ID code: '3R9W' 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' --------------------------------------------------------------------------------- 2443 C1' C B1506 beta 2438 2444 2441 2463 C1' A B1507 beta 2458 2464 2461 2485 C1' A B1508 beta 2480 2486 2483 2507 C1' C B1509 beta 2502 2508 2505 2527 C1' C B1510 beta 2522 2528 2525 2547 C1' G B1511 beta 2542 2548 2545 2570 C1' U B1512 beta 2565 2571 2568 2590 C1' A B1513 beta 2585 2591 2588 2612 C1' G B1514 beta 2607 2613 2610 2635 C1' G B1515 beta 2630 2636 2633 2658 C1' G B1516 beta 2653 2659 2656 2681 C1' G B1517 beta 2676 2682 2679 2704 C1' A B1518 beta 2699 2705 2702 2726 C1' A B1519 beta 2721 2727 2724 2748 C1' C B1520 beta 2743 2749 2746 2768 C1' C B1521 beta 2763 2769 2766 2788 C1' U B1522 beta 2783 2789 2786 2808 C1' G B1523 beta 2803 2809 2806 2831 C1' C B1524 beta 2826 2832 2829 2851 C1' G B1525 beta 2846 2852 2849 2874 C1' G B1526 beta 2869 2875 2872 2897 C1' U B1527 beta 2892 2898 2895 2917 C1' U B1528 beta 2912 2918 2915 2937 C1' G B1529 beta 2932 2938 2935 2960 C1' G B1530 beta 2955 2961 2958 2983 C1' A B1531 beta 2978 2984 2981 3005 C1' U B1532 beta 3000 3006 3003 3025 C1' C B1533 beta 3020 3026 3023 3045 C1' A B1534 beta 3040 3046 3043 3067 C1' C B1535 beta 3062 3068 3065 3087 C1' C B1536 beta 3082 3088 3085 3107 C1' U B1537 beta 3102 3108 3105 3127 C1' C B1538 beta 3122 3128 3125 3147 C1' C B1539 beta 3142 3148 3145 3178 C1' GNP A 402 beta 3173 3179 3176 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2441 C2' C B1506 OK 2443 2439 2442 2461 C2' A B1507 OK 2463 2459 2462 2483 C2' A B1508 OK 2485 2481 2484 2505 C2' C B1509 OK 2507 2503 2506 2525 C2' C B1510 OK 2527 2523 2526 2545 C2' G B1511 OK 2547 2543 2546 2568 C2' U B1512 OK 2570 2566 2569 2588 C2' A B1513 OK 2590 2586 2589 2610 C2' G B1514 OK 2612 2608 2611 2633 C2' G B1515 OK 2635 2631 2634 2656 C2' G B1516 OK 2658 2654 2657 2679 C2' G B1517 OK 2681 2677 2680 2702 C2' A B1518 OK 2704 2700 2703 2724 C2' A B1519 OK 2726 2722 2725 2746 C2' C B1520 OK 2748 2744 2747 2766 C2' C B1521 OK 2768 2764 2767 2786 C2' U B1522 OK 2788 2784 2787 2806 C2' G B1523 OK 2808 2804 2807 2829 C2' C B1524 OK 2831 2827 2830 2849 C2' G B1525 OK 2851 2847 2850 2872 C2' G B1526 OK 2874 2870 2873 2895 C2' U B1527 OK 2897 2893 2896 2915 C2' U B1528 OK 2917 2913 2916 2935 C2' G B1529 OK 2937 2933 2936 2958 C2' G B1530 OK 2960 2956 2959 2981 C2' A B1531 OK 2983 2979 2982 3003 C2' U B1532 OK 3005 3001 3004 3023 C2' C B1533 OK 3025 3021 3024 3043 C2' A B1534 OK 3045 3041 3044 3065 C2' C B1535 OK 3067 3063 3066 3085 C2' C B1536 OK 3087 3083 3086 3105 C2' U B1537 OK 3107 3103 3106 3125 C2' C B1538 OK 3127 3123 3126 3145 C2' C B1539 OK 3147 3143 3146 3176 C2' GNP A 402 OK 3178 3174 3177 