ID code: '2IRN' 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' --------------------------------------------------------------------------------- 13 C1' G A 1 alpha beta 8 31 14 11 48 C1' C A 2 alpha beta 43 63 49 46 79 C1' U A 3 alpha beta 74 94 80 77 109 C1' G A 4 alpha beta 104 127 110 107 143 C1' A A 5 alpha beta 138 160 144 141 176 C1' G A 6 alpha beta 171 194 177 174 210 C1' G A 7 alpha beta 205 228 211 208 244 C1' C A 8 alpha beta 239 259 245 242 275 C1' U A 9 alpha beta 270 291 276 273 308 C1' G B 10 alpha beta 303 326 309 306 343 C1' C B 11 alpha beta 338 358 344 341 374 C1' U B 12 alpha beta 369 389 375 372 404 C1' G B 13 alpha beta 399 422 405 402 438 C1' A B 14 alpha beta 433 455 439 436 471 C1' G B 15 alpha beta 466 489 472 469 505 C1' G B 16 alpha beta 500 523 506 503 539 C1' C B 17 alpha beta 534 554 540 537 570 C1' U B 18 alpha beta 565 586 571 568 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK OK 13 9 29 12 46 C2' C A 2 OK OK 48 44 61 47 77 C2' U A 3 OK OK 79 75 92 78 107 C2' G A 4 OK OK 109 105 125 108 141 C2' A A 5 OK OK 143 139 158 142 174 C2' G A 6 OK OK 176 172 192 175 208 C2' G A 7 OK OK 210 206 226 209 242 C2' C A 8 OK OK 244 240 257 243 273 C2' U A 9 OK OK 275 271 289 274 306 C2' G B 10 OK OK 308 304 324 307 341 C2' C B 11 OK OK 343 339 356 342 372 C2' U B 12 OK OK 374 370 387 373 402 C2' G B 13 OK OK 404 400 420 403 436 C2' A B 14 OK OK 438 434 453 437 469 C2' G B 15 OK OK 471 467 487 470 503 C2' G B 16 OK OK 505 501 521 504 537 C2' C B 17 OK OK 539 535 552 538 568 C2' U B 18 OK OK 570 566 584 569 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK OK 7 28 10 11 44 C3' C A 2 OK OK 42 60 45 46 75 C3' U A 3 OK OK 73 91 76 77 105 C3' G A 4 OK OK 103 124 106 107 139 C3' A A 5 OK OK 137 157 140 141 172 C3' G A 6 OK OK 170 191 173 174 206 C3' G A 7 OK OK 204 225 207 208 240 C3' C A 8 OK OK 238 256 241 242 271 C3' U A 9 OK OK 269 287 272 273 304 C3' G B 10 OK OK 302 323 305 306 339 C3' C B 11 OK OK 337 355 340 341 370 C3' U B 12 OK OK 368 386 371 372 400 C3' G B 13 OK OK 398 419 401 402 434 C3' A B 14 OK OK 432 452 435 436 467 C3' G B 15 OK OK 465 486 468 469 501 C3' G B 16 OK OK 499 520 502 503 535 C3' C B 17 OK OK 533 551 536 537 566 C3' U B 18 OK OK 564 582 567 568 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK OK 9 27 6 8 42 C4' C A 2 OK OK 44 59 41 43 73 C4' U A 3 OK OK 75 90 72 74 103 C4' G A 4 OK OK 105 123 102 104 137 C4' A A 5 OK OK 139 156 136 138 170 C4' G A 6 OK OK 172 190 169 171 204 C4' G A 7 OK OK 206 224 203 205 238 C4' C A 8 OK OK 240 255 237 239 269 C4' U A 9 OK OK 271 286 268 270 302 C4' G B 10 OK OK 304 322 301 303 337 C4' C B 11 OK OK 339 354 336 338 368 C4' U B 12 OK OK 370 385 367 369 398 C4' G B 13 OK OK 400 418 397 399 432 C4' A B 14 OK OK 434 451 431 433 465 C4' G B 15 OK OK 467 485 464 466 499 C4' G B 16 OK OK 501 519 498 500 533 C4' C B 17 OK OK 535 550 532 534 564 C4' U B 18 OK OK 566 581 563 565 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 OK OK 5 25 26 7 41 C5' C A 2 OK OK 40 57 58 42 72 C5' U A 3 OK OK 71 88 89 73 102 C5' G A 4 OK OK 101 121 122 103 136 C5' A A 5 OK OK 135 154 155 137 169 C5' G A 6 OK OK 168 188 189 170 203 C5' G A 7 OK OK 202 222 223 204 237 C5' C A 8 OK OK 236 253 254 238 268 C5' U A 9 OK OK 267 284 285 269 301 C5' G B 10 OK OK 300 320 321 302 336 C5' C B 11 OK OK 335 352 353 337 367 C5' U B 12 OK OK 366 383 384 368 397 C5' G B 13 OK OK 396 416 417 398 431 C5' A B 14 OK OK 430 449 450 432 464 C5' G B 15 OK OK 463 483 484 465 498 C5' G B 16 OK OK 497 517 518 499 532 C5' C B 17 OK OK 531 548 549 533 563 C5' U B 18 OK OK 562 579 580 564 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 distorted distorted 3 4 5 37 P C A 2 distorted distorted 10 38 39 40 68 P U A 3 distorted distorted 45 69 70 71 98 P G A 4 distorted distorted 76 99 100 101 132 P A A 5 distorted distorted 106 133 134 135 165 P G A 6 distorted distorted 140 166 167 168 199 P G A 7 distorted distorted 173 200 201 202 233 P C A 8 distorted distorted 207 234 235 236 264 P U A 9 distorted distorted 241 265 266 267 297 P G B 10 OK OK 298 299 300 332 P C B 11 distorted distorted 305 333 334 335 363 P U B 12 distorted distorted 340 364 365 366 393 P G B 13 distorted distorted 371 394 395 396 427 P A B 14 distorted distorted 401 428 429 430 460 P G B 15 distorted distorted 435 461 462 463 494 P G B 16 distorted distorted 468 495 496 497 528 P C B 17 distorted distorted 502 529 530 531 559 P U B 18 distorted distorted 536 560 561 562 ---------------------------------------------------------------------------------