ID code: '1ZBN' 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 1 alpha beta 8 31 14 11 48 C1' G A 2 alpha beta 43 66 49 46 82 C1' C A 3 alpha beta 77 97 83 80 113 C1' U A 4 alpha beta 108 128 114 111 143 C1' C A 5 alpha beta 138 158 144 141 174 C1' G A 6 alpha beta 169 192 175 172 208 C1' U A 7 alpha beta 203 223 209 206 238 C1' G A 8 alpha beta 233 256 239 236 272 C1' U A 9 alpha beta 267 287 273 270 302 C1' A A 10 alpha beta 297 319 303 300 335 C1' G A 11 alpha beta 330 353 336 333 369 C1' C A 12 alpha beta 364 384 370 367 400 C1' U A 13 alpha beta 395 415 401 398 430 C1' C A 14 alpha beta 425 445 431 428 461 C1' A A 15 alpha beta 456 478 462 459 494 C1' U A 16 alpha beta 489 509 495 492 524 C1' U A 17 alpha beta 519 539 525 522 554 C1' A A 18 alpha beta 549 571 555 552 587 C1' G A 19 alpha beta 582 605 588 585 621 C1' C A 20 alpha beta 616 636 622 619 652 C1' U A 21 alpha beta 647 667 653 650 682 C1' C A 22 alpha beta 677 697 683 680 713 C1' C A 23 alpha beta 708 728 714 711 744 C1' G A 24 alpha beta 739 762 745 742 778 C1' A A 25 alpha beta 773 795 779 776 811 C1' G A 26 alpha beta 806 829 812 809 845 C1' C A 27 alpha beta 840 860 846 843 876 C1' C A 28 alpha beta 871 892 877 874 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' G A 1 OK OK 13 9 29 12 46 C2' G A 2 OK OK 48 44 64 47 80 C2' C A 3 OK OK 82 78 95 81 111 C2' U A 4 OK OK 113 109 126 112 141 C2' C A 5 OK OK 143 139 156 142 172 C2' G A 6 OK OK 174 170 190 173 206 C2' U A 7 OK OK 208 204 221 207 236 C2' G A 8 OK OK 238 234 254 237 270 C2' U A 9 OK OK 272 268 285 271 300 C2' A A 10 OK OK 302 298 317 301 333 C2' G A 11 OK OK 335 331 351 334 367 C2' C A 12 OK OK 369 365 382 368 398 C2' U A 13 OK OK 400 396 413 399 428 C2' C A 14 OK OK 430 426 443 429 459 C2' A A 15 OK OK 461 457 476 460 492 C2' U A 16 OK OK 494 490 507 493 522 C2' U A 17 OK OK 524 520 537 523 552 C2' A A 18 OK OK 554 550 569 553 585 C2' G A 19 OK OK 587 583 603 586 619 C2' C A 20 OK OK 621 617 634 620 650 C2' U A 21 OK OK 652 648 665 651 680 C2' C A 22 OK OK 682 678 695 681 711 C2' C A 23 OK OK 713 709 726 712 742 C2' G A 24 OK OK 744 740 760 743 776 C2' A A 25 OK OK 778 774 793 777 809 C2' G A 26 OK OK 811 807 827 810 843 C2' C A 27 OK OK 845 841 858 844 874 C2' C A 28 OK OK 876 872 890 875 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' G A 1 OK OK 7 28 10 11 44 C3' G A 2 OK OK 42 63 45 46 78 C3' C A 3 OK OK 76 94 79 80 109 C3' U A 4 OK OK 107 125 110 111 139 C3' C A 5 OK OK 137 155 140 141 170 C3' G A 6 OK OK 168 189 171 172 204 C3' U A 7 OK OK 202 220 205 206 234 C3' G A 8 OK OK 232 253 235 236 268 C3' U A 9 OK OK 266 284 269 270 298 C3' A A 10 OK OK 296 316 299 300 331 C3' G A 11 OK OK 329 350 332 333 365 C3' C A 12 OK OK 363 381 366 367 396 C3' U A 13 OK OK 394 412 397 398 426 C3' C A 14 OK OK 424 442 427 428 457 C3' A A 15 OK OK 455 475 458 459 490 C3' U A 16 OK OK 488 506 491 492 520 C3' U A 17 OK OK 518 536 521 522 550 C3' A A 18 OK OK 548 568 551 552 583 C3' G A 19 OK OK 581 602 584 585 617 C3' C A 20 OK OK 615 633 618 619 648 C3' U A 21 OK OK 646 664 649 650 678 C3' C A 22 OK OK 676 694 679 680 709 C3' C A 23 OK OK 707 725 710 711 740 C3' G A 24 OK OK 738 759 741 742 774 C3' A A 25 OK OK 772 792 775 776 807 C3' G A 26 OK OK 805 826 808 809 841 C3' C A 27 OK OK 839 857 842 843 872 C3' C A 28 OK OK 870 888 873 874 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' G A 1 OK OK 9 27 6 8 42 C4' G A 2 OK OK 44 62 41 43 76 C4' C A 3 OK OK 78 