ID code: '2NUG' 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' A C 2 beta 8 14 11 35 C1' A C 3 beta 30 36 33 57 C1' G C 4 beta 52 58 55 80 C1' G C 5 beta 75 81 78 103 C1' U C 6 beta 98 104 101 123 C1' C C 7 beta 118 124 121 143 C1' A C 8 beta 138 144 141 165 C1' U C 9 beta 160 166 163 185 C1' U C 10 beta 180 186 183 205 C1' C C 11 beta 200 206 203 225 C1' G C 12 beta 220 226 223 341 C1' U E 19 beta 336 342 339 361 C1' G E 20 beta 356 362 359 384 C1' G E 21 beta 379 385 382 407 C1' C E 22 beta 402 408 405 427 C1' C E 23 beta 422 428 425 447 C1' U E 24 beta 442 448 445 467 C1' U E 25 beta 462 468 465 487 C1' G E 26 beta 482 488 485 510 C1' C E 27 beta 505 511 508 532 C1' A D 2 beta 527 533 530 554 C1' A D 3 beta 549 555 552 576 C1' G D 4 beta 571 577 574 599 C1' G D 5 beta 594 600 597 622 C1' U D 6 beta 617 623 620 642 C1' C D 7 beta 637 643 640 662 C1' A D 8 beta 657 663 660 684 C1' U D 9 beta 679 685 682 704 C1' U D 10 beta 699 705 702 724 C1' C D 11 beta 719 725 722 744 C1' G D 12 beta 739 745 742 860 C1' U F 19 beta 855 861 858 880 C1' G F 20 beta 875 881 878 903 C1' G F 21 beta 898 904 901 926 C1' C F 22 beta 921 927 924 946 C1' C F 23 beta 941 947 944 966 C1' U F 24 beta 961 967 964 986 C1' U F 25 beta 981 987 984 1006 C1' G F 26 beta 1001 1007 1004 1029 C1' C F 27 beta 1024 1030 1027 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' A C 2 OK 13 9 12 33 C2' A C 3 OK 35 31 34 55 C2' G C 4 OK 57 53 56 78 C2' G C 5 OK 80 76 79 101 C2' U C 6 OK 103 99 102 121 C2' C C 7 OK 123 119 122 141 C2' A C 8 OK 143 139 142 163 C2' U C 9 OK 165 161 164 183 C2' U C 10 OK 185 181 184 203 C2' C C 11 OK 205 201 204 223 C2' G C 12 OK 225 221 224 339 C2' U E 19 OK 341 337 340 359 C2' G E 20 OK 361 357 360 382 C2' G E 21 OK 384 380 383 405 C2' C E 22 OK 407 403 406 425 C2' C E 23 OK 427 423 426 445 C2' U E 24 OK 447 443 446 465 C2' U E 25 OK 467 463 466 485 C2' G E 26 OK 487 483 486 508 C2' C E 27 OK 510 506 509 530 C2' A D 2 OK 532 528 531 552 C2' A D 3 OK 554 550 553 574 C2' G D 4 OK 576 572 575 597 C2' G D 5 OK 599 595 598 620 C2' U D 6 OK 622 618 621 640 C2' C D 7 OK 642 638 641 660 C2' A D 8 OK 662 658 661 682 C2' U D 9 OK 684 680 683 702 C2' U D 10 OK 704 700 703 722 C2' C D 11 OK 724 720 723 742 C2' G D 12 OK 744 740 743 858 C2' U F 19 OK 860 856 859 878 C2' G F 20 OK 880 876 879 901 C2' G F 21 OK 903 899 902 924 C2' C F 22 OK 926 922 925 944 C2' C F 23 OK 946 942 945 964 C2' U F 24 OK 966 962 965 984 C2' U F 25 OK 986 982 985 1004 C2' G F 26 OK 1006 1002 1005 1027 C2' C F 27 OK 1029 1025 1028 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' A C 2 OK 7 10 11 31 C3' A C 3 OK 29 32 33 53 C3' G C 4 OK 51 54 55 76 C3' G C 5 