ID code: '5VZB' 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' --------------------------------------------------------------------------------- 2714 C1' DC T 1 beta 2710 2715 2713 2733 C1' DG T 2 beta 2729 2734 2732 2755 C1' DG T 3 beta 2751 2756 2754 2777 C1' DC T 4 beta 2773 2778 2776 2796 C1' DA T 5 beta 2792 2797 2795 2817 C1' DT T 6 beta 2813 2818 2816 2837 C1' DA T 7 beta 2833 2838 2836 2858 C1' DC T 8 beta 2854 2859 2857 2877 C1' DG T 9 beta 2873 2878 2876 2897 C1' DC P 1 beta 2893 2898 2896 2916 C1' DG P 2 beta 2912 2917 2915 2938 C1' DT P 3 beta 2934 2939 2937 2958 C1' DA P 4 beta 2954 2959 2957 2986 C1' DG D 1 beta 2982 2987 2985 3008 C1' DC D 2 beta 3004 3009 3007 3121 C1' UTP A 506 beta 3120 3126 3122 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2713 C2' DC T 1 2714 2711 2732 C2' DG T 2 2733 2730 2754 C2' DG T 3 2755 2752 2776 C2' DC T 4 2777 2774 2795 C2' DA T 5 2796 2793 2816 C2' DT T 6 2817 2814 2836 C2' DA T 7 2837 2834 2857 C2' DC T 8 2858 2855 2876 C2' DG T 9 2877 2874 2896 C2' DC P 1 2897 2894 2915 C2' DG P 2 2916 2913 2937 C2' DT P 3 2938 2935 2957 C2' DA P 4 2958 2955 2985 C2' DG D 1 2986 2983 3007 C2' DC D 2 3008 3005 3122 C2' UTP A 506 OK 3121 3124 3123 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2711 C3' DC T 1 OK 2709 2712 2713 2730 C3' DG T 2 OK 2728 2731 2732 2752 C3' DG T 3 OK 2750 2753 2754 2774 C3' DC T 4 OK 2772 2775 2776 2793 C3' DA T 5 OK 2791 2794 2795 2814 C3' DT T 6 OK 2812 2815 2816 2834 C3' DA T 7 OK 2832 2835 2836 2855 C3' DC T 8 OK 2853 2856 2857 2874 C3' DG T 9 OK 2872 2875 2876 2894 C3' DC P 1 OK 2892 2895 2896 2913 C3' DG P 2 OK 2911 2914 2915 2935 C3' DT P 3 OK 2933 2936 2937 2955 C3' DA P 4 OK 2953 2956 2957 2983 C3' DG D 1 OK 2981 2984 2985 3005 C3' DC D 2 OK 3003 3006 3007 3124 C3' UTP A 506 OK 3119 3125 3122 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2709 C4' DC T 1 OK 2711 2708 2710 2728 C4' DG T 2 OK 2730 2727 2729 2750 C4' DG T 3 OK 2752 2749 2751 2772 C4' DC T 4 OK 2774 2771 2773 2791 C4' DA T 5 OK 2793 2790 2792 2812 C4' DT T 6 OK 2814 2811 2813 2832 C4' DA T 7 OK 2834 2831 2833 2853 C4' DC T 8 OK 2855 2852 2854 2872 C4' DG T 9 OK 2874 2871 2873 2892 C4' DC P 1 OK 2894 2891 2893 2911 C4' DG P 2 OK 2913 2910 2912 2933 C4' DT P 3 OK 2935 2932 2934 2953 C4' DA P 4 OK 2955 2952 2954 2981 C4' DG D 1 OK 2983 2980 2982 3003 C4' DC D 2 OK 3005 3002 3004 3119 C4' UTP A 506 OK 3124 3118 3120 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2708 C5' DC T 1 2707 2709 2727 C5' DG T 2 2726 2728 2749 C5' DG T 3 2748 2750 2771 C5' DC T 4 2770 2772 2790 C5' DA T 5 2789 2791 2811 C5' DT T 6 2810 2812 2831 C5' DA T 7 2830 2832 2852 C5' DC T 8 2851 2853 2871 C5' DG T 9 2870 2872 2891 C5' DC P 1 2890 2892 2910 C5' DG P 2 2909 2911 2932 C5' DT P 3 2931 2933 2952 C5' DA P 4 2951 2953 2973 C5' U P 5 2972 2980 C5' DG D 1 2979 2981 3002 C5' DC D 2 3001 3003 3118 C5' UTP A 506 3109 3119 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2723 P DG T 2 distorted distorted 2712 2724 2725 2726 2745 P DG T 3 distorted distorted 2731 2746 2747 2748 2767 P DC T 4 distorted distorted 2753 2768 2769 2770 2786 P DA T 5 distorted distorted 2775 2787 2788 2789 2807 P DT T 6 distorted distorted 2794 2808 2809 2810 2827 P DA T 7 distorted distorted 2815 2828 2829 2830 2848 P DC T 8 distorted distorted 2835 2849 2850 2851 2867 P DG T 9 distorted distorted 2856 2868 2869 2870 2906 P DG P 2 distorted distorted 2895 2907 2908 2909 2928 P DT P 3 distorted distorted 2914 2929 2930 2931 2948 P DA P 4 distorted distorted 2936 2949 2950 2951 2969 P U P 5 distorted distorted 2956 2970 2971 2972 2976 P DG D 1 OK OK 2977 2978 2979 2998 P DC D 2 distorted distorted 2984 2999 3000 3001 3017 P DC D 3 3006 3018 P DC D 3 3006 3055 P DG D 4 3056 P DG D 4 ---------------------------------------------------------------------------------