ID code: '5ZNA' 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' --------------------------------------------------------------------------------- 8 C1' G A 1 alpha beta 4 24 9 7 41 C1' C A 2 alpha beta 37 54 42 40 71 C1' G A 3 alpha beta 67 87 72 70 104 C1' C A 4 alpha beta 100 117 105 103 134 C1' G A 5 alpha beta 130 150 135 133 167 C1' C A 6 alpha beta 163 180 168 166 197 C1' G A 7 alpha beta 193 213 198 196 230 C1' C A 8 alpha beta 226 243 231 229 260 C1' G A 9 alpha beta 256 276 261 259 293 C1' C A 10 alpha beta 289 306 294 292 323 C1' G A 11 alpha beta 319 339 324 322 356 C1' C A 12 alpha beta 352 369 357 355 386 C1' G A 13 alpha beta 382 402 387 385 419 C1' C A 14 alpha beta 415 432 420 418 449 C1' G A 15 alpha beta 445 465 450 448 482 C1' C A 16 alpha beta 478 495 483 481 510 C1' G B 17 alpha beta 506 526 511 509 543 C1' C B 18 alpha beta 539 556 544 542 573 C1' G B 19 alpha beta 569 589 574 572 606 C1' C B 20 alpha beta 602 619 607 605 636 C1' G B 21 alpha beta 632 652 637 635 669 C1' C B 22 alpha beta 665 682 670 668 699 C1' G B 23 alpha beta 695 715 700 698 732 C1' C B 24 alpha beta 728 745 733 731 762 C1' G B 25 alpha beta 758 778 763 761 795 C1' C B 26 alpha beta 791 808 796 794 825 C1' G B 27 alpha beta 821 841 826 824 858 C1' C B 28 alpha beta 854 871 859 857 888 C1' G B 29 alpha beta 884 904 889 887 921 C1' C B 30 alpha beta 917 934 922 920 951 C1' G B 31 alpha beta 947 967 952 950 984 C1' C B 32 alpha beta 980 997 985 983 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 8 5 29 30 40 C2' C A 2 OK OK 41 38 60 59 70 C2' G A 3 OK OK 71 68 92 93 103 C2' C A 4 OK OK 104 101 123 122 133 C2' G A 5 OK OK 134 131 155 156 166 C2' C A 6 OK OK 167 164 186 185 196 C2' G A 7 OK OK 197 194 218 219 229 C2' C A 8 OK OK 230 227 249 248 259 C2' G A 9 OK OK 260 257 281 282 292 C2' C A 10 OK OK 293 290 312 311 322 C2' G A 11 OK OK 323 320 344 345 355 C2' C A 12 OK OK 356 353 375 374 385 C2' G A 13 OK OK 386 383 407 408 418 C2' C A 14 OK OK 419 416 438 437 448 C2' G A 15 OK OK 449 446 470 471 481 C2' C A 16 OK OK 482 479 501 500 509 C2' G B 17 OK OK 510 507 531 532 542 C2' C B 18 OK OK 543 540 562 561 572 C2' G B 19 OK OK 573 570 594 595 605 C2' C B 20 OK OK 606 603 625 624 635 C2' G B 21 OK OK 636 633 657 658 668 C2' C B 22 OK OK 669 666 688 687 698 C2' G B 23 OK OK 699 696 720 721 731 C2' C B 24 OK OK 732 729 751 750 761 C2' G B 25 OK OK 762 759 783 784 794 C2' C B 26 OK OK 795 792 814 813 824 C2' G B 27 OK OK 825 822 846 847 857 C2' C B 28 OK OK 858 855 877 876 887 C2' G B 29 OK OK 888 885 909 910 920 C2' C B 30 OK OK 921 918 940 939 950 C2' G B 31 OK OK 951 948 972 973 983 C2' C B 32 OK OK 984 981 1003 1002 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK OK 3 23 6 7 38 C3' C A 2 OK OK 36 53 39 40 68 C3' G A 3 OK OK 66 86 69 70 101 C3' C A 4 OK OK 99 116 102 103 131 C3' G A 5 OK OK 129 149 132 133 164 C3' C A 6 OK OK 162 179 165 166 194 C3' G A 7 OK OK 192 212 195 196 227 C3' C A 8 OK OK 225 242 228 229 257 C3' G A 9 OK OK 255 275 258 259 290 C3' C A 10 OK OK 288 305 291 292 320 C3' G A 11 OK OK 318 338 321 322 353 C3' C A 12 OK OK 351 368 354 355 383 C3' G A 13 OK OK 381 401 384 385 416 C3' C A 14 OK OK 414 431 417 418 446 C3' G A 15 OK OK 444 464 447 448 479 C3' C A 16 OK OK 477 494 480 481 507 C3' G B 17 OK OK 505 525 508 509 540 C3' C B 18 OK OK 538 555 541 542 570 C3' G B 19 OK OK 568 588 571 572 603 C3' C B 20 OK OK 601 618 604 605 633 C3' G B 21 OK OK 631 651 634 635 666 C3' C B 22 OK OK 664 681 667 668 696 C3' G B 23 OK OK 694 714 697 698 729 C3' C B 24 OK OK 727 744 730 731 759 C3' G B 25 OK OK 757 777 760 761 792 C3' C B 26 OK OK 790 807 793 794 822 C3' G B 27 OK OK 820 840 823 824 855 C3' C B 28 OK OK 853 870 856 857 885 C3' G B 29 OK OK 883 903 886 887 918 C3' C B 30 OK OK 916 933 919 920 948 C3' G B 31 OK OK 946 966 949 950 981 C3' C B 32 OK OK 979 996 982 983 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK