ID code: '1BN0' 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' G A 2 alpha beta 39 62 45 42 78 C1' A A 3 alpha beta 73 95 79 76 111 C1' C A 4 alpha beta 106 126 112 109 142 C1' U A 5 alpha beta 137 157 143 140 172 C1' A A 6 alpha beta 167 189 173 170 205 C1' G A 7 alpha beta 200 223 206 203 239 C1' C A 8 alpha beta 234 254 240 237 270 C1' G A 9 alpha beta 265 288 271 268 304 C1' G A 10 alpha beta 299 322 305 302 338 C1' A A 11 alpha beta 333 355 339 336 371 C1' G A 12 alpha beta 366 389 372 369 405 C1' G A 13 alpha beta 400 423 406 403 439 C1' C A 14 alpha beta 434 454 440 437 470 C1' U A 15 alpha beta 465 485 471 468 500 C1' A A 16 alpha beta 495 517 501 498 533 C1' G A 17 alpha beta 528 551 534 531 567 C1' U A 18 alpha beta 562 582 568 565 597 C1' C A 19 alpha beta 592 612 598 595 628 C1' C A 20 alpha beta 623 644 629 626 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' G A 2 OK OK 44 40 60 43 76 C2' A A 3 OK OK 78 74 93 77 109 C2' C A 4 OK OK 111 107 124 110 140 C2' U A 5 OK OK 142 138 155 141 170 C2' A A 6 OK OK 172 168 187 171 203 C2' G A 7 OK OK 205 201 221 204 237 C2' C A 8 OK OK 239 235 252 238 268 C2' G A 9 OK OK 270 266 286 269 302 C2' G A 10 OK OK 304 300 320 303 336 C2' A A 11 OK OK 338 334 353 337 369 C2' G A 12 OK OK 371 367 387 370 403 C2' G A 13 OK OK 405 401 421 404 437 C2' C A 14 OK OK 439 435 452 438 468 C2' U A 15 OK OK 470 466 483 469 498 C2' A A 16 OK OK 500 496 515 499 531 C2' G A 17 OK OK 533 529 549 532 565 C2' U A 18 OK OK 567 563 580 566 595 C2' C A 19 OK OK 597 593 610 596 626 C2' C A 20 OK OK 628 624 642 627 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 40 C3' G A 2 OK OK 38 59 41 42 74 C3' A A 3 OK OK 72 92 75 76 107 C3' C A 4 OK OK 105 123 108 109 138 C3' U A 5 OK OK 136 154 139 140 168 C3' A A 6 OK OK 166 186 169 170 201 C3' G A 7 OK OK 199 220 202 203 235 C3' C A 8 OK OK 233 251 236 237 266 C3' G A 9 OK OK 264 285 267 268 300 C3' G A 10 OK OK 298 319 301 302 334 C3' A A 11 OK OK 332 352 335 336 367 C3' G A 12 OK OK 365 386 368 369 401 C3' G A 13 OK OK 399 420 402 403 435 C3' C A 14 OK OK 433 451 436 437 466 C3' U A 15 OK OK 464 482 467 468 496 C3' A A 16 OK OK 494 514 497 498 529 C3' G A 17 OK OK 527 548 530 531 563 C3' U A 18 OK OK 561 579 564 565 593 C3' C A 19 OK OK 591 609 594 595 624 C3' C A 20 OK OK 622 640 625 626 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 38 C4' G A 2 OK OK 40 58 37 39 72 C4' A A 3 OK OK 74 91 71 73 105 C4' C A 4 OK OK 107 122 104 106 136 C4' U A 5 OK OK 138 153 135 137 166 C4' A A 6 OK OK 168 185 165 167 199 C4' G A 7 OK OK 201 219 198 200 233 C4' C A 8 OK OK 235 250 232 234 264 C4' G A 9 OK OK 266 284 263 265 298 C4' G A 10 OK OK 300 318 297 299 332 C4' A A 11 OK OK 334 351 331 333 365 C4' G A 12 OK OK 367 385 364 366 399 C4' G A 13 OK OK 401 419 398 400 433 C4' C A 14 OK OK 435 450 432 434 464 C4' U A 15 OK OK 466 481 463 465 494 C4' A A 16 OK OK 496 513 493 495 527 C4' G A 17 OK OK 529 547 526 528 561 C4' U A 18 OK OK 563 578 560 562 591 C4' C A 19 OK OK 593 608 590 592 622 C4' C A 20 OK OK 624 639 621 623 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' G A 2 OK OK 36 56 57 38 71 C5' A A 3 OK OK 70 89 90 72 104 C5' C A 4 OK OK 103 120 121 105 135 C5' U A 5 OK OK 134 151 152 136 165 C5' A A 6 OK OK 164 183 184 166 198 C5' G A 7 OK OK 197 217 218 199 232 C5' C A 8 OK OK 231 248 249 233 263 C5' G A 9 OK OK 262 282 283 264 297 C5' G A 10 OK OK 296 316 317 298 331 C5' A A 11 OK OK 330 349 350 332 364 C5' G A 12 OK OK 363 383 384 365 398 C5' G A 13 OK OK 397 417 418 399 432 C5' C A 14 OK OK 431 448 449 433 463 C5' U A 15 OK OK 462 479 480 464 493 C5' A A 16 OK OK 492 511 512 494 526 C5' G A 17 OK OK 525 545 546 527 560 C5' U A 18 OK OK 559 576 577 561 590 C5' C A 19 OK OK 589 606 607 591 621 C5' C A 20 OK OK 620 637 638 622 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P A A 3 distorted distorted 41 68 69 70 100 P C A 4 distorted distorted 75 101 102 103 131 P U A 5 distorted distorted 108 132 133 134 161 P A A 6 distorted distorted 139 162 163 164 194 P G A 7 distorted distorted 169 195 196 197 228 P C A 8 distorted distorted 202 229 230 231 259 P G A 9 distorted distorted 236 260 261 262 293 P G A 10 distorted distorted 267 294 295 296 327 P A A 11 distorted distorted 301 328 329 330 360 P G A 12 distorted distorted 335 361 362 363 394 P G A 13 distorted distorted 368 395 396 397 428 P C A 14 distorted distorted 402 429 430 431 459 P U A 15 distorted distorted 436 460 461 462 489 P A A 16 distorted distorted 467 490 491 492 522 P G A 17 distorted distorted 497 523 524 525 556 P U A 18 distorted distorted 530 557 558 559 586 P C A 19 distorted distorted 564 587 588 589 617 P C A 20 distorted distorted 594 618 619 620 ---------------------------------------------------------------------------------