ID code: '3MDA' 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' --------------------------------------------------------------------------------- 2537 C1' DC T 1 beta 2533 2538 2536 2556 C1' DG T 2 beta 2552 2557 2555 2578 C1' DG T 3 beta 2574 2579 2577 2600 C1' DC T 4 beta 2596 2601 2599 2619 C1' DG T 5 beta 2615 2620 2618 2641 C1' DG T 6 beta 2637 2642 2640 2663 C1' DT T 7 beta 2659 2664 2662 2683 C1' DA T 8 beta 2679 2684 2682 2704 C1' DC T 9 beta 2700 2705 2703 2723 C1' DT T 10 beta 2719 2724 2722 2743 C1' DG T 11 beta 2739 2744 2742 2763 C1' DC P 1 beta 2759 2764 2762 2782 C1' DA P 2 beta 2778 2783 2781 2803 C1' DG P 3 beta 2799 2804 2802 2825 C1' DT P 4 beta 2821 2826 2824 2845 C1' DA P 5 beta 2841 2846 2844 2866 C1' DC P 6 beta 2862 2867 2865 2886 C1' CAR P 7 beta 2881 2887 2884 2907 C1' DG D 1 beta 2903 2908 2906 2929 C1' DC D 2 beta 2925 2930 2928 2948 C1' DC D 3 beta 2944 2949 2947 2967 C1' DG D 4 beta 2963 2968 2966 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2536 C2' DC T 1 2537 2534 2555 C2' DG T 2 2556 2553 2577 C2' DG T 3 2578 2575 2599 C2' DC T 4 2600 2597 2618 C2' DG T 5 2619 2616 2640 C2' DG T 6 2641 2638 2662 C2' DT T 7 2663 2660 2682 C2' DA T 8 2683 2680 2703 C2' DC T 9 2704 2701 2722 C2' DT T 10 2723 2720 2742 C2' DG T 11 2743 2740 2762 C2' DC P 1 2763 2760 2781 C2' DA P 2 2782 2779 2802 C2' DG P 3 2803 2800 2824 C2' DT P 4 2825 2822 2844 C2' DA P 5 2845 2842 2865 C2' DC P 6 2866 2863 2884 C2' CAR P 7 distorted 2886 2882 2885 2906 C2' DG D 1 2907 2904 2928 C2' DC D 2 2929 2926 2947 C2' DC D 3 2948 2945 2966 C2' DG D 4 2967 2964 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2534 C3' DC T 1 OK 2532 2535 2536 2553 C3' DG T 2 OK 2551 2554 2555 2575 C3' DG T 3 OK 2573 2576 2577 2597 C3' DC T 4 OK 2595 2598 2599 2616 C3' DG T 5 OK 2614 2617 2618 2638 C3' DG T 6 OK 2636 2639 2640 2660 C3' DT T 7 OK 2658 2661 2662 2680 C3' DA T 8 OK 2678 2681 2682 2701 C3' DC T 9 OK 2699 2702 2703 2720 C3' DT T 10 OK 2718 2721 2722 2740 C3' DG T 11 OK 2738 2741 2742 2760 C3' DC P 1 OK 2758 2761 2762 2779 C3' DA P 2 OK 2777 2780 2781 2800 C3' DG P 3 OK 2798 2801 2802 2822 C3' DT P 4 OK 2820 2823 2824 2842 C3' DA P 5 OK 2840 2843 2844 2863 C3' DC P 6 OK 2861 2864 2865 2882 C3' CAR P 7 OK 2880 2883 2884 2904 C3' DG D 1 OK 2902 2905 2906 2926 C3' DC D 2 OK 2924 2927 2928 2945 C3' DC D 3 OK 2943 2946 2947 2964 C3' DG D 4 OK 2962 2965 2966 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2532 C4' DC T 1 OK 2534 2531 2533 2551 C4' DG T 2 OK 2553 2550 2552 2573 C4' DG T 3 OK 2575 2572 2574 2595 C4' DC T 4 OK 2597 2594 2596 2614 C4' DG T 5 OK 2616 2613 2615 2636 C4' DG T 6 OK 2638 2635 2637 2658 C4' DT T 7 OK 2660 2657 2659 2678 C4' DA T 8 OK 2680 2677 2679 2699 C4' DC T 9 OK 2701 2698 2700 2718 C4' DT T 10 OK 2720 2717 2719 2738 C4' DG T 11 OK 2740 2737 2739 2758 C4' DC P 1 OK 2760 2757 2759 2777 C4' DA P 2 OK 2779 2776 2778 2798 C4' DG P 3 OK 2800 2797 2799 2820 C4' DT P 4 OK 2822 2819 2821 2840 C4' DA P 5 OK 2842 2839 2841 2861 C4' DC P 6 OK 2863 2860 2862 2880 C4' CAR P 7 OK 2882 2879 2881 2902 C4' DG D 1 OK 2904 2901 2903 2924 C4' DC D 2 OK 2926 2923 2925 2943 C4' DC D 3 OK 2945 2942 2944 2962 C4' DG D 4 OK 2964 2961 2963 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2531 C5' DC T 1 2530 2532 2550 C5' DG T 2 2549 2551 2572 C5' DG T 3 2571 2573 2594 C5' DC T 4 2593 2595 2613 C5' DG T 5 2612 2614 2635 C5' DG T 6 2634 2636 2657 C5' DT T 7 2656 2658 2677 C5' DA T 8 2676 2678 2698 C5' DC T 9 2697 2699 2717 C5' DT T 10 2716 2718 2737 C5' DG T 11 2736 2738 2757 C5' DC P 1 2756 2758 2776 C5' DA P 2 2775 2777 2797 C5' DG P 3 2796 2798 2819 C5' DT P 4 2818 2820 2839 C5' DA P 5 2838 2840 2860 C5' DC P 6 2859 2861 2879 C5' CAR P 7 2878 2880 2901 C5' DG D 1 2900 2902 2923 C5' DC D 2 2922 2924 2942 C5' DC D 3 2941 2943 2961 C5' DG D 4 2960 2962 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2546 P DG T 2 distorted distorted 2535 2547 2548 2549 2568 P DG T 3 distorted distorted 2554 2569 2570 2571 2590 P DC T 4 distorted distorted 2576 2591 2592 2593 2609 P DG T 5 distorted distorted 2598 2610 2611 2612 2631 P DG T 6 distorted distorted 2617 2632 2633 2634 2653 P DT T 7 distorted distorted 2639 2654 2655 2656 2673 P DA T 8 distorted distorted 2661 2674 2675 2676 2694 P DC T 9 distorted distorted 2681 2695 2696 2697 2713 P DT T 10 distorted distorted 2702 2714 2715 2716 2733 P DG T 11 distorted distorted 2721 2734 2735 2736 2772 P DA P 2 distorted distorted 2761 2773 2774 2775 2793 P DG P 3 distorted distorted 2780 2794 2795 2796 2815 P DT P 4 distorted distorted 2801 2816 2817 2818 2835 P DA P 5 distorted distorted 2823 2836 2837 2838 2856 P DC P 6 distorted distorted 2843 2857 2858 2859 2875 P CAR P 7 distorted distorted 2864 2876 2877 2878 2897 P DG D 1 OK OK 2898 2899 2900 2919 P DC D 2 distorted distorted 2905 2920 2921 2922 2938 P DC D 3 distorted distorted 2927 2939 2940 2941 2957 P DG D 4 distorted distorted 2946 2958 2959 2960 ---------------------------------------------------------------------------------