ID code: '3TZR' 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' C A 48 beta 4 10 7 29 C1' G A 49 beta 24 30 27 52 C1' A A 50 beta 47 53 50 74 C1' G A 51 beta 69 75 72 97 C1' G A 52 beta 92 98 95 120 C1' A A 53 beta 115 121 118 142 C1' A A 54 beta 137 143 140 164 C1' C A 55 beta 159 165 162 184 C1' U A 56 beta 179 185 182 204 C1' A A 57 beta 199 205 202 226 C1' C A 58 beta 221 227 224 246 C1' U A 59 beta 241 247 244 266 C1' G A 60 beta 261 267 264 289 C1' U A 61 beta 284 290 287 309 C1' C A 62 beta 304 310 307 329 C1' U A 63 beta 324 330 327 349 C1' U A 64 beta 344 350 347 369 C1' C A 65 beta 364 370 367 389 C1' C A 66 beta 384 390 387 409 C1' C A 67 beta 404 410 407 427 C1' G B 101 beta 422 428 425 450 C1' G B 102 beta 445 451 448 473 C1' U B 103 beta 468 474 471 493 C1' C B 104 beta 488 494 491 513 C1' G B 105 beta 508 514 511 536 C1' U B 106 beta 531 537 534 556 C1' G B 107 beta 551 557 554 579 C1' C B 108 beta 574 580 577 599 C1' A B 109 beta 594 600 597 621 C1' G B 110 beta 616 622 619 644 C1' C B 111 beta 639 645 642 664 C1' C B 112 beta 659 665 662 684 C1' U B 113 beta 679 685 682 704 C1' C B 114 beta 699 705 702 724 C1' G B 115 beta 719 725 722 747 C1' G B 116 beta 742 748 745 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 48 OK 9 5 8 27 C2' G A 49 OK 29 25 28 50 C2' A A 50 OK 52 48 51 72 C2' G A 51 OK 74 70 73 95 C2' G A 52 OK 97 93 96 118 C2' A A 53 OK 120 116 119 140 C2' A A 54 OK 142 138 141 162 C2' C A 55 OK 164 160 163 182 C2' U A 56 OK 184 180 183 202 C2' A A 57 OK 204 200 203 224 C2' C A 58 OK 226 222 225 244 C2' U A 59 OK 246 242 245 264 C2' G A 60 OK 266 262 265 287 C2' U A 61 OK 289 285 288 307 C2' C A 62 OK 309 305 308 327 C2' U A 63 OK 329 325 328 347 C2' U A 64 OK 349 345 348 367 C2' C A 65 OK 369 365 368 387 C2' C A 66 OK 389 385 388 407 C2' C A 67 OK 409 405 408 425 C2' G B 101 OK 427 423 426 448 C2' G B 102 OK 450 446 449 471 C2' U B 103 OK 473 469 472 491 C2' C B 104 OK 493 489 492 511 C2' G B 105 OK 513 509 512 534 C2' U B 106 OK 536 532 535 554 C2' G B 107 OK 556 552 555 577 C2' C B 108 OK 579 575 578 597 C2' A B 109 OK 599 595 598 619 C2' G B 110 OK 621 617 620 642 C2' C B 111 OK 644 640 643 662 C2' C B 112 OK 664 660 663 682 C2' U B 113 OK 684 680 683 702 C2' C B 114 OK 704 700 703 722 C2' G B 115 OK 724 720 723 745 C2' G B 116 OK 747 743 746 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 48 OK 3 6 7 25 C3' G A 49 OK 23 26 27 48 C3' A A 50 OK 46 49 50 70 C3' G A 51 OK 68 71 72 93 C3' G A 52 OK 91 94 95 116 C3' A A 53 OK 114 117 118 138 C3' A A 54 OK 136 139 140 160 C3' C A 55 OK 158 161 162 180 C3' U A 56 OK 178 181 182 200 C3' A A 57 OK 198 201 202 222 C3' C A 58 OK 220 223 224 242 C3' U A 59 OK 240 243 244 262 C3' G A 60 OK 260 263 264 285 C3' U A 61 OK 283 286 287 305 C3' C A 62 OK 303 306 307 325 C3' U A 63 OK 323 326 327 345 C3' U A 64 OK 343 346 347 365 C3' C A 65 OK 363 366 367 385 C3' C A 66 OK 383 386 387 405 C3' C A 67 OK 403 406 407 423 C3' G B 101 OK 421 424 425 446 C3' G B 102 OK 444 447 448 469 C3' U B 103 OK 467 470 471 489 C3' C B 104 OK 487 490 491 509 C3' G B 105 OK 507 510 511 532 C3' U B 106 OK 530 533 534 552 C3' G B 107 OK 550 553 554 575 C3' C B 108 OK 573 576 577 595 C3' A B 109 OK 593 596 597 617 C3' G B 110 OK 615 618 619 640 C3' C B 111 OK 638 641 642 660 C3' C B 112 OK 658 661 662 680 C3' U B 113 OK 678 681 682 700 C3' C B 114 OK 698 701 702 720 C3' G B 115 OK 718 721 722 743 C3' G B 116 OK 741 744 745 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 48 OK 5 2 4 23 C4' G A 49 OK 25 22 24 46 C4' A A 50 OK 48 45 47 68 C4' G A 51 OK 70 67 69 91 C4' G A 52 OK 93 90 