ID code: '2MFD' 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' --------------------------------------------------------------------------------- 13 C1' G A 55 alpha beta 8 31 14 11 48 C1' G A 56 alpha beta 43 66 49 46 82 C1' C A 57 alpha beta 77 97 83 80 113 C1' G A 58 alpha beta 108 131 114 111 147 C1' U A 59 alpha beta 142 162 148 145 177 C1' U A 60 alpha beta 172 192 178 175 207 C1' C A 61 alpha beta 202 222 208 205 238 C1' G A 62 alpha beta 233 256 239 236 272 C1' C A 63 alpha beta 267 287 273 270 303 C1' U A 64 alpha beta 298 318 304 301 333 C1' U A 65 alpha beta 328 348 334 331 363 C1' A A 66 alpha beta 358 380 364 361 396 C1' G A 67 alpha beta 391 414 397 394 430 C1' A A 68 alpha beta 425 447 431 428 463 C1' A A 69 alpha beta 458 480 464 461 496 C1' C A 70 alpha beta 491 511 497 494 527 C1' G A 71 alpha beta 522 545 528 525 561 C1' U A 72 alpha beta 556 576 562 559 591 C1' C A 73 alpha beta 586 607 592 589 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 55 OK OK 13 9 29 12 46 C2' G A 56 OK OK 48 44 64 47 80 C2' C A 57 OK OK 82 78 95 81 111 C2' G A 58 OK OK 113 109 129 112 145 C2' U A 59 OK OK 147 143 160 146 175 C2' U A 60 OK OK 177 173 190 176 205 C2' C A 61 OK OK 207 203 220 206 236 C2' G A 62 OK OK 238 234 254 237 270 C2' C A 63 OK OK 272 268 285 271 301 C2' U A 64 OK OK 303 299 316 302 331 C2' U A 65 OK OK 333 329 346 332 361 C2' A A 66 OK OK 363 359 378 362 394 C2' G A 67 OK OK 396 392 412 395 428 C2' A A 68 OK OK 430 426 445 429 461 C2' A A 69 OK OK 463 459 478 462 494 C2' C A 70 OK OK 496 492 509 495 525 C2' G A 71 OK OK 527 523 543 526 559 C2' U A 72 OK OK 561 557 574 560 589 C2' C A 73 OK OK 591 587 605 590 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 55 OK OK 7 28 10 11 44 C3' G A 56 OK OK 42 63 45 46 78 C3' C A 57 OK OK 76 94 79 80 109 C3' G A 58 OK OK 107 128 110 111 143 C3' U A 59 OK OK 141 159 144 145 173 C3' U A 60 OK OK 171 189 174 175 203 C3' C A 61 OK OK 201 219 204 205 234 C3' G A 62 OK OK 232 253 235 236 268 C3' C A 63 OK OK 266 284 269 270 299 C3' U A 64 OK OK 297 315 300 301 329 C3' U A 65 OK OK 327 345 330 331 359 C3' A A 66 OK OK 357 377 360 361 392 C3' G A 67 OK OK 390 411 393 394 426 C3' A A 68 OK OK 424 444 427 428 459 C3' A A 69 OK OK 457 477 460 461 492 C3' C A 70 OK OK 490 508 493 494 523 C3' G A 71 OK OK 521 542 524 525 557 C3' U A 72 OK OK 555 573 558 559 587 C3' C A 73 OK OK 585 603 588 589 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 55 OK OK 9 27 6 8 42 C4' G A 56 OK OK 44 62 41 43 76 C4' C A 57 OK OK 78 93 75 77 107 C4' G A 58 OK OK 109 127 106 108 141 C4' U A 59 OK OK 143 158 140 142 171 C4' U A 60 OK OK 173 188 170 172 201 C4' C A 61 OK OK 203 218 200 202 232 C4' G A 62 OK OK 234 252 231 233 266 C4' C A 63 OK OK 268 283 265 267 297 C4' U A 64 OK OK 299 314 296 298 327 C4' U A 65 OK OK 329 344 326 328 357 C4' A A 66 OK OK 359 376 356 358 390 C4' G A 67 OK OK 392 410 389 391 424 C4' A A 68 OK OK 426 443 423 425 457 C4' A A 69 OK OK 459 476 456 458 490 C4' C A 70 OK OK 492 507 489 491 521 C4' G A 71 OK OK 523 541 520 522 555 C4' U A 72 OK OK 557 572 554 556 585 C4' C A 73 OK OK 587 602 584 586 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 55 OK OK 5 25 26 7 41 C5' G A 56 OK OK 40 60 61 42 75 C5' C A 57 OK OK 74 91 92 76 106 C5' G A 58 OK OK 105 125 126 107 140 C5' U A 59 OK OK 139 156 157 141 170 C5' U A 60 OK OK 169 186 187 171 200 C5' C A 61 OK OK 199 216 217 201 231 C5' G A 62 OK OK 230 250 251 232 265 C5' C A 63 OK OK 264 281 282 266 296 C5' U A 64 OK OK 295 312 313 297 326 C5' U A 65 OK OK 325 342 343 327 356 C5' A A 66 OK OK 355 374 375 357 389 C5' G A 67 OK OK 388 408 409 390 423 C5' A A 68 OK OK 422 441 442 424 456 C5' A A 69 OK OK 455 474 475 457 489 C5' C A 70 OK OK 488 505 506 490 520 C5' G A 71 OK OK 519 539 540 521 554 C5' U A 72 OK OK 553 570 571 555 584 C5' C A 73 OK OK 583 600 601 585 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 55 distorted distorted 3 4 5 37 P G A 56 distorted distorted 10 38 39 40 71 P C A 57 distorted distorted 45 72 73 74 102 P G A 58 distorted distorted 79 103 104 105 136 P U A 59 distorted distorted 110 137 138 139 166 P U A 60 distorted distorted 144 167 168 169 196 P C A 61 distorted distorted 174 197 198 199 227 P G A 62 distorted distorted 204 228 229 230 261 P C A 63 distorted distorted 235 262 263 264 292 P U A 64 distorted distorted 269 293 294 295 322 P U A 65 distorted distorted 300 323 324 325 352 P A A 66 distorted distorted 330 353 354 355 385 P G A 67 distorted distorted 360 386 387 388 419 P A A 68 distorted distorted 393 420 421 422 452 P A A 69 distorted distorted 427 453 454 455 485 P C A 70 distorted distorted 460 486 487 488 516 P G A 71 distorted distorted 493 517 518 519 550 P U A 72 distorted distorted 524 551 552 553 580 P C A 73 distorted distorted 558 581 582 583 ---------------------------------------------------------------------------------