ID code: '2JXS' 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' A A 6 alpha beta 170 192 176 173 208 C1' G A 7 alpha beta 203 226 209 206 242 C1' A A 8 alpha beta 237 259 243 240 275 C1' G A 9 alpha beta 270 293 276 273 309 C1' C A 10 alpha beta 304 324 310 307 340 C1' G A 11 alpha beta 335 359 341 338 373 C1' C B 12 alpha beta 368 388 374 371 405 C1' G B 13 alpha beta 400 423 406 403 439 C1' C B 14 alpha beta 434 454 440 437 470 C1' U B 15 alpha beta 465 485 471 468 500 C1' C B 16 alpha beta 495 515 501 498 531 C1' U B 17 alpha beta 526 546 532 529 561 C1' C B 18 alpha beta 556 576 562 559 592 C1' U B 19 alpha beta 587 607 593 590 622 C1' G B 20 alpha beta 617 640 623 620 656 C1' C B 21 alpha beta 651 672 657 654 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A A 6 OK OK 175 171 190 174 206 C2' G A 7 OK OK 208 204 224 207 240 C2' A A 8 OK OK 242 238 257 241 273 C2' G A 9 OK OK 275 271 291 274 307 C2' C A 10 OK OK 309 305 322 308 338 C2' G A 11 OK OK 340 336 357 339 371 C2' C B 12 OK OK 373 369 386 372 403 C2' G B 13 OK OK 405 401 421 404 437 C2' C B 14 OK OK 439 435 452 438 468 C2' U B 15 OK OK 470 466 483 469 498 C2' C B 16 OK OK 500 496 513 499 529 C2' U B 17 OK OK 531 527 544 530 559 C2' C B 18 OK OK 561 557 574 560 590 C2' U B 19 OK OK 592 588 605 591 620 C2' G B 20 OK OK 622 618 638 621 654 C2' C B 21 OK OK 656 652 670 655 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 6 OK OK 169 189 172 173 204 C3' G A 7 OK OK 202 223 205 206 238 C3' A A 8 OK OK 236 256 239 240 271 C3' G A 9 OK OK 269 290 272 273 305 C3' C A 10 OK OK 303 321 306 307 336 C3' G A 11 OK OK 334 355 337 338 369 C3' C B 12 OK OK 367 385 370 371 401 C3' G B 13 OK OK 399 420 402 403 435 C3' C B 14 OK OK 433 451 436 437 466 C3' U B 15 OK OK 464 482 467 468 496 C3' C B 16 OK OK 494 512 497 498 527 C3' U B 17 OK OK 525 543 528 529 557 C3' C B 18 OK OK 555 573 558 559 588 C3' U B 19 OK OK 586 604 589 590 618 C3' G B 20 OK OK 616 637 619 620 652 C3' C B 21 OK OK 650 668 653 654 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 6 OK OK 171 188 168 170 202 C4' G A 7 OK OK 204 222 201 203 236 C4' A A 8 OK OK 238 255 235 237 269 C4' G A 9 OK OK 271 289 268 270 303 C4' C A 10 OK OK 305 320 302 304 334 C4' G A 11 OK OK 336 354 333 335 367 C4' C B 12 OK OK 369 384 366 368 399 C4' G B 13 OK OK 401 419 398 400 433 C4' C B 14 OK OK 435 450 432 434 464 C4' U B 15 OK OK 466 481 463 465 494 C4' C B 16 OK OK 496 511 493 495 525 C4' U B 17 OK OK 527 542 524 526 555 C4' C B 18 OK OK 557 572 554 556 586 C4' U B 19 OK OK 588 603 585 587 616 C4' G B 20 OK OK 618 636 615 617 650 C4' C B 21 OK OK 652 667 649 651 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A A 6 OK OK 167 186 187 169 201 C5' G A 7 OK OK 200 220 221 202 235 C5' A A 8 OK OK 234 253 254 236 268 C5' G A 9 OK OK 267 287 288 269 302 C5' C A 10 OK OK 301 318 319 303 333 C5' G A 11 OK OK 332 352 353 334 366 C5' C B 12 OK OK 365 382 383 367 398 C5' G B 13 OK OK 397 417 418 399 432 C5' C B 14 OK OK 431 448 449 433 463 C5' U B 15 OK OK 462 479 480 464 493 C5' C B 16 OK OK 492 509 510 494 524 C5' U B 17 OK OK 523 540 541 525 554 C5' C B 18 OK OK 553 570 571 555 585 C5' U B 19 OK OK 584 601 602 586 615 C5' G B 20 OK OK 614 634 635 616 649 C5' C B 21 OK OK 648 665 666 650 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 A A 6 distorted distorted 139 165 166 167 197 P G A 7 distorted distorted 172 198 199 200 231 P A A 8 distorted distorted 205 232 233 234 264 P G A 9 distorted distorted 239 265 266 267 298 P C A 10 distorted distorted 272 299 300 301 329 P G A 11 distorted distorted 306 330 331 332 394 P G B 13 distorted distorted 370 395 396 397 428 P C B 14 distorted distorted 402 429 430 431 459 P U B 15 distorted distorted 436 460 461 462 489 P C B 16 distorted distorted 467 490 491 492 520 P U B 17 distorted distorted 497 521 522 523 550 P C B 18 distorted distorted 528 551 552 553 581 P U B 19 distorted distorted 558 582 583 584 611 P G B 20 distorted distorted 589 612 613 614 645 P C B 21 distorted distorted 619 646 647 648 ---------------------------------------------------------------------------------