92 114 C4' A A 53 OK 116 113 115 136 C4' A A 54 OK 138 135 137 158 C4' C A 55 OK 160 157 159 178 C4' U A 56 OK 180 177 179 198 C4' A A 57 OK 200 197 199 220 C4' C A 58 OK 222 219 221 240 C4' U A 59 OK 242 239 241 260 C4' G A 60 OK 262 259 261 283 C4' U A 61 OK 285 282 284 303 C4' C A 62 OK 305 302 304 323 C4' U A 63 OK 325 322 324 343 C4' U A 64 OK 345 342 344 363 C4' C A 65 OK 365 362 364 383 C4' C A 66 OK 385 382 384 403 C4' C A 67 OK 405 402 404 421 C4' G B 101 OK 423 420 422 444 C4' G B 102 OK 446 443 445 467 C4' U B 103 OK 469 466 468 487 C4' C B 104 OK 489 486 488 507 C4' G B 105 OK 509 506 508 530 C4' U B 106 OK 532 529 531 550 C4' G B 107 OK 552 549 551 573 C4' C B 108 OK 575 572 574 593 C4' A B 109 OK 595 592 594 615 C4' G B 110 OK 617 614 616 638 C4' C B 111 OK 640 637 639 658 C4' C B 112 OK 660 657 659 678 C4' U B 113 OK 680 677 679 698 C4' C B 114 OK 700 697 699 718 C4' G B 115 OK 720 717 719 741 C4' G B 116 OK 743 740 742 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 48 1 3 22 C5' G A 49 21 23 45 C5' A A 50 44 46 67 C5' G A 51 66 68 90 C5' G A 52 89 91 113 C5' A A 53 112 114 135 C5' A A 54 134 136 157 C5' C A 55 156 158 177 C5' U A 56 176 178 197 C5' A A 57 196 198 219 C5' C A 58 218 220 239 C5' U A 59 238 240 259 C5' G A 60 258 260 282 C5' U A 61 281 283 302 C5' C A 62 301 303 322 C5' U A 63 321 323 342 C5' U A 64 341 343 362 C5' C A 65 361 363 382 C5' C A 66 381 383 402 C5' C A 67 401 403 420 C5' G B 101 419 421 443 C5' G B 102 442 444 466 C5' U B 103 465 467 486 C5' C B 104 485 487 506 C5' G B 105 505 507 529 C5' U B 106 528 530 549 C5' G B 107 548 550 572 C5' C B 108 571 573 592 C5' A B 109 591 593 614 C5' G B 110 613 615 637 C5' C B 111 636 638 657 C5' C B 112 656 658 677 C5' U B 113 676 678 697 C5' C B 114 696 698 717 C5' G B 115 716 718 740 C5' G B 116 739 741 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G A 49 distorted distorted 6 19 20 21 41 P A A 50 distorted distorted 26 42 43 44 63 P G A 51 distorted distorted 49 64 65 66 86 P G A 52 distorted distorted 71 87 88 89 109 P A A 53 distorted distorted 94 110 111 112 131 P A A 54 distorted distorted 117 132 133 134 153 P C A 55 distorted distorted 139 154 155 156 173 P U A 56 distorted distorted 161 174 175 176 193 P A A 57 distorted distorted 181 194 195 196 215 P C A 58 distorted distorted 201 216 217 218 235 P U A 59 distorted distorted 223 236 237 238 255 P G A 60 distorted distorted 243 256 257 258 278 P U A 61 distorted distorted 263 279 280 281 298 P C A 62 distorted distorted 286 299 300 301 318 P U A 63 distorted distorted 306 319 320 321 338 P U A 64 distorted distorted 326 339 340 341 358 P C A 65 distorted distorted 346 359 360 361 378 P C A 66 distorted distorted 366 379 380 381 398 P C A 67 distorted distorted 386 399 400 401 439 P G B 102 distorted distorted 424 440 441 442 462 P U B 103 distorted distorted 447 463 464 465 482 P C B 104 distorted distorted 470 483 484 485 502 P G B 105 distorted distorted 490 503 504 505 525 P U B 106 distorted distorted 510 526 527 528 545 P G B 107 distorted distorted 533 546 547 548 568 P C B 108 distorted distorted 553 569 570 571 588 P A B 109 distorted distorted 576 589 590 591 610 P G B 110 distorted distorted 596 611 612 613 633 P C B 111 distorted distorted 618 634 635 636 653 P C B 112 distorted distorted 641 654 655 656 673 P U B 113 distorted distorted 661 674 675 676 693 P C B 114 distorted distorted 681 694 695 696 713 P G B 115 distorted distorted 701 714 715 716 736 P G B 116 distorted distorted 721 737 738 739 ---------------------------------------------------------------------------------