ID code: '2K3Z' 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' G A 1 alpha beta 4 27 10 7 44 C1' U A 2 alpha beta 39 59 45 42 74 C1' C A 3 alpha beta 69 89 75 72 105 C1' G A 4 alpha beta 100 123 106 103 139 C1' A A 5 alpha beta 134 156 140 137 172 C1' G A 6 alpha beta 167 190 173 170 206 C1' C A 7 alpha beta 201 221 207 204 237 C1' U A 8 alpha beta 232 252 238 235 267 C1' G A 9 alpha beta 262 286 268 265 300 C1' C B 10 alpha beta 295 315 301 298 332 C1' A B 11 alpha beta 327 349 333 330 365 C1' G B 12 alpha beta 360 383 366 363 399 C1' C B 13 alpha beta 394 414 400 397 430 C1' C B 14 alpha beta 425 445 431 428 461 C1' G B 15 alpha beta 456 479 462 459 495 C1' A B 16 alpha beta 490 512 496 493 528 C1' C B 17 alpha beta 523 544 529 526 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK OK 9 5 25 8 42 C2' U A 2 OK OK 44 40 57 43 72 C2' C A 3 OK OK 74 70 87 73 103 C2' G A 4 OK OK 105 101 121 104 137 C2' A A 5 OK OK 139 135 154 138 170 C2' G A 6 OK OK 172 168 188 171 204 C2' C A 7 OK OK 206 202 219 205 235 C2' U A 8 OK OK 237 233 250 236 265 C2' G A 9 OK OK 267 263 284 266 298 C2' C B 10 OK OK 300 296 313 299 330 C2' A B 11 OK OK 332 328 347 331 363 C2' G B 12 OK OK 365 361 381 364 397 C2' C B 13 OK OK 399 395 412 398 428 C2' C B 14 OK OK 430 426 443 429 459 C2' G B 15 OK OK 461 457 477 460 493 C2' A B 16 OK OK 495 491 510 494 526 C2' C B 17 OK OK 528 524 542 527 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' U A 2 OK OK 38 56 41 42 70 C3' C A 3 OK OK 68 86 71 72 101 C3' G A 4 OK OK 99 120 102 103 135 C3' A A 5 OK OK 133 153 136 137 168 C3' G A 6 OK OK 166 187 169 170 202 C3' C A 7 OK OK 200 218 203 204 233 C3' U A 8 OK OK 231 249 234 235 263 C3' G A 9 OK OK 261 282 264 265 296 C3' C B 10 OK OK 294 312 297 298 328 C3' A B 11 OK OK 326 346 329 330 361 C3' G B 12 OK OK 359 380 362 363 395 C3' C B 13 OK OK 393 411 396 397 426 C3' C B 14 OK OK 424 442 427 428 457 C3' G B 15 OK OK 455 476 458 459 491 C3' A B 16 OK OK 489 509 492 493 524 C3' C B 17 OK OK 522 540 525 526 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' U A 2 OK OK 40 55 37 39 68 C4' C A 3 OK OK 70 85 67 69 99 C4' G A 4 OK OK 101 119 98 100 133 C4' A A 5 OK OK 135 152 132 134 166 C4' G A 6 OK OK 168 186 165 167 200 C4' C A 7 OK OK 202 217 199 201 231 C4' U A 8 OK OK 233 248 230 232 261 C4' G A 9 OK OK 263 281 260 262 294 C4' C B 10 OK OK 296 311 293 295 326 C4' A B 11 OK OK 328 345 325 327 359 C4' G B 12 OK OK 361 379 358 360 393 C4' C B 13 OK OK 395 410 392 394 424 C4' C B 14 OK OK 426 441 423 425 455 C4' G B 15 OK OK 457 475 454 456 489 C4' A B 16 OK OK 491 508 488 490 522 C4' C B 17 OK OK 524 539 521 523 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 21 22 3 37 C5' U A 2 OK OK 36 53 54 38 67 C5' C A 3 OK OK 66 83 84 68 98 C5' G A 4 OK OK 97 117 118 99 132 C5' A A 5 OK OK 131 150 151 133 165 C5' G A 6 OK OK 164 184 185 166 199 C5' C A 7 OK OK 198 215 216 200 230 C5' U A 8 OK OK 229 246 247 231 260 C5' G A 9 OK OK 259 279 280 261 293 C5' C B 10 OK OK 292 309 310 294 325 C5' A B 11 OK OK 324 343 344 326 358 C5' G B 12 OK OK 357 377 378 359 392 C5' C B 13 OK OK 391 408 409 393 423 C5' C B 14 OK OK 422 439 440 424 454 C5' G B 15 OK OK 453 473 474 455 488 C5' A B 16 OK OK 487 506 507 489 521 C5' C B 17 OK OK 520 537 538 522 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P U A 2 distorted distorted 6 34 35 36 63 P C A 3 distorted distorted 41 64 65 66 94 P G A 4 distorted distorted 71 95 96 97 128 P A A 5 distorted distorted 102 129 130 131 161 P G A 6 distorted distorted 136 162 163 164 195 P C A 7 distorted distorted 169 196 197 198 226 P U A 8 distorted distorted 203 227 228 229 256 P G A 9 distorted distorted 234 257 258 259 321 P A B 11 distorted distorted 297 322 323 324 354 P G B 12 distorted distorted 329 355 356 357 388 P C B 13 distorted distorted 362 389 390 391 419 P C B 14 distorted distorted 396 420 421 422 450 P G B 15 distorted distorted 427 451 452 453 484 P A B 16 distorted distorted 458 485 486 487 517 P C B 17 distorted distorted 492 518 519 520 ---------------------------------------------------------------------------------