ID code: '3LZJ' 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' --------------------------------------------------------------------------------- 7397 C1' DT T 1 beta 7393 7398 7396 7417 C1' DC T 2 beta 7413 7418 7416 7436 C1' DA T 3 beta 7432 7437 7435 7457 C1' 8OG T 4 beta 7453 7458 7456 7480 C1' DG T 5 beta 7476 7481 7479 7502 C1' DT T 6 beta 7498 7503 7501 7522 C1' DA T 7 beta 7518 7523 7521 7543 C1' DA T 8 beta 7539 7544 7542 7564 C1' DG T 9 beta 7560 7565 7563 7586 C1' DC T 10 beta 7582 7587 7585 7605 C1' DA T 11 beta 7601 7606 7604 7626 C1' DG T 12 beta 7622 7627 7625 7648 C1' DT T 13 beta 7644 7649 7647 7668 C1' DC T 14 beta 7664 7669 7667 7687 C1' DC T 15 beta 7683 7688 7686 7706 C1' DG T 16 beta 7702 7707 7705 7728 C1' DC T 17 beta 7724 7729 7727 7747 C1' DG T 18 beta 7743 7748 7746 7767 C1' DG P 103 beta 7763 7768 7766 7789 C1' DC P 104 beta 7785 7790 7788 7808 C1' DG P 105 beta 7804 7809 7807 7830 C1' DG P 106 beta 7826 7831 7829 7852 C1' DA P 107 beta 7848 7853 7851 7873 C1' DC P 108 beta 7869 7874 7872 7892 C1' DT P 109 beta 7888 7893 7891 7912 C1' DG P 110 beta 7908 7913 7911 7934 C1' DC P 111 beta 7930 7935 7933 7953 C1' DT P 112 beta 7949 7954 7952 7973 C1' DT P 113 beta 7969 7974 7972 7993 C1' DA P 114 beta 7989 7994 7992 8012 C1' DOC P 115 beta 8016 8004 8013 8031 C1' CTP A 904 beta 8035 8023 8032 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7396 C2' DT T 1 7397 7394 7416 C2' DC T 2 7417 7414 7435 C2' DA T 3 7436 7433 7456 C2' 8OG T 4 7457 7454 7479 C2' DG T 5 7480 7477 7501 C2' DT T 6 7502 7499 7521 C2' DA T 7 7522 7519 7542 C2' DA T 8 7543 7540 7563 C2' DG T 9 7564 7561 7585 C2' DC T 10 7586 7583 7604 C2' DA T 11 7605 7602 7625 C2' DG T 12 7626 7623 7647 C2' DT T 13 7648 7645 7667 C2' DC T 14 7668 7665 7686 C2' DC T 15 7687 7684 7705 C2' DG T 16 7706 7703 7727 C2' DC T 17 7728 7725 7746 C2' DG T 18 7747 7744 7766 C2' DG P 103 7767 7764 7788 C2' DC P 104 7789 7786 7807 C2' DG P 105 7808 7805 7829 C2' DG P 106 7830 7827 7851 C2' DA P 107 7852 7849 7872 C2' DC P 108 7873 7870 7891 C2' DT P 109 7892 7889 7911 C2' DG P 110 7912 7909 7933 C2' DC P 111 7934 7931 7952 C2' DT P 112 7953 7950 7972 C2' DT P 113 7973 7970 7992 C2' DA P 114 7993 7990 8013 C2' DOC P 115 8012 8014 8032 C2' CTP A 904 8031 8033 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7394 C3' DT T 1 OK 7392 7395 7396 7414 C3' DC T 2 OK 7412 7415 7416 7433 C3' DA T 3 OK 7431 7434 7435 7454 C3' 8OG T 4 OK 7452 7455 7456 7477 C3' DG T 5 OK 7475 7478 7479 7499 C3' DT T 6 OK 7497 7500 7501 7519 C3' DA T 7 OK 7517 7520 7521 7540 C3' DA T 8 OK 7538 7541 7542 7561 C3' DG T 9 OK 7559 7562 7563 7583 C3' DC T 10 OK 7581 7584 7585 7602 C3' DA T 11 OK 7600 7603 7604 7623 C3' DG T 12 OK 7621 7624 7625 7645 C3' DT T 13 OK 7643 7646 7647 7665 C3' DC T 14 OK 7663 7666 7667 7684 C3' DC T 15 OK 7682 7685 7686 7703 C3' DG T 16 OK 7701 7704 7705 7725 C3' DC T 17 OK 7723 7726 7727 7744 C3' DG T 18 OK 7742 7745 7746 7764 C3' DG P 103 OK 7762 7765 7766 7786 C3' DC P 104 OK 7784 7787 7788 7805 C3' DG P 105 OK 7803 7806 7807 7827 C3' DG P 106 OK 7825 7828 7829 7849 C3' DA P 107 OK 7847 7850 7851 7870 C3' DC P 108 OK 7868 7871 7872 7889 C3' DT P 109 OK 7887 7890 7891 7909 C3' DG P 110 OK 7907 7910 7911 7931 C3' DC P 111 OK 7929 7932 7933 7950 C3' DT P 112 OK 7948 7951 7952 7970 C3' DT P 113 OK 7968 7971 7972 7990 C3' DA P 114 OK 7988 7991 7992 8014 C3' DOC P 115 8015 8013 8033 C3' CTP A 904 OK 8034 8036 8032 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7392 C4' DT T 1 OK 7394 7391 7393 7412 C4' DC T 2 OK 7414 7411 7413 7431 C4' DA T 3 OK 7433 7430 7432 7452 C4' 8OG T 4 distorted 7454 7451 7453 7475 C4' DG T 5 OK 7477 7474 