ID code: '2JXQ' 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' C A 2 alpha beta 39 59 45 42 75 C1' A A 3 alpha beta 70 92 76 73 108 C1' G A 4 alpha beta 103 126 109 106 142 C1' A A 5 alpha beta 137 159 143 140 175 C1' G A 6 alpha beta 170 193 176 173 209 C1' A A 7 alpha beta 204 226 210 207 242 C1' G A 8 alpha beta 237 260 243 240 276 C1' C A 9 alpha beta 271 291 277 274 307 C1' G A 10 alpha beta 302 326 308 305 340 C1' C B 11 alpha beta 335 355 341 338 372 C1' G B 12 alpha beta 367 390 373 370 406 C1' C B 13 alpha beta 401 421 407 404 437 C1' U B 14 alpha beta 432 452 438 435 467 C1' C B 15 alpha beta 462 482 468 465 498 C1' U B 16 alpha beta 493 513 499 496 528 C1' C B 17 alpha beta 523 543 529 526 559 C1' U B 18 alpha beta 554 574 560 557 589 C1' G B 19 alpha beta 584 607 590 587 623 C1' C B 20 alpha beta 618 639 624 621 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' C A 2 OK OK 44 40 57 43 73 C2' A A 3 OK OK 75 71 90 74 106 C2' G A 4 OK OK 108 104 124 107 140 C2' A A 5 OK OK 142 138 157 141 173 C2' G A 6 OK OK 175 171 191 174 207 C2' A A 7 OK OK 209 205 224 208 240 C2' G A 8 OK OK 242 238 258 241 274 C2' C A 9 OK OK 276 272 289 275 305 C2' G A 10 OK OK 307 303 324 306 338 C2' C B 11 OK OK 340 336 353 339 370 C2' G B 12 OK OK 372 368 388 371 404 C2' C B 13 OK OK 406 402 419 405 435 C2' U B 14 OK OK 437 433 450 436 465 C2' C B 15 OK OK 467 463 480 466 496 C2' U B 16 OK OK 498 494 511 497 526 C2' C B 17 OK OK 528 524 541 527 557 C2' U B 18 OK OK 559 555 572 558 587 C2' G B 19 OK OK 589 585 605 588 621 C2' C B 20 OK OK 623 619 637 622 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' C A 2 OK OK 38 56 41 42 71 C3' A A 3 OK OK 69 89 72 73 104 C3' G A 4 OK OK 102 123 105 106 138 C3' A A 5 OK OK 136 156 139 140 171 C3' G A 6 OK OK 169 190 172 173 205 C3' A A 7 OK OK 203 223 206 207 238 C3' G A 8 OK OK 236 257 239 240 272 C3' C A 9 OK OK 270 288 273 274 303 C3' G A 10 OK OK 301 322 304 305 336 C3' C B 11 OK OK 334 352 337 338 368 C3' G B 12 OK OK 366 387 369 370 402 C3' C B 13 OK OK 400 418 403 404 433 C3' U B 14 OK OK 431 449 434 435 463 C3' C B 15 OK OK 461 479 464 465 494 C3' U B 16 OK OK 492 510 495 496 524 C3' C B 17 OK OK 522 540 525 526 555 C3' U B 18 OK OK 553 571 556 557 585 C3' G B 19 OK OK 583 604 586 587 619 C3' C B 20 OK OK 617 635 620 621 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' C A 2 OK OK 40 55 37 39 69 C4' A A 3 OK OK 71 88 68 70 102 C4' G A 4 OK OK 104 122 101 103 136 C4' A A 5 OK OK 138 155 135 137 169 C4' G A 6 OK OK 171 189 168 170 203 C4' A A 7 OK OK 205 222 202 204 236 C4' G A 8 OK OK 238 256 235 237 270 C4' C A 9 OK OK 272 287 269 271 301 C4' G A 10 OK OK 303 321 300 302 334 C4' C B 11 OK OK 336 351 333 335 366 C4' G B 12 OK OK 368 386 365 367 400 C4' C B 13 OK OK 402 417 399 401 431 C4' U B 14 OK OK 433 448 430 432 461 C4' C B 15 OK OK 463 478 460 462 492 C4' U B 16 OK OK 494 509 491 493 522 C4' C B 17 OK OK 524 539 521 523 553 C4' U B 18 OK OK 555 570 552 554 583 C4' G B 19 OK OK 585 603 582 584 617 C4' C B 20 OK OK 619 634 616 618 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' C A 2 OK OK 36 53 54 38 68 C5' A A 3 OK OK 67 86 87 69 101 C5' G A 4 OK OK 100 120 121 102 135 C5' A A 5 OK OK 134 153 154 136 168 C5' G A 6 OK OK 167 187 188 169 202 C5' A A 7 OK OK 201 220 221 203 235 C5' G A 8 OK OK 234 254 255 236 269 C5' C A 9 OK OK 268 285 286 270 300 C5' G A 10 OK OK 299 319 320 301 333 C5' C B 11 OK OK 332 349 350 334 365 C5' G B 12 OK OK 364 384 385 366 399 C5' C B 13 OK OK 398 415 416 400 430 C5' U B 14 OK OK 429 446 447 431 460 C5' C B 15 OK OK 459 476 477 461 491 C5' U B 16 OK OK 490 507 508 492 521 C5' C B 17 OK OK 520 537 538 522 552 C5' U B 18 OK OK 551 568 569 553 582 C5' G B 19 OK OK 581 601 602 583 616 C5' C B 20 OK OK 615 632 633 617 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P C A 2 distorted distorted 6 34 35 36 64 P A A 3 distorted distorted 41 65 66 67 97 P G A 4 distorted distorted 72 98 99 100 131 P A A 5 distorted distorted 105 132 133 134 164 P G A 6 distorted distorted 139 165 166 167 198 P A A 7 distorted distorted 172 199 200 201 231 P G A 8 distorted distorted 206 232 233 234 265 P C A 9 distorted distorted 239 266 267 268 296 P G A 10 distorted distorted 273 297 298 299 361 P G B 12 distorted distorted 337 362 363 364 395 P C B 13 distorted distorted 369 396 397 398 426 P U B 14 distorted distorted 403 427 428 429 456 P C B 15 distorted distorted 434 457 458 459 487 P U B 16 distorted distorted 464 488 489 490 517 P C B 17 distorted distorted 495 518 519 520 548 P U B 18 distorted distorted 525 549 550 551 578 P G B 19 distorted distorted 556 579 580 581 612 P C B 20 distorted distorted 586 613 614 615 ---------------------------------------------------------------------------------