ID code: '1ZBH' 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 F 6 beta 4 10 7 32 C1' G F 7 beta 27 33 30 55 C1' C F 8 beta 50 56 53 75 C1' U F 9 beta 70 76 73 95 C1' C F 10 beta 90 96 93 115 C1' U F 11 beta 110 116 113 135 C1' U F 12 beta 130 136 133 155 C1' U F 13 beta 150 156 153 175 C1' U F 14 beta 170 176 173 195 C1' C F 15 beta 190 196 193 215 C1' A F 16 beta 210 216 213 237 C1' G F 17 beta 232 238 235 260 C1' A F 18 beta 255 261 258 282 C1' G F 19 beta 277 283 280 305 C1' C F 20 beta 300 306 303 325 C1' C F 21 beta 320 326 323 343 C1' G E 6 beta 338 344 341 366 C1' G E 7 beta 361 367 364 389 C1' C E 8 beta 384 390 387 409 C1' U E 9 beta 404 410 407 429 C1' C E 10 beta 424 430 427 449 C1' U E 11 beta 444 450 447 469 C1' U E 12 beta 464 470 467 489 C1' U E 13 beta 484 490 487 509 C1' U E 14 beta 504 510 507 529 C1' C E 15 beta 524 530 527 549 C1' A E 16 beta 544 550 547 571 C1' G E 17 beta 566 572 569 594 C1' A E 18 beta 589 595 592 616 C1' G E 19 beta 611 617 614 639 C1' C E 20 beta 634 640 637 659 C1' C E 21 beta 654 660 657 9041 C1' AMP A1002 beta 9036 9042 9039 9066 C1' AMP B2002 beta 9061 9067 9064 9091 C1' AMP C3002 beta 9086 9092 9089 9116 C1' AMP D4002 beta 9111 9117 9114 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G F 6 OK 9 5 8 30 C2' G F 7 OK 32 28 31 53 C2' C F 8 OK 55 51 54 73 C2' U F 9 OK 75 71 74 93 C2' C F 10 OK 95 91 94 113 C2' U F 11 OK 115 111 114 133 C2' U F 12 OK 135 131 134 153 C2' U F 13 OK 155 151 154 173 C2' U F 14 OK 175 171 174 193 C2' C F 15 OK 195 191 194 213 C2' A F 16 OK 215 211 214 235 C2' G F 17 OK 237 233 236 258 C2' A F 18 OK 260 256 259 280 C2' G F 19 OK 282 278 281 303 C2' C F 20 OK 305 301 304 323 C2' C F 21 OK 325 321 324 341 C2' G E 6 OK 343 339 342 364 C2' G E 7 OK 366 362 365 387 C2' C E 8 OK 389 385 388 407 C2' U E 9 OK 409 405 408 427 C2' C E 10 OK 429 425 428 447 C2' U E 11 OK 449 445 448 467 C2' U E 12 OK 469 465 468 487 C2' U E 13 OK 489 485 488 507 C2' U E 14 OK 509 505 508 527 C2' C E 15 OK 529 525 528 547 C2' A E 16 OK 549 545 548 569 C2' G E 17 OK 571 567 570 592 C2' A E 18 OK 594 590 593 614 C2' G E 19 OK 616 612 615 637 C2' C E 20 OK 639 635 638 657 C2' C E 21 OK 659 655 658 9039 C2' AMP A1002 OK 9041 9037 9040 9064 C2' AMP B2002 OK 9066 9062 9065 9089 C2' AMP C3002 OK 9091 9087 9090 9114 C2' AMP D4002 OK 9116 9112 9115 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G F 6 OK 3 6 7 28 C3' G F 7 OK 26 29 30 51 C3' C F 8 OK 49 52 53 71 C3' U F 9 OK 69 72 73 91 C3' C F 10 OK 89 92 93 111 C3' U F 11 OK 109 112 113 131 C3' U F 12 OK 129 132 133 151 C3' U F 13 OK 149 152 153 171 C3' U F 14 OK 169 172 173 191 C3' C F 15 OK 189 192 193 211 C3' A F 16 OK 209 212 213 233 C3' G F 17 OK 231 234 235 256 C3' A F 18 OK 254 257 258 278 C3' G F 19 OK 276 279 280 301 C3' C F 20 OK 299 302 303 321 C3' C F 21 OK 319 322 323 339 C3' G E 6 OK 337 340 341 362 C3' G E 7 OK 360 363 364 385 C3' C E 8 OK 383 386 387 405 C3' U E 9 OK 403 406 407 425 C3' C E 10 OK 423 426 427 445 C3' U E 11 OK 443 446 447 465 C3' U E 12 OK 463 466 467 485 C3' U E 13 OK 483 486 487 505 C3' U E 14 OK 503 506 507 525 C3' C E 15 OK 523 526 527 545 C3' A E 16 OK 543 546 547 567 C3' G E 17 OK 565 568 569 590 C3' A E 18 OK 588 591 592 612 C3' G E 19 OK 610 613 614 635 C3' C E 20 OK 633 636 637 655 C3' C E 21 OK 653 656 657 9037 C3' AMP A1002 OK 9035 9038 9039 9062 C3' AMP B2002 OK 9060 9063 9064 9087 C3' AMP C3002 OK 9085 9088 9089 9112 C3' AMP D4002 OK 9110 9113 9114 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G F 6 OK 5 2 4 26 C4' G F 7 OK 28 25 27 49 C4' C F 8 OK 51 48 50 69 C4' U F 9 OK 71 68 70 89 