OK 74 77 78 99 C3' U C 6 OK 97 100 101 119 C3' C C 7 OK 117 120 121 139 C3' A C 8 OK 137 140 141 161 C3' U C 9 OK 159 162 163 181 C3' U C 10 OK 179 182 183 201 C3' C C 11 OK 199 202 203 221 C3' G C 12 OK 219 222 223 337 C3' U E 19 OK 335 338 339 357 C3' G E 20 OK 355 358 359 380 C3' G E 21 OK 378 381 382 403 C3' C E 22 OK 401 404 405 423 C3' C E 23 OK 421 424 425 443 C3' U E 24 OK 441 444 445 463 C3' U E 25 OK 461 464 465 483 C3' G E 26 OK 481 484 485 506 C3' C E 27 OK 504 507 508 528 C3' A D 2 OK 526 529 530 550 C3' A D 3 OK 548 551 552 572 C3' G D 4 OK 570 573 574 595 C3' G D 5 OK 593 596 597 618 C3' U D 6 OK 616 619 620 638 C3' C D 7 OK 636 639 640 658 C3' A D 8 OK 656 659 660 680 C3' U D 9 OK 678 681 682 700 C3' U D 10 OK 698 701 702 720 C3' C D 11 OK 718 721 722 740 C3' G D 12 OK 738 741 742 856 C3' U F 19 OK 854 857 858 876 C3' G F 20 OK 874 877 878 899 C3' G F 21 OK 897 900 901 922 C3' C F 22 OK 920 923 924 942 C3' C F 23 OK 940 943 944 962 C3' U F 24 OK 960 963 964 982 C3' U F 25 OK 980 983 984 1002 C3' G F 26 OK 1000 1003 1004 1025 C3' C F 27 OK 1023 1026 1027 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' A C 2 OK 9 6 8 29 C4' A C 3 OK 31 28 30 51 C4' G C 4 OK 53 50 52 74 C4' G C 5 OK 76 73 75 97 C4' U C 6 OK 99 96 98 117 C4' C C 7 OK 119 116 118 137 C4' A C 8 OK 139 136 138 159 C4' U C 9 OK 161 158 160 179 C4' U C 10 OK 181 178 180 199 C4' C C 11 OK 201 198 200 219 C4' G C 12 OK 221 218 220 335 C4' U E 19 OK 337 334 336 355 C4' G E 20 OK 357 354 356 378 C4' G E 21 OK 380 377 379 401 C4' C E 22 OK 403 400 402 421 C4' C E 23 OK 423 420 422 441 C4' U E 24 OK 443 440 442 461 C4' U E 25 OK 463 460 462 481 C4' G E 26 OK 483 480 482 504 C4' C E 27 OK 506 503 505 526 C4' A D 2 OK 528 525 527 548 C4' A D 3 OK 550 547 549 570 C4' G D 4 OK 572 569 571 593 C4' G D 5 OK 595 592 594 616 C4' U D 6 OK 618 615 617 636 C4' C D 7 OK 638 635 637 656 C4' A D 8 OK 658 655 657 678 C4' U D 9 OK 680 677 679 698 C4' U D 10 OK 700 697 699 718 C4' C D 11 OK 720 717 719 738 C4' G D 12 OK 740 737 739 854 C4' U F 19 OK 856 853 855 874 C4' G F 20 OK 876 873 875 897 C4' G F 21 OK 899 896 898 920 C4' C F 22 OK 922 919 921 940 C4' C F 23 OK 942 939 941 960 C4' U F 24 OK 962 959 961 980 C4' U F 25 OK 982 979 981 1000 C4' G F 26 OK 1002 999 1001 1023 C4' C F 27 OK 1025 1022 1024 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' A C 2 5 7 28 C5' A C 3 27 29 50 C5' G C 4 49 51 73 C5' G C 5 72 74 96 C5' U C 6 95 97 116 C5' C C 7 115 117 136 C5' A C 8 135 137 158 C5' U C 9 157 159 178 C5' U C 10 177 179 198 C5' C C 11 197 199 218 C5' G C 12 217 219 334 C5' U E 19 333 335 354 C5' G E 20 353 355 377 C5' G E 21 376 378 400 C5' C E 22 399 401 420 C5' C