ID code: '3JPQ' 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' --------------------------------------------------------------------------------- 2627 C1' DG D 1 beta 2623 2628 2626 2649 C1' DT D 2 beta 2645 2650 2648 2669 C1' DC D 3 beta 2665 2670 2668 2688 C1' DG D 4 beta 2684 2689 2687 2710 C1' DG D 5 beta 2706 2711 2709 2730 C1' DG P 1 beta 2726 2731 2729 2752 C1' DC P 2 beta 2748 2753 2751 2771 C1' DT P 3 beta 2767 2772 2770 2791 C1' DG P 4 beta 2787 2792 2790 2813 C1' DA P 5 beta 2809 2814 2812 2834 C1' DT P 6 beta 2830 2835 2833 2854 C1' DG P 7 beta 2850 2855 2853 2876 C1' DC P 8 beta 2872 2877 2875 2895 C1' DG P 9 beta 2891 2896 2894 2915 C1' DOC P 10 beta 2919 2907 2916 2933 C1' DC T 1 beta 2929 2934 2932 2952 C1' DC T 2 beta 2948 2953 2951 2971 C1' DG T 3 beta 2967 2972 2970 2993 C1' DA T 4 beta 2989 2994 2992 3014 C1' DC T 5 beta 3010 3015 3013 3033 C1' DC T 6 beta 3029 3034 3032 3052 C1' DG T 7 beta 3048 3053 3051 3074 C1' DC T 8 beta 3070 3075 3073 3093 C1' DG T 9 beta 3089 3094 3092 3115 C1' DC T 10 beta 3111 3116 3114 3134 C1' DA T 11 beta 3130 3135 3133 3155 C1' DT T 12 beta 3151 3156 3154 3175 C1' DC T 13 beta 3171 3176 3174 3194 C1' DA T 14 beta 