OK 5 22 2 4 36 C4' C A 2 OK OK 38 52 35 37 66 C4' G A 3 OK OK 68 85 65 67 99 C4' C A 4 OK OK 101 115 98 100 129 C4' G A 5 OK OK 131 148 128 130 162 C4' C A 6 OK OK 164 178 161 163 192 C4' G A 7 OK OK 194 211 191 193 225 C4' C A 8 OK OK 227 241 224 226 255 C4' G A 9 OK OK 257 274 254 256 288 C4' C A 10 OK OK 290 304 287 289 318 C4' G A 11 OK OK 320 337 317 319 351 C4' C A 12 OK OK 353 367 350 352 381 C4' G A 13 OK OK 383 400 380 382 414 C4' C A 14 OK OK 416 430 413 415 444 C4' G A 15 OK OK 446 463 443 445 477 C4' C A 16 OK OK 479 493 476 478 505 C4' G B 17 OK OK 507 524 504 506 538 C4' C B 18 OK OK 540 554 537 539 568 C4' G B 19 OK OK 570 587 567 569 601 C4' C B 20 OK OK 603 617 600 602 631 C4' G B 21 OK OK 633 650 630 632 664 C4' C B 22 OK OK 666 680 663 665 694 C4' G B 23 OK OK 696 713 693 695 727 C4' C B 24 OK OK 729 743 726 728 757 C4' G B 25 OK OK 759 776 756 758 790 C4' C B 26 OK OK 792 806 789 791 820 C4' G B 27 OK OK 822 839 819 821 853 C4' C B 28 OK OK 855 869 852 854 883 C4' G B 29 OK OK 885 902 882 884 916 C4' C B 30 OK OK 918 932 915 917 946 C4' G B 31 OK OK 948 965 945 947 979 C4' C B 32 OK OK 981 995 978 980 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 OK OK 1 20 21 3 35 C5' C A 2 OK OK 34 50 51 36 65 C5' G A 3 OK OK 64 83 84 66 98 C5' C A 4 OK OK 97 113 114 99 128 C5' G A 5 OK OK 127 146 147 129 161 C5' C A 6 OK OK 160 176 177 162 191 C5' G A 7 OK OK 190 209 210 192 224 C5' C A 8 OK OK 223 239 240 225 254 C5' G A 9 OK OK 253 272 273 255 287 C5' C A 10 OK OK 286 302 303 288 317 C5' G A 11 OK OK 316 335 336 318 350 C5' C A 12 OK OK 349 365 366 351 380 C5' G A 13 OK OK 379 398 399 381 413 C5' C A 14 OK OK 412 428 429 414 443 C5' G A 15 OK OK 442 461 462 444 476 C5' C A 16 OK OK 475 491 492 477 504 C5' G B 17 OK OK 503 522 523 505 537 C5' C B 18 OK OK 536 552 553 538 567 C5' G B 19 OK OK 566 585 586 568 600 C5' C B 20 OK OK 599 615 616 601 630 C5' G B 21 OK OK 629 648 649 631 663 C5' C B 22 OK OK 662 678 679 664 693 C5' G B 23 OK OK 692 711 712 694 726 C5' C B 24 OK OK 725 741 742 727 756 C5' G B 25 OK OK 755 774 775 757 789 C5' C B 26 OK OK 788 804 805 790 819 C5' G B 27 OK OK 818 837 838 820 852 C5' C B 28 OK OK 851 867 868 853 882 C5' G B 29 OK OK 881 900 901 883 915 C5' C B 30 OK OK 914 930 931 916 945 C5' G B 31 OK OK 944 963 964 946 978 C5' C B 32 OK OK 977 993 994 979 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 31 P C A 2 distorted distorted 6 32 33 34 61 P G A 3 distorted distorted 39 62 63 64 94 P C A 4 distorted distorted 69 95 96 97 124 P G A 5 distorted distorted 102 125 126 127 157 P C A 6 distorted distorted 132 158 159 160 187 P G A 7 distorted distorted 165 188 189 190 220 P C A 8 distorted distorted 195 221 222 223 250 P G A 9 distorted distorted 228 251 252 253 283 P C A 10 distorted distorted 258 284 285 286 313 P G A 11 distorted distorted 291 314 315 316 346 P C A 12 distorted distorted 321 347 348 349 376 P G A 13 distorted distorted 354 377 378 379 409 P C A 14 distorted distorted 384 410 411 412 439 P G A 15 distorted distorted 417 440 441 442 472 P C A 16 distorted distorted 447 473 474 475 533 P C B 18 distorted distorted 508 534 535 536 563 P G B 19 distorted distorted 541 564 565 566 596 P C B 20 distorted distorted 571 597 598 599 626 P G B 21 distorted distorted 604 627 628 629 659 P C B 22 distorted distorted 634 660 661 662 689 P G B 23 distorted distorted 667 690 691 692 722 P C B 24 distorted distorted 697 723 724 725 752 P G B 25 distorted distorted 730 753 754 755 785 P C B 26 distorted distorted 760 786 787 788 815 P G B 27 distorted distorted 793 816 817 818 848 P C B 28 distorted distorted 823 849 850 851 878 P G B 29 distorted distorted 856 879 880 881 911 P C B 30 distorted distorted 886 912 913 914 941 P G B 31 distorted distorted 919 942 943 944 974 P C B 32 distorted distorted 949 975 976 977 ---------------------------------------------------------------------------------