ID code: '5MWI' 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 beta 4 10 7 32 C1' C A 2 beta 27 33 30 52 C1' U A 3 beta 47 53 50 72 C1' G A 4 beta 67 73 70 95 C1' C A 5 beta 90 96 93 115 C1' U A 6 beta 110 116 113 135 C1' G A 7 beta 130 136 133 158 C1' C A 8 beta 153 159 156 178 C1' U A 9 beta 173 179 176 198 C1' G A 10 beta 193 199 196 221 C1' C A 11 beta 216 222 219 281 C1' G A 13 beta 276 282 279 304 C1' C A 14 beta 299 305 302 364 C1' G A 16 beta 359 365 362 387 C1' C A 17 beta 382 388 385 407 C1' U A 18 beta 402 408 405 427 C1' G A 19 beta 422 428 425 450 C1' C A 20 beta 445 451 448 470 C1' U A 21 beta 465 471 468 490 C1' G A 22 beta 485 491 488 513 C1' C A 23 beta 508 514 511 533 C1' U A 24 beta 528 534 531 553 C1' G A 25 beta 548 554 551 576 C1' C A 26 beta 571 577 574 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 9 5 8 30 C2' C A 2 OK 32 28 31 50 C2' U A 3 OK 52 48 51 70 C2' G A 4 OK 72 68 71 93 C2' C A 5 OK 95 91 94 113 C2' U A 6 OK 115 111 114 133 C2' G A 7 OK 135 131 134 156 C2' C A 8 OK 158 154 157 176 C2' U A 9 OK 178 174 177 196 C2' G A 10 OK 198 194 197 219 C2' C A 11 OK 221 217 220 279 C2' G A 13 OK 281 277 280 302 C2' C A 14 OK 304 300 303 362 C2' G A 16 OK 364 360 363 385 C2' C A 17 OK 387 383 386 405 C2' U A 18 OK 407 403 406 425 C2' G A 19 OK 427 423 426 448 C2' C A 20 OK 450 446 449 468 C2' U A 21 OK 470 466 469 488 C2' G A 22 OK 490 486 489 511 C2' C A 23 OK 513 509 512 531 C2' U A 24 OK 533 529 532 551 C2' G A 25 OK 553 549 552 574 C2' C A 26 OK 576 572 575 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' C A 2 OK 26 29 30 48 C3' U A 3 OK 46 49 50 68 C3' G A 4 OK 66 69 70 91 C3' C A 5 OK 89 92 93 111 C3' U A 6 OK 109 112 113 131 C3' G A 7 OK 129 132 133 154 C3' C A 8 OK 152 155 156 174 C3' U A 9 OK 172 175 176 194 C3' G A 10 OK 192 195 196 217 C3' C A 11 OK 215 218 219 277 C3' G A 13 OK 275 278 279 300 C3' C A 14 OK 298 301 302 360 C3' G A 16 OK 358 361 362 383 C3' C A 17 OK 381 384 385 403 C3' U A 18 OK 401 404 405 423 C3' G A 19 OK 421 424 425 446 C3' C A 20 OK 444 447 448 466 C3' U A 21 OK 464 467 468 486 C3' G A 22 OK 484 487 488 509 C3' C A 23 OK 507 510 511 529 C3' U A 24 OK 527 530 531 549 C3' G A 25 OK 547 550 551 572 C3' C A 26 OK 570 573 574 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' C A 2 OK 28 25 27 46 C4' U A 3 OK 48 45 47 66 C4' G A 4 OK 68 65 67 89 C4' C A 5 OK 91 88 90 109 C4' U A 6 OK 111 108 110 129 C4' G A 7 OK 131 128 130 152 C4' C A 8 OK 154 151 153 172 C4' U A 9 OK 174 171 173 192 C4' G A 10 OK 194 191 193 215 C4' C A 11 OK 217 214 216 275 C4' G A 13 OK 277 274 276 298 C4' C A 14 OK 300 297 299 358 C4' G A 16 OK 360 357 359 381 C4' C A 17 OK 383 380 382 401 C4' U A 18 OK 403 400 402 421 C4' G A 19 OK 423 420 422 444 C4' C A 20 OK 446 443 445 464 C4' U A 21 OK 466 463 465 484 C4' G A 22 OK 486 483 485 507 C4' C A 23 OK 509 506 508 527 C4' U A 24 OK 529 526 528 547 C4' G A 25 OK 549 546 548 570 C4' C A 26 OK 572 569 571 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' C A 2 24 26 45 C5' U A 3 44 46 65 C5' G A 4 64 66 88 C5' C A 5 87 89 108 C5' U A 6 107 109 128 C5' G A 7 127 129 151 C5' C A 8 150 152 171 C5' U A 9 170 172 191 C5' G A 10 190 192 214 C5' C A 11 213 215 274 C5' G A 13 273 275 297 C5' C A 14 296 298 357 C5' G A 16 356 358 380 C5' C A 17 379 381 400 C5' U A 18 399 401 420 C5' G A 19 419 421 443 C5' C A 20 442 444 463 C5' U A 21 462 464 483 C5' G A 22 482 484 506 C5' C A 23 505 507 526 C5' U A 24 525 527 546 C5' G A 25 545 547 569 C5' C A 26 568 570 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 2 distorted distorted 6 22 23 24 41 P U A 3 distorted distorted 29 42 43 44 61 P G A 4 distorted distorted 49 62 63 64 84 P C A 5 distorted distorted 69 85 86 87 104 P U A 6 distorted distorted 92 105 106 107 124 P G A 7 distorted distorted 112 125 126 127 147 P C A 8 distorted distorted 132 148 149 150 167 P U A 9 distorted distorted 155 168 169 170 187 P G A 10 distorted distorted 175 188 189 190 210 P C A 11 distorted distorted 195 211 212 213 230 P U A 12 218 231 P U A 12 218 270 P G A 13 distorted distorted 271 272 273 293 P C A 14 distorted distorted 278 294 295 296 313 P U A 15 301 314 P U A 15 301 353 P G A 16 distorted distorted 354 355 356 376 P C A 17 distorted distorted 361 377 378 379 396 P U A 18 distorted distorted 384 397 398 399 416 P G A 19 distorted distorted 404 417 418 419 439 P C A 20 distorted distorted 424 440 441 442 459 P U A 21 distorted distorted 447 460 461 462 479 P G A 22 distorted distorted 467 480 481 482 502 P C A 23 distorted distorted 487 503 504 505 522 P U A 24 distorted distorted 510 523 524 525 542 P G A 25 distorted distorted 530 543 544 545 565 P C A 26 distorted distorted 550 566 567 568 ---------------------------------------------------------------------------------