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2439 C3' C B1506 OK 2437 2440 2441 2459 C3' A B1507 OK 2457 2460 2461 2481 C3' A B1508 OK 2479 2482 2483 2503 C3' C B1509 OK 2501 2504 2505 2523 C3' C B1510 OK 2521 2524 2525 2543 C3' G B1511 OK 2541 2544 2545 2566 C3' U B1512 OK 2564 2567 2568 2586 C3' A B1513 OK 2584 2587 2588 2608 C3' G B1514 OK 2606 2609 2610 2631 C3' G B1515 OK 2629 2632 2633 2654 C3' G B1516 OK 2652 2655 2656 2677 C3' G B1517 OK 2675 2678 2679 2700 C3' A B1518 OK 2698 2701 2702 2722 C3' A B1519 OK 2720 2723 2724 2744 C3' C B1520 OK 2742 2745 2746 2764 C3' C B1521 OK 2762 2765 2766 2784 C3' U B1522 OK 2782 2785 2786 2804 C3' G B1523 OK 2802 2805 2806 2827 C3' C B1524 OK 2825 2828 2829 2847 C3' G B1525 OK 2845 2848 2849 2870 C3' G B1526 OK 2868 2871 2872 2893 C3' U B1527 OK 2891 2894 2895 2913 C3' U B1528 OK 2911 2914 2915 2933 C3' G B1529 OK 2931 2934 2935 2956 C3' G B1530 OK 2954 2957 2958 2979 C3' A B1531 OK 2977 2980 2981 3001 C3' U B1532 OK 2999 3002 3003 3021 C3' C B1533 OK 3019 3022 3023 3041 C3' A B1534 OK 3039 3042 3043 3063 C3' C B1535 OK 3061 3064 3065 3083 C3' C B1536 OK 3081 3084 3085 3103 C3' U B1537 OK 3101 3104 3105 3123 C3' C B1538 OK 3121 3124 3125 3143 C3' C B1539 OK 3141 3144 3145 3174 C3' GNP A 402 OK 3172 3175 3176 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2437 C4' C B1506 OK 2439 2436 2438 2457 C4' A B1507 OK 2459 2456 2458 2479 C4' A B1508 OK 2481 2478 2480 2501 C4' C B1509 OK 2503 2500 2502 2521 C4' C B1510 OK 2523 2520 2522 2541 C4' G B1511 OK 2543 2540 2542 2564 C4' U B1512 OK 2566 2563 2565 2584 C4' A B1513 OK 2586 2583 2585 2606 C4' G B1514 OK 2608 2605 2607 2629 C4' G B1515 OK 2631 2628 2630 2652 C4' G B1516 OK 2654 2651 2653 2675 C4' G B1517 OK 2677 2674 2676 2698 C4' A B1518 OK 2700 2697 2699 2720 C4' A B1519 OK 2722 2719 2721 2742 C4' C B1520 OK 2744 2741 2743 2762 C4' C B1521 OK 2764 2761 2763 2782 C4' U B1522 OK 2784 2781 2783 2802 C4' G B1523 OK 2804 2801 2803 2825 C4' C B1524 OK 2827 2824 2826 2845 C4' G B1525 OK 2847 2844 2846 2868 C4' G B1526 OK 2870 2867 2869 2891 C4' U B1527 OK 2893 2890 2892 2911 C4' U B1528 OK 2913 2910 2912 2931 C4' G B1529 OK 2933 2930 2932 2954 C4' G B1530 OK 2956 2953 2955 2977 C4' A B1531 OK 2979 2976 2978 2999 C4' U B1532 OK 3001 2998 3000 3019 C4' C B1533 OK 3021 3018 3020 3039 C4' A B1534 OK 3041 3038 3040 3061 C4' C B1535 OK 3063 3060 3062 3081 C4' C B1536 OK 3083 3080 3082 3101 C4' U B1537 OK 3103 3100 3102 3121 C4' C B1538 OK 3123 3120 3122 3141 C4' C B1539 OK 3143 3140 3142 3172 C4' GNP A 402 OK 3174 3171 3173 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2436 C5' C B1506 2435 2437 2456 C5' A B1507 2455 2457 2478 C5' A B1508 2477 2479 2500 C5' C B1509 2499 2501 2520 C5' C B1510 2519 2521 2540 C5' G B1511 2539 2541 2563 C5' U