ID code: '2MVY' 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 78 C1' A 1 3 alpha beta 73 95 79 76 111 C1' C 1 4 alpha beta 106 126 112 109 142 C1' U 1 5 alpha beta 137 157 143 140 172 C1' A 1 6 alpha beta 167 189 173 170 205 C1' G 1 7 alpha beta 200 223 206 203 239 C1' U 1 8 alpha beta 234 254 240 237 269 C1' C 1 9 alpha beta 264 284 270 267 300 C1' C 1 10 alpha beta 295 316 301 298 330 C1' G 2 11 alpha beta 325 348 331 328 365 C1' G 2 12 alpha beta 360 383 366 363 399 C1' A 2 13 alpha beta 394 416 400 397 432 C1' C 2 14 alpha beta 427 447 433 430 463 C1' U 2 15 alpha beta 458 478 464 461 493 C1' A 2 16 alpha beta 488 510 494 491 526 C1' G 2 17 alpha beta 521 544 527 524 560 C1' U 2 18 alpha beta 555 575 561 558 590 C1' C 2 19 alpha beta 585 605 591 588 621 C1' C 2 20 alpha beta 616 637 622 619 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 76 C2' A 1 3 OK OK 78 74 93 77 109 C2' C 1 4 OK OK 111 107 124 110 140 C2' U 1 5 OK OK 142 138 155 141 170 C2' A 1 6 OK OK 172 168 187 171 203 C2' G 1 7 OK OK 205 201 221 204 237 C2' U 1 8 OK OK 239 235 252 238 267 C2' C 1 9 OK OK 269 265 282 268 298 C2' C 1 10 OK OK 300 296 314 299 328 C2' G 2 11 OK OK 330 326 346 329 363 C2' G 2 12 OK OK 365 361 381 364 397 C2' A 2 13 OK OK 399 395 414 398 430 C2' C 2 14 OK OK 432 428 445 431 461 C2' U 2 15 OK OK 463 459 476 462 491 C2' A 2 16 OK OK 493 489 508 492 524 C2' G 2 17 OK OK 526 522 542 525 558 C2' U 2 18 OK OK 560 556 573 559 588 C2' C 2 19 OK OK 590 586 603 589 619 C2' C 2 20 OK OK 621 617 635 620 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 74 C3' A 1 3 OK OK 72 92 75 76 107 C3' C 1 4 OK OK 105 123 108 109 138 C3' U 1 5 OK OK 136 154 139 140 168 C3' A 1 6 OK OK 166 186 169 170 201 C3' G 1 7 OK OK 199 220 202 203 235 C3' U 1 8 OK OK 233 251 236 237 265 C3' C 1 9 OK OK 263 281 266 267 296 C3' C 1 10 OK OK 294 312 297 298 326 C3' G 2 11 OK OK 324 345 327 328 361 C3' G 2 12 OK OK 359 380 362 363 395 C3' A 2 13 OK OK 393 413 396 397 428 C3' C 2 14 OK OK 426 444 429 430 459 C3' U 2 15 OK OK 457 475 460 461 489 C3' A 2 16 OK OK 487 507 490 491 522 C3' G 2 17 OK OK 520 541 523 524 556 C3' U 2 18 OK OK 554 572 557 558 586 C3' C 2 19 OK OK 584 602 587 588 617 C3' C 2 20 OK OK 615 633 618 619 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 72 C4' A 1 3 OK OK 74 91 71 73 105 C4' C 1 4 OK OK 107 122 104 106 136 C4' U 1 5 OK OK 138 153 135 137 166 C4' A 1 6 OK OK 168 185 165 167 199 C4' G 1 7 OK OK 201 219 198 200 233 C4' U 1 8 OK OK 235 250 232 234 263 C4' C 1 9 OK OK 265 280 262 264 294 C4' C 1 10 OK OK 296 311 293 295 324 C4' G 2 11 OK OK 326 344 323 325 359 C4' G 2 12 OK OK 361 379 358 360 393 C4' A 2 13 OK OK 395 412 392 394 426 C4' C 2 14 OK OK 428 443 425 427 457 C4' U 2 15 OK OK 459 474 456 458 487 C4' A 2 16 OK OK 489 506 486 488 520 C4' G 2 17 OK OK 522 540 519 521 554 C4' U 2 18 OK OK 556 571 553 555 584 C4' C 2 19 OK OK 586 601 583 585 615 C4' C 2 20 OK OK 617 632 614 616 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 71 C5' A 1 3 OK OK 70 89 90 72 104 C5' C 1 4 OK OK 103 120 121 105 135 C5' U 1 5 OK OK 134 151 152 136 165 C5' A 1 6 OK OK 164 183 184 166 198 C5' G 1 7 OK OK 197 217 218 199 232 C5' U 1 8 OK OK 231 248 249 233 262 C5' C 1 9 OK OK 261 278 279 263 293 C5' C 1 10 OK OK 292 309 310 294 323 C5' G 2 11 OK OK 322 342 343 324 358 C5' G 2 12 OK OK 357 377 378 359 392 C5' A 2 13 OK OK 391 410 411 393 425 C5' C 2 14 OK OK 424 441 442 426 456 C5' U 2 15 OK OK 455 472 473 457 486 C5' A 2 16 OK OK 485 504 505 487 519 C5' G 2 17 OK OK 518 538 539 520 553 C5' U 2 18 OK OK 552 569 570 554 583 C5' C 2 19 OK OK 582 599 600 584 614 C5' C 2 20 OK OK 613 630 631 615 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G 1 2 distorted distorted 6 34 35 36 67 P A 1 3 distorted distorted 41 68 69 70 100 P C 1 4 distorted distorted 75 101 102 103 131 P U 1 5 distorted distorted 108 132 133 134 161 P A 1 6 distorted distorted 139 162 163 164 194 P G 1 7 distorted distorted 169 195 196 197 228 P U 1 8 distorted distorted 202 229 230 231 258 P C 1 9 distorted distorted 236 259 260 261 289 P C 1 10 distorted distorted 266 290 291 292 354 P G 2 12 distorted distorted 327 355 356 357 388 P A 2 13 distorted distorted 362 389 390 391 421 P C 2 14 distorted distorted 396 422 423 424 452 P U 2 15 distorted distorted 429 453 454 455 482 P A 2 16 distorted distorted 460 483 484 485 515 P G 2 17 distorted distorted 490 516 517 518 549 P U 2 18 distorted distorted 523 550 551 552 579 P C 2 19 distorted distorted 557 580 581 582 610 P C 2 20 distorted distorted 587 611 612 613 ---------------------------------------------------------------------------------