ID code: '2MVS' 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 1 1 alpha beta 4 27 10 7 44 C1' G 1 2 alpha beta 39 62 45 42 84 C1' 6MZ 1 3 alpha beta 83 92 72 85 114 C1' C 1 4 alpha beta 109 129 115 112 145 C1' U 1 5 alpha beta 140 160 146 143 175 C1' A 1 6 alpha beta 170 192 176 173 208 C1' G 1 7 alpha beta 203 226 209 206 242 C1' U 1 8 alpha beta 237 257 243 240 272 C1' C 1 9 alpha beta 267 287 273 270 303 C1' C 1 10 alpha beta 298 319 304 301 333 C1' G 2 11 alpha beta 328 351 334 331 368 C1' G 2 12 alpha beta 363 386 369 366 408 C1' 6MZ 2 13 alpha beta 407 416 396 409 438 C1' C 2 14 alpha beta 433 453 439 436 469 C1' U 2 15 alpha beta 464 484 470 467 499 C1' A 2 16 alpha beta 494 516 500 497 532 C1' G 2 17 alpha beta 527 550 533 530 566 C1' U 2 18 alpha beta 561 581 567 564 596 C1' C 2 19 alpha beta 591 611 597 594 627 C1' C 2 20 alpha beta 622 643 628 625 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G 1 1 OK OK 9 5 25 8 42 C2' G 1 2 OK OK 44 40 60 43 85 C2' 6MZ 1 3 OK OK 84 87 99 86 112 C2' C 1 4 OK OK 114 110 127 113 143 C2' U 1 5 OK OK 145 141 158 144 173 C2' A 1 6 OK OK 175 171 190 174 206 C2' G 1 7 OK OK 208 204 224 207 240 C2' U 1 8 OK OK 242 238 255 241 270 C2' C 1 9 OK OK 272 268 285 271 301 C2' C 1 10 OK OK 303 299 317 302 331 C2' G 2 11 OK OK 333 329 349 332 366 C2' G 2 12 OK OK 368 364 384 367 409 C2' 6MZ 2 13 OK OK 408 411 423 410 436 C2' C 2 14 OK OK 438 434 451 437 467 C2' U 2 15 OK OK 469 465 482 468 497 C2' A 2 16 OK OK 499 495 514 498 530 C2' G 2 17 OK OK 532 528 548 531 564 C2' U 2 18 OK OK 566 562 579 565 594 C2' C 2 19 OK OK 596 592 609 595 625 C2' C 2 20 OK OK 627 623 641 626 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G 1 1 OK OK 3 24 6 7 40 C3' G 1 2 OK OK 38 59 41 42 87 C3' 6MZ 1 3 OK OK 82 98 88 85 110 C3' C 1 4 OK OK 108 126 111 112 141 C3' U 1 5 OK OK 139 157 142 143 171 C3' A 1 6 OK OK 169 189 172 173 204 C3' G 1 7 OK OK 202 223 205 206 238 C3' U 1 8 OK OK 236 254 239 240 268 C3' C 1 9 OK OK 266 284 269 270 299 C3' C 1 10 OK OK 297 315 300 301 329 C3' G 2 11 OK OK 327 348 330 331 364 C3' G 2 12 OK OK 362 383 365 366 411 C3' 6MZ 2 13 OK OK 406 422 412 409 434 C3' C 2 14 OK OK 432 450 435 436 465 C3' U 2 15 OK OK 463 481 466 467 495 C3' A 2 16 OK OK 493 513 496 497 528 C3' G 2 17 OK OK 526 547 529 530 562 C3' U 2 18 OK OK 560 578 563 564 592 C3' C 2 19 OK OK 590 608 593 594 623 C3' C 2 20 OK OK 621 639 624 625 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G 1 1 OK OK 5 23 2 4 38 C4' G 1 2 OK OK 40 58 37 39 82 C4' 6MZ 1 3 OK OK 87 97 81 83 108 C4' C 1 4 OK OK 110 125 107 109 139 C4' U 1 5 OK OK 141 156 138 140 169 C4' A 1 6 OK OK 171 188 168 170 202 C4' G 1 7 OK OK 204 222 201 203 236 C4' U 1 8 OK OK 238 253 235 237 266 C4' C 1 9 OK OK 268 283 265 267 297 C4' C 1 10 OK OK 299 314 296 298 327 C4' G 2 11 OK OK 329 347 326 328 362 C4' G 2 12 OK OK 364 382 361 363 406 C4' 6MZ 2 13 OK OK 411 421 405 407 432 C4' C 2 14 OK OK 434 449 431 433 463 C4' U 2 15 OK OK 465 480 462 464 493 C4' A 2 16 OK OK 495 512 492 494 526 C4' G 2 17 OK OK 528 546 525 527 560 C4' U 2 18 OK OK 562 577 559 561 590 C4' C 2 19 OK OK 592 607 589 591 621 C4' C 2 20 OK OK 623 638 620 622 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G 1 1 OK OK 1 21 22 3 37 C5' G 1 2 OK OK 36 56 57 38 81 C5' 6MZ 1 3 OK OK 80 95 96 82 107 C5' C 1 4 OK OK 106 123 124 108 138 C5' U 1 5 OK OK 137 154 155 139 168 C5' A 1 6 OK OK 167 186 187 169 201 C5' G 1 7 OK OK 200 220 221 202 235 C5' U 1 8 OK OK 234 251 252 236 265 C5' C 1 9 OK OK 264 281 282 266 296 C5' C 1 10 OK OK 295 312 313 297 326 C5' G 2 11 OK OK 325 345 346 327 361 C5' G 2 12 OK OK 360 380 381 362 405 C5' 6MZ 2 13 OK OK 404 419 420 406 431 C5' C 2 14 OK OK 430 447 448 432 462 C5' U 2 15 OK OK 461 478 479 463 492 C5' A 2 16 OK OK 491 510 511 493 525 C5' G 2 17 OK OK 524 544 545 526 559 C5' U 2 18 OK OK 558 575 576 560 589 C5' C 2 19 OK OK 588 605 606 590 620 C5' C 2 20 OK OK 619 636 637 621 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G 1 2 distorted distorted 6 34 35 36 89 P 6MZ 1 3 distorted distorted 41 70 71 80 103 P C 1 4 distorted distorted 88 104 105 106 134 P U 1 5 distorted distorted 111 135 136 137 164 P A 1 6 distorted distorted 142 165 166 167 197 P G 1 7 distorted distorted 172 198 199 200 231 P U 1 8 distorted distorted 205 232 233 234 261 P C 1 9 distorted distorted 239 262 263 264 292 P C 1 10 distorted distorted 269 293 294 295 357 P G 2 12 distorted distorted 330 358 359 360 413 P 6MZ 2 13 OK OK 365 394 395 404 427 P C 2 14 distorted distorted 412 428 429 430 458 P U 2 15 distorted distorted 435 459 460 461 488 P A 2 16 distorted distorted 466 489 490 491 521 P G 2 17 distorted distorted 496 522 523 524 555 P U 2 18 distorted distorted 529 556 557 558 585 P C 2 19 distorted distorted 563 586 587 588 616 P C 2 20 distorted distorted 593 617 618 619 ---------------------------------------------------------------------------------