C4' C F 10 OK 91 88 90 109 C4' U F 11 OK 111 108 110 129 C4' U F 12 OK 131 128 130 149 C4' U F 13 OK 151 148 150 169 C4' U F 14 OK 171 168 170 189 C4' C F 15 OK 191 188 190 209 C4' A F 16 OK 211 208 210 231 C4' G F 17 OK 233 230 232 254 C4' A F 18 OK 256 253 255 276 C4' G F 19 OK 278 275 277 299 C4' C F 20 OK 301 298 300 319 C4' C F 21 OK 321 318 320 337 C4' G E 6 OK 339 336 338 360 C4' G E 7 OK 362 359 361 383 C4' C E 8 OK 385 382 384 403 C4' U E 9 OK 405 402 404 423 C4' C E 10 OK 425 422 424 443 C4' U E 11 OK 445 442 444 463 C4' U E 12 OK 465 462 464 483 C4' U E 13 OK 485 482 484 503 C4' U E 14 OK 505 502 504 523 C4' C E 15 OK 525 522 524 543 C4' A E 16 OK 545 542 544 565 C4' G E 17 OK 567 564 566 588 C4' A E 18 OK 590 587 589 610 C4' G E 19 OK 612 609 611 633 C4' C E 20 OK 635 632 634 653 C4' C E 21 OK 655 652 654 9035 C4' AMP A1002 OK 9037 9034 9036 9060 C4' AMP B2002 OK 9062 9059 9061 9085 C4' AMP C3002 OK 9087 9084 9086 9110 C4' AMP D4002 OK 9112 9109 9111 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G F 6 1 3 25 C5' G F 7 24 26 48 C5' C F 8 47 49 68 C5' U F 9 67 69 88 C5' C F 10 87 89 108 C5' U F 11 107 109 128 C5' U F 12 127 129 148 C5' U F 13 147 149 168 C5' U F 14 167 169 188 C5' C F 15 187 189 208 C5' A F 16 207 209 230 C5' G F 17 229 231 253 C5' A F 18 252 254 275 C5' G F 19 274 276 298 C5' C F 20 297 299 318 C5' C F 21 317 319 336 C5' G E 6 335 337 359 C5' G E 7 358 360 382 C5' C E 8 381 383 402 C5' U E 9 401 403 422 C5' C E 10 421 423 442 C5' U E 11 441 443 462 C5' U E 12 461 463 482 C5' U E 13 481 483 502 C5' U E 14 501 503 522 C5' C E 15 521 523 542 C5' A E 16 541 543 564 C5' G E 17 563 565 587 C5' A E 18 586 588 609 C5' G E 19 608 610 632 C5' C E 20 631 633 652 C5' C E 21 651 653 9034 C5' AMP A1002 9033 9035 9059 C5' AMP B2002 9058 9060 9084 C5' AMP C3002 9083 9085 9109 C5' AMP D4002 9108 9110 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P G F 7 distorted distorted 6 22 23 24 44 P C F 8 OK OK 29 45 46 47 64 P U F 9 distorted distorted 52 65 66 67 84 P C F 10 distorted distorted 72 85 86 87 104 P U F 11 distorted distorted 92 105 106 107 124 P U F 12 distorted distorted 112 125 126 127 144 P U F 13 distorted distorted 132 145 146 147 164 P U F 14 distorted distorted 152 165 166 167 184 P C F 15 distorted distorted 172 185 186 187 204 P A F 16 distorted distorted 192 205 206 207 226 P G F 17 distorted distorted 212 227 228 229 249 P A F 18 distorted distorted 234 250 251 252 271 P G F 19 distorted distorted 257 272 273 274 294 P C F 20 distorted distorted 279 295 296 297 314 P C F 21 distorted distorted 302 315 316 317 355 P G E 7 distorted distorted 340 356 357 358 378 P C E 8 OK OK 363 379 380 381 398 P U E 9 distorted distorted 386 399 400 401 418 P C E 10 distorted distorted 406 419 420 421 438 P U E 11 distorted distorted 426 439 440 441 458 P U E 12 distorted distorted 446 459 460 461 478 P U E 13 distorted distorted 466 479 480 481 498 P U E 14 distorted distorted 486 499 500 501 518 P C E 15 distorted distorted 506 519 520 521 538 P A E 16 distorted distorted 526 539 540 541 560 P G E 17 distorted distorted 546 561 562 563 583 P A E 18 distorted distorted 568 584 585 586 605 P G E 19 distorted distorted 591 606 607 608 628 P C E 20 distorted distorted 613 629 630 631 648 P C E 21 distorted distorted 636 649 650 651 9029 P AMP A1002 distorted distorted 9030 9031 9033 9054 P AMP B2002 distorted distorted 9055 9056 9058 9079 P AMP C3002 distorted distorted 9080 9081 9083 9104 P AMP D4002 distorted distorted 9105 9106 9108 ---------------------------------------------------------------------------------