B1512 2562 2564 2583 C5' A B1513 2582 2584 2605 C5' G B1514 2604 2606 2628 C5' G B1515 2627 2629 2651 C5' G B1516 2650 2652 2674 C5' G B1517 2673 2675 2697 C5' A B1518 2696 2698 2719 C5' A B1519 2718 2720 2741 C5' C B1520 2740 2742 2761 C5' C B1521 2760 2762 2781 C5' U B1522 2780 2782 2801 C5' G B1523 2800 2802 2824 C5' C B1524 2823 2825 2844 C5' G B1525 2843 2845 2867 C5' G B1526 2866 2868 2890 C5' U B1527 2889 2891 2910 C5' U B1528 2909 2911 2930 C5' G B1529 2929 2931 2953 C5' G B1530 2952 2954 2976 C5' A B1531 2975 2977 2998 C5' U B1532 2997 2999 3018 C5' C B1533 3017 3019 3038 C5' A B1534 3037 3039 3060 C5' C B1535 3059 3061 3080 C5' C B1536 3079 3081 3100 C5' U B1537 3099 3101 3120 C5' C B1538 3119 3121 3140 C5' C B1539 3139 3141 3171 C5' GNP A 402 3170 3172 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2432 P C B1506 OK OK 2433 2434 2435 2452 P A B1507 distorted distorted 2440 2453 2454 2455 2474 P A B1508 distorted distorted 2460 2475 2476 2477 2496 P C B1509 distorted distorted 2482 2497 2498 2499 2516 P C B1510 distorted distorted 2504 2517 2518 2519 2536 P G B1511 distorted distorted 2524 2537 2538 2539 2559 P U B1512 distorted distorted 2544 2560 2561 2562 2579 P A B1513 distorted distorted 2567 2580 2581 2582 2601 P G B1514 distorted distorted 2587 2602 2603 2604 2624 P G B1515 distorted distorted 2609 2625 2626 2627 2647 P G B1516 distorted distorted 2632 2648 2649 2650 2670 P G B1517 distorted distorted 2655 2671 2672 2673 2693 P A B1518 distorted distorted 2678 2694 2695 2696 2715 P A B1519 distorted distorted 2701 2716 2717 2718 2737 P C B1520 distorted distorted 2723 2738 2739 2740 2757 P C B1521 distorted distorted 2745 2758 2759 2760 2777 P U B1522 distorted distorted 2765 2778 2779 2780 2797 P G B1523 distorted distorted 2785 2798 2799 2800 2820 P C B1524 distorted distorted 2805 2821 2822 2823 2840 P G B1525 distorted distorted 2828 2841 2842 2843 2863 P G B1526 distorted distorted 2848 2864 2865 2866 2886 P U B1527 distorted distorted 2871 2887 2888 2889 2906 P U B1528 distorted distorted 2894 2907 2908 2909 2926 P G B1529 distorted distorted 2914 2927 2928 2929 2949 P G B1530 distorted distorted 2934 2950 2951 2952 2972 P A B1531 distorted distorted 2957 2973 2974 2975 2994 P U B1532 distorted distorted 2980 2995 2996 2997 3014 P C B1533 distorted distorted 3002 3015 3016 3017 3034 P A B1534 distorted distorted 3022 3035 3036 3037 3056 P C B1535 distorted distorted 3042 3057 3058 3059 3076 P C B1536 distorted distorted 3064 3077 3078 3079 3096 P U B1537 distorted distorted 3084 3097 3098 3099 3116 P C B1538 distorted distorted 3104 3117 3118 3119 3136 P C B1539 distorted distorted 3124 3137 3138 3139 ---------------------------------------------------------------------------------