ID code: '2RLU' 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' U A 3 alpha beta 73 93 79 76 108 C1' U A 4 alpha beta 103 123 109 106 138 C1' G A 5 alpha beta 133 156 139 136 172 C1' C A 6 alpha beta 167 187 173 170 203 C1' G A 7 alpha beta 198 221 204 201 237 C1' G A 8 alpha beta 232 255 238 235 271 C1' G A 9 alpha beta 266 289 272 269 305 C1' U A 10 alpha beta 300 320 306 303 335 C1' C A 11 alpha beta 330 350 336 333 366 C1' U A 12 alpha beta 361 381 367 364 396 C1' C A 13 alpha beta 391 411 397 394 427 C1' G A 14 alpha beta 422 445 428 425 461 C1' C A 15 alpha beta 456 476 462 459 492 C1' A A 16 alpha beta 487 509 493 490 525 C1' A A 17 alpha beta 520 542 526 523 558 C1' C A 18 alpha beta 553 573 559 556 589 C1' C A 19 alpha beta 584 605 590 587 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' U A 3 OK OK 78 74 91 77 106 C2' U A 4 OK OK 108 104 121 107 136 C2' G A 5 OK OK 138 134 154 137 170 C2' C A 6 OK OK 172 168 185 171 201 C2' G A 7 OK OK 203 199 219 202 235 C2' G A 8 OK OK 237 233 253 236 269 C2' G A 9 OK OK 271 267 287 270 303 C2' U A 10 OK OK 305 301 318 304 333 C2' C A 11 OK OK 335 331 348 334 364 C2' U A 12 OK OK 366 362 379 365 394 C2' C A 13 OK OK 396 392 409 395 425 C2' G A 14 OK OK 427 423 443 426 459 C2' C A 15 OK OK 461 457 474 460 490 C2' A A 16 OK OK 492 488 507 491 523 C2' A A 17 OK OK 525 521 540 524 556 C2' C A 18 OK OK 558 554 571 557 587 C2' C A 19 OK OK 589 585 603 588 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 72 90 75 76 104 C3' U A 4 OK OK 102 120 105 106 134 C3' G A 5 OK OK 132 153 135 136 168 C3' C A 6 OK OK 166 184 169 170 199 C3' G A 7 OK OK 197 218 200 201 233 C3' G A 8 OK OK 231 252 234 235 267 C3' G A 9 OK OK 265 286 268 269 301 C3' U A 10 OK OK 299 317 302 303 331 C3' C A 11 OK OK 329 347 332 333 362 C3' U A 12 OK OK 360 378 363 364 392 C3' C A 13 OK OK 390 408 393 394 423 C3' G A 14 OK OK 421 442 424 425 457 C3' C A 15 OK OK 455 473 458 459 488 C3' A A 16 OK OK 486 506 489 490 521 C3' A A 17 OK OK 519 539 522 523 554 C3' C A 18 OK OK 552 570 555 556 585 C3' C A 19 OK OK 583 601 586 587 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 74 89 71 73 102 C4' U A 4 OK OK 104 119 101 103 132 C4' G A 5 OK OK 134 152 131 133 166 C4' C A 6 OK OK 168 183 165 167 197 C4' G A 7 OK OK 199 217 196 198 231 C4' G A 8 OK OK 233 251 230 232 265 C4' G A 9 OK OK 267 285 264 266 299 C4' U A 10 OK OK 301 316 298 300 329 C4' C A 11 OK OK 331 346 328 330 360 C4' U A 12 OK OK 362 377 359 361 390 C4' C A 13 OK OK 392 407 389 391 421 C4' G A 14 OK OK 423 441 420 422 455 C4' C A 15 OK OK 457 472 454 456 486 C4' A A 16 OK OK 488 505 485 487 519 C4' A A 17 OK OK 521 538 518 520 552 C4' C A 18 OK OK 554 569 551 553 583 C4' C A 19 OK OK 585 600 582 584 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' U A 3 OK OK 70 87 88 72 101 C5' U A 4 OK OK 100 117 118 102 131 C5' G A 5 OK OK 130 150 151 132 165 C5' C A 6 OK OK 164 181 182 166 196 C5' G A 7 OK OK 195 215 216 197 230 C5' G A 8 OK OK 229 249 250 231 264 C5' G A 9 OK OK 263 283 284 265 298 C5' U A 10 OK OK 297 314 315 299 328 C5' C A 11 OK OK 327 344 345 329 359 C5' U A 12 OK OK 358 375 376 360 389 C5' C A 13 OK OK 388 405 406 390 420 C5' G A 14 OK OK 419 439 440 421 454 C5' C A 15 OK OK 453 470 471 455 485 C5' A A 16 OK OK 484 503 504 486 518 C5' A A 17 OK OK 517 536 537 519 551 C5' C A 18 OK OK 550 567 568 552 582 C5' C A 19 OK OK 581 598 599 583 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 33 P G A 2 distorted distorted 6 34 35 36 67 P U A 3 distorted distorted 41 68 69 70 97 P U A 4 distorted distorted 75 98 99 100 127 P G A 5 distorted distorted 105 128 129 130 161 P C A 6 distorted distorted 135 162 163 164 192 P G A 7 distorted distorted 169 193 194 195 226 P G A 8 distorted distorted 200 227 228 229 260 P G A 9 distorted distorted 234 261 262 263 294 P U A 10 distorted distorted 268 295 296 297 324 P C A 11 distorted distorted 302 325 326 327 355 P U A 12 distorted distorted 332 356 357 358 385 P C A 13 distorted distorted 363 386 387 388 416 P G A 14 distorted distorted 393 417 418 419 450 P C A 15 distorted distorted 424 451 452 453 481 P A A 16 distorted distorted 458 482 483 484 514 P A A 17 distorted distorted 489 515 516 517 547 P C A 18 distorted distorted 522 548 549 550 578 P C A 19 distorted distorted 555 579 580 581 ---------------------------------------------------------------------------------