ID code: '1MFJ' 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 43 C1' A A 2 alpha beta 38 60 44 41 76 C1' C A 3 alpha beta 71 91 77 74 107 C1' A A 4 alpha beta 102 124 108 105 140 C1' G A 5 alpha beta 135 158 141 138 174 C1' U A 6 alpha beta 169 189 175 172 204 C1' C A 7 alpha beta 199 219 205 202 235 C1' U A 8 alpha beta 230 250 236 233 265 C1' C A 9 alpha beta 260 280 266 263 296 C1' U A 10 alpha beta 291 311 297 294 326 C1' A A 11 alpha beta 321 343 327 324 359 C1' C A 12 alpha beta 354 374 360 357 390 C1' G A 13 alpha beta 385 408 391 388 424 C1' G A 14 alpha beta 419 442 425 422 458 C1' A A 15 alpha beta 453 475 459 456 491 C1' G A 16 alpha beta 486 509 492 489 525 C1' A A 17 alpha beta 520 542 526 523 558 C1' C A 18 alpha beta 553 573 559 556 589 C1' U A 19 alpha beta 584 604 590 587 619 C1' G A 20 alpha beta 614 637 620 617 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 41 C2' A A 2 OK OK 43 39 58 42 74 C2' C A 3 OK OK 76 72 89 75 105 C2' A A 4 OK OK 107 103 122 106 138 C2' G A 5 OK OK 140 136 156 139 172 C2' U A 6 OK OK 174 170 187 173 202 C2' C A 7 OK OK 204 200 217 203 233 C2' U A 8 OK OK 235 231 248 234 263 C2' C A 9 OK OK 265 261 278 264 294 C2' U A 10 OK OK 296 292 309 295 324 C2' A A 11 OK OK 326 322 341 325 357 C2' C A 12 OK OK 359 355 372 358 388 C2' G A 13 OK OK 390 386 406 389 422 C2' G A 14 OK OK 424 420 440 423 456 C2' A A 15 OK OK 458 454 473 457 489 C2' G A 16 OK OK 491 487 507 490 523 C2' A A 17 OK OK 525 521 540 524 556 C2' C A 18 OK OK 558 554 571 557 587 C2' U A 19 OK OK 589 585 602 588 617 C2' G A 20 OK OK 619 615 635 618 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 24 6 7 39 C3' A A 2 OK OK 37 57 40 41 72 C3' C A 3 OK OK 70 88 73 74 103 C3' A A 4 OK OK 101 121 104 105 136 C3' G A 5 OK OK 134 155 137 138 170 C3' U A 6 OK OK 168 186 171 172 200 C3' C A 7 OK OK 198 216 201 202 231 C3' U A 8 OK OK 229 247 232 233 261 C3' C A 9 OK OK 259 277 262 263 292 C3' U A 10 OK OK 290 308 293 294 322 C3' A A 11 OK OK 320 340 323 324 355 C3' C A 12 OK OK 353 371 356 357 386 C3' G A 13 OK OK 384 405 387 388 420 C3' G A 14 OK OK 418 439 421 422 454 C3' A A 15 OK OK 452 472 455 456 487 C3' G A 16 OK OK 485 506 488 489 521 C3' A A 17 OK OK 519 539 522 523 554 C3' C A 18 OK OK 552 570 555 556 585 C3' U A 19 OK OK 583 601 586 587 615 C3' G A 20 OK OK 613 634 616 617 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 23 2 4 37 C4' A A 2 OK OK 39 56 36 38 70 C4' C A 3 OK OK 72 87 69 71 101 C4' A A 4 OK OK 103 120 100 102 134 C4' G A 5 OK OK 136 154 133 135 168 C4' U A 6 OK OK 170 185 167 169 198 C4' C A 7 OK OK 200 215 197 199 229 C4' U A 8 OK OK 231 246 228 230 259 C4' C A 9 OK OK 261 276 258 260 290 C4' U A 10 OK OK 292 307 289 291 320 C4' A A 11 OK OK 322 339 319 321 353 C4' C A 12 OK OK 355 370 352 354 384 C4' G A 13 OK OK 386 404 383 385 418 C4' G A 14 OK OK 420 438 417 419 452 C4' A A 15 OK OK 454 471 451 453 485 C4' G A 16 OK OK 487 505 484 486 519 C4' A A 17 OK OK 521 538 518 520 552 C4' C A 18 OK OK 554 569 551 553 583 C4' U A 19 OK OK 585 600 582 584 613 C4' G A 20 OK OK 615 633 612 614 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 36 C5' A A 2 OK OK 35 54 55 37 69 C5' C A 3 OK OK 68 85 86 70 100 C5' A A 4 OK OK 99 118 119 101 133 C5' G A 5 OK OK 132 152 153 134 167 C5' U A 6 OK OK 166 183 184 168 197 C5' C A 7 OK OK 196 213 214 198 228 C5' U A 8 OK OK 227 244 245 229 258 C5' C A 9 OK OK 257 274 275 259 289 C5' U A 10 OK OK 288 305 306 290 319 C5' A A 11 OK OK 318 337 338 320 352 C5' C A 12 OK OK 351 368 369 353 383 C5' G A 13 OK OK 382 402 403 384 417 C5' G A 14 OK OK 416 436 437 418 451 C5' A A 15 OK OK 450 469 470 452 484 C5' G A 16 OK OK 483 503 504 485 518 C5' A A 17 OK OK 517 536 537 519 551 C5' C A 18 OK OK 550 567 568 552 582 C5' U A 19 OK OK 581 598 599 583 612 C5' G A 20 OK OK 611 631 632 613 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 32 P A A 2 distorted distorted 6 33 34 35 65 P C A 3 distorted distorted 40 66 67 68 96 P A A 4 distorted distorted 73 97 98 99 129 P G A 5 distorted distorted 104 130 131 132 163 P U A 6 distorted distorted 137 164 165 166 193 P C A 7 distorted distorted 171 194 195 196 224 P U A 8 distorted distorted 201 225 226 227 254 P C A 9 distorted distorted 232 255 256 257 285 P U A 10 distorted distorted 262 286 287 288 315 P A A 11 distorted distorted 293 316 317 318 348 P C A 12 distorted distorted 323 349 350 351 379 P G A 13 distorted distorted 356 380 381 382 413 P G A 14 distorted distorted 387 414 415 416 447 P A A 15 distorted distorted 421 448 449 450 480 P G A 16 distorted distorted 455 481 482 483 514 P A A 17 distorted distorted 488 515 516 517 547 P C A 18 distorted distorted 522 548 549 550 578 P U A 19 distorted distorted 555 579 580 581 608 P G A 20 distorted distorted 586 609 610 611 ---------------------------------------------------------------------------------