E 23 419 421 440 C5' U E 24 439 441 460 C5' U E 25 459 461 480 C5' G E 26 479 481 503 C5' C E 27 502 504 525 C5' A D 2 524 526 547 C5' A D 3 546 548 569 C5' G D 4 568 570 592 C5' G D 5 591 593 615 C5' U D 6 614 616 635 C5' C D 7 634 636 655 C5' A D 8 654 656 677 C5' U D 9 676 678 697 C5' U D 10 696 698 717 C5' C D 11 716 718 737 C5' G D 12 736 738 853 C5' U F 19 852 854 873 C5' G F 20 872 874 896 C5' G F 21 895 897 919 C5' C F 22 918 920 939 C5' C F 23 938 940 959 C5' U F 24 958 960 979 C5' U F 25 978 980 999 C5' G F 26 998 1000 1022 C5' C F 27 1021 1023 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P A C 2 OK OK 3 4 5 24 P A C 3 distorted distorted 10 25 26 27 46 P G C 4 distorted distorted 32 47 48 49 69 P G C 5 distorted distorted 54 70 71 72 92 P U C 6 distorted distorted 77 93 94 95 112 P C C 7 distorted distorted 100 113 114 115 132 P A C 8 distorted distorted 120 133 134 135 154 P U C 9 distorted distorted 140 155 156 157 174 P U C 10 distorted distorted 162 175 176 177 194 P C C 11 distorted distorted 182 195 196 197 214 P G C 12 distorted distorted 202 215 216 217 240 P A E 17 241 P A E 17 284 P G E 18 285 P G E 18 330 P U E 19 distorted distorted 331 332 333 350 P G E 20 distorted distorted 338 351 352 353 373 P G E 21 distorted distorted 358 374 375 376 396 P C E 22 distorted distorted 381 397 398 399 416 P C E 23 distorted distorted 404 417 418 419 436 P U E 24 distorted distorted 424 437 438 439 456 P U E 25 distorted distorted 444 457 458 459 476 P G E 26 distorted distorted 464 477 478 479 499 P C E 27 distorted distorted 484 500 501 502 521 P A D 2 OK OK 522 523 524 543 P A D 3 distorted distorted 529 544 545 546 565 P G D 4 distorted distorted 551 566 567 568 588 P G D 5 distorted distorted 573 589 590 591 611 P U D 6 distorted distorted 596 612 613 614 631 P C D 7 distorted distorted 619 632 633 634 651 P A D 8 distorted distorted 639 652 653 654 673 P U D 9 distorted distorted 659 674 675 676 693 P U D 10 distorted distorted 681 694 695 696 713 P C D 11 distorted distorted 701 714 715 716 733 P G D 12 distorted distorted 721 734 735 736 759 P A F 17 760 P A F 17 803 P G F 18 804 P G F 18 849 P U F 19 distorted distorted 850 851 852 869 P G F 20 distorted distorted 857 870 871 872 892 P G F 21 distorted distorted 877 893 894 895 915 P C F 22 distorted distorted 900 916 917 918 935 P C F 23 distorted distorted 923 936 937 938 955 P U F 24 distorted distorted 943 956 957 958 975 P U F 25 distorted distorted 963 976 977 978 995 P G F 26 distorted distorted 983 996 997 998 1018 P C F 27 distorted distorted 1003 1019 1020 1021 ---------------------------------------------------------------------------------