 C3' G B 3 OK 302 305 306 327 C3' G B 4 OK 325 328 329 350 C3' C B 5 OK 348 351 352 370 C3' G B 6 OK 368 371 372 393 C3' C B 7 OK 391 394 395 453 C3' G B 9 OK 451 454 455 476 C3' G B 10 OK 474 477 478 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' C A 2 OK 25 22 24 135 C4' C A 5 OK 137 134 136 155 C4' G A 6 OK 157 154 156 178 C4' C A 7 OK 180 177 179 198 C4' C A 8 OK 200 197 199 218 C4' G A 9 OK 220 217 219 241 C4' G A 10 OK 243 240 242 262 C4' C B 1 OK 264 261 263 282 C4' C B 2 OK 284 281 283 302 C4' G B 3 OK 304 301 303 325 C4' G B 4 OK 327 324 326 348 C4' C B 5 OK 350 347 349 368 C4' G B 6 OK 370 367 369 391 C4' C B 7 OK 393 390 392 451 C4' G B 9 OK 453 450 452 474 C4' G B 10 OK 476 473 475 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' C A 2 21 23 134 C5' C A 5 133 135 154 C5' G A 6 153 155 177 C5' C A 7 176 178 197 C5' C A 8 196 198 217 C5' G A 9 216 218 240 C5' G A 10 239 241 261 C5' C B 1 260 262 281 C5' C B 2 280 282 301 C5' G B 3 300 302 324 C5' G B 4 323 325 347 C5' C B 5 346 348 367 C5' G B 6 366 368 390 C5' C B 7 389 391 450 C5' G B 9 449 451 473 C5' G B 10 472 474 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C A 2 distorted distorted 6 19 20 21 38 P G A 3 26 39 P G A 3 26 84 P G A 4 85 P G A 4 130 P C A 5 distorted distorted 131 132 133 150 P G A 6 distorted distorted 151 152 153 173 P C A 7 distorted distorted 158 174 175 176 193 P C A 8 distorted distorted 194 195 196 213 P G A 9 distorted distorted 201 214 215 216 236 P G A 10 distorted distorted 221 237 238 239 277 P C B 2 distorted distorted 265 278 279 280 297 P G B 3 distorted distorted 285 298 299 300 320 P G B 4 distorted distorted 321 322 323 343 P C B 5 distorted distorted 328 344 345 346 363 P G B 6 distorted distorted 364 365 366 386 P C B 7 distorted distorted 371 387 388 389 406 P C B 8 407 P C B 8 446 P G B 9 distorted distorted 447 448 449 469 P G B 10 distorted distorted 454 470 471 472 ---------------------------------------------------------------------------------