93 75 77 107 C4' U A 4 OK OK 109 124 106 108 137 C4' C A 5 OK OK 139 154 136 138 168 C4' G A 6 OK OK 170 188 167 169 202 C4' U A 7 OK OK 204 219 201 203 232 C4' G A 8 OK OK 234 252 231 233 266 C4' U A 9 OK OK 268 283 265 267 296 C4' A A 10 OK OK 298 315 295 297 329 C4' G A 11 OK OK 331 349 328 330 363 C4' C A 12 OK OK 365 380 362 364 394 C4' U A 13 OK OK 396 411 393 395 424 C4' C A 14 OK OK 426 441 423 425 455 C4' A A 15 OK OK 457 474 454 456 488 C4' U A 16 OK OK 490 505 487 489 518 C4' U A 17 OK OK 520 535 517 519 548 C4' A A 18 OK OK 550 567 547 549 581 C4' G A 19 OK OK 583 601 580 582 615 C4' C A 20 OK OK 617 632 614 616 646 C4' U A 21 OK OK 648 663 645 647 676 C4' C A 22 OK OK 678 693 675 677 707 C4' C A 23 OK OK 709 724 706 708 738 C4' G A 24 OK OK 740 758 737 739 772 C4' A A 25 OK OK 774 791 771 773 805 C4' G A 26 OK OK 807 825 804 806 839 C4' C A 27 OK OK 841 856 838 840 870 C4' C A 28 OK OK 872 887 869 871 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' G A 1 OK OK 5 25 26 7 41 C5' G A 2 OK OK 40 60 61 42 75 C5' C A 3 OK OK 74 91 92 76 106 C5' U A 4 OK OK 105 122 123 107 136 C5' C A 5 OK OK 135 152 153 137 167 C5' G A 6 OK OK 166 186 187 168 201 C5' U A 7 OK OK 200 217 218 202 231 C5' G A 8 OK OK 230 250 251 232 265 C5' U A 9 OK OK 264 281 282 266 295 C5' A A 10 OK OK 294 313 314 296 328 C5' G A 11 OK OK 327 347 348 329 362 C5' C A 12 OK OK 361 378 379 363 393 C5' U A 13 OK OK 392 409 410 394 423 C5' C A 14 OK OK 422 439 440 424 454 C5' A A 15 OK OK 453 472 473 455 487 C5' U A 16 OK OK 486 503 504 488 517 C5' U A 17 OK OK 516 533 534 518 547 C5' A A 18 OK OK 546 565 566 548 580 C5' G A 19 OK OK 579 599 600 581 614 C5' C A 20 OK OK 613 630 631 615 645 C5' U A 21 OK OK 644 661 662 646 675 C5' C A 22 OK OK 674 691 692 676 706 C5' C A 23 OK OK 705 722 723 707 737 C5' G A 24 OK OK 736 756 757 738 771 C5' A A 25 OK OK 770 789 790 772 804 C5' G A 26 OK OK 803 823 824 805 838 C5' C A 27 OK OK 837 854 855 839 869 C5' C A 28 OK OK 868 885 886 870 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P G A 1 distorted distorted 3 4 5 37 P G A 2 distorted distorted 10 38 39 40 71 P C A 3 distorted distorted 45 72 73 74 102 P U A 4 distorted distorted 79 103 104 105 132 P C A 5 distorted distorted 110 133 134 135 163 P G A 6 distorted distorted 140 164 165 166 197 P U A 7 distorted distorted 171 198 199 200 227 P G A 8 distorted distorted 205 228 229 230 261 P U A 9 distorted distorted 235 262 263 264 291 P A A 10 distorted distorted 269 292 293 294 324 P G A 11 distorted distorted 299 325 326 327 358 P C A 12 distorted distorted 332 359 360 361 389 P U A 13 distorted distorted 366 390 391 392 419 P C A 14 distorted distorted 397 420 421 422 450 P A A 15 distorted distorted 427 451 452 453 483 P U A 16 distorted distorted 458 484 485 486 513 P U A 17 distorted distorted 491 514 515 516 543 P A A 18 distorted distorted 521 544 545 546 576 P G A 19 distorted distorted 551 577 578 579 610 P C A 20 distorted distorted 584 611 612 613 641 P U A 21 distorted distorted 618 642 643 644 671 P C A 22 distorted distorted 649 672 673 674 702 P C A 23 distorted distorted 679 703 704 705 733 P G A 24 distorted distorted 710 734 735 736 767 P A A 25 distorted distorted 741 768 769 770 800 P G A 26 distorted distorted 775 801 802 803 834 P C A 27 distorted distorted 808 835 836 837 865 P C A 28 distorted distorted 842 866 867 868 ---------------------------------------------------------------------------------