7476 7497 C4' DT T 6 OK 7499 7496 7498 7517 C4' DA T 7 OK 7519 7516 7518 7538 C4' DA T 8 OK 7540 7537 7539 7559 C4' DG T 9 OK 7561 7558 7560 7581 C4' DC T 10 OK 7583 7580 7582 7600 C4' DA T 11 OK 7602 7599 7601 7621 C4' DG T 12 OK 7623 7620 7622 7643 C4' DT T 13 OK 7645 7642 7644 7663 C4' DC T 14 OK 7665 7662 7664 7682 C4' DC T 15 OK 7684 7681 7683 7701 C4' DG T 16 OK 7703 7700 7702 7723 C4' DC T 17 OK 7725 7722 7724 7742 C4' DG T 18 OK 7744 7741 7743 7762 C4' DG P 103 OK 7764 7761 7763 7784 C4' DC P 104 OK 7786 7783 7785 7803 C4' DG P 105 OK 7805 7802 7804 7825 C4' DG P 106 OK 7827 7824 7826 7847 C4' DA P 107 OK 7849 7846 7848 7868 C4' DC P 108 OK 7870 7867 7869 7887 C4' DT P 109 OK 7889 7886 7888 7907 C4' DG P 110 OK 7909 7906 7908 7929 C4' DC P 111 OK 7931 7928 7930 7948 C4' DT P 112 OK 7950 7947 7949 7968 C4' DT P 113 OK 7970 7967 7969 7988 C4' DA P 114 OK 7990 7987 7989 8015 C4' DOC P 115 OK 8014 8017 8016 8034 C4' CTP A 904 OK 8033 8037 8035 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7391 C5' DT T 1 7390 7392 7411 C5' DC T 2 7410 7412 7430 C5' DA T 3 7429 7431 7451 C5' 8OG T 4 7450 7452 7474 C5' DG T 5 7473 7475 7496 C5' DT T 6 7495 7497 7516 C5' DA T 7 7515 7517 7537 C5' DA T 8 7536 7538 7558 C5' DG T 9 7557 7559 7580 C5' DC T 10 7579 7581 7599 C5' DA T 11 7598 7600 7620 C5' DG T 12 7619 7621 7642 C5' DT T 13 7641 7643 7662 C5' DC T 14 7661 7663 7681 C5' DC T 15 7680 7682 7700 C5' DG T 16 7699 7701 7722 C5' DC T 17 7721 7723 7741 C5' DG T 18 7740 7742 7761 C5' DG P 103 7760 7762 7783 C5' DC P 104 7782 7784 7802 C5' DG P 105 7801 7803 7824 C5' DG P 106 7823 7825 7846 C5' DA P 107 7845 7847 7867 C5' DC P 108 7866 7868 7886 C5' DT P 109 7885 7887 7906 C5' DG P 110 7905 7907 7928 C5' DC P 111 7927 7929 7947 C5' DT P 112 7946 7948 7967 C5' DT P 113 7966 7968 7987 C5' DA P 114 7986 7988 8017 C5' DOC P 115 8018 8015 8037 C5' CTP A 904 8038 8034 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7387 P DT T 1 distorted distorted 7388 7389 7390 7407 P DC T 2 distorted distorted 7395 7408 7409 7410 7426 P DA T 3 distorted distorted 7415 7427 7428 7429 7447 P 8OG T 4 distorted distorted 7434 7448 7449 7450 7470 P DG T 5 distorted distorted 7455 7471 7472 7473 7492 P DT T 6 distorted distorted 7478 7493 7494 7495 7512 P DA T 7 distorted distorted 7500 7513 7514 7515 7533 P DA T 8 distorted distorted 7520 7534 7535 7536 7554 P DG T 9 distorted distorted 7541 7555 7556 7557 7576 P DC T 10 distorted distorted 7562 7577 7578 7579 7595 P DA T 11 distorted distorted 7584 7596 7597 7598 7616 P DG T 12 distorted distorted 7603 7617 7618 7619 7638 P DT T 13 distorted distorted 7624 7639 7640 7641 7658 P DC T 14 distorted distorted 7646 7659 7660 7661 7677 P DC T 15 distorted distorted 7666 7678 7679 7680 7696 P DG T 16 distorted distorted 7685 7697 7698 7699 7718 P DC T 17 distorted distorted 7704 7719 7720 7721 7737 P DG T 18 distorted distorted 7726 7738 7739 7740 7779 P DC P 104 distorted distorted 7765 7780 7781 7782 7798 P DG P 105 distorted distorted 7787 7799 7800 7801 7820 P DG P 106 distorted distorted 7806 7821 7822 7823 7842 P DA P 107 distorted distorted 7828 7843 7844 7845 7863 P DC P 108 distorted distorted 7850 7864 7865 7866 7882 P DT P 109 distorted distorted 7871 7883 7884 7885 7902 P DG P 110 distorted distorted 7890 7903 7904 7905 7924 P DC P 111 distorted distorted 7910 7925 7926 7927 7943 P DT P 112 distorted distorted 7932 7944 7945 7946 7963 P DT P 113 distorted distorted 7951 7964 7965 7966 7983 P DA P 114 distorted distorted 7971 7984 7985 7986 8019 P DOC P 115 distorted distorted 7991 8020 8021 8018 ---------------------------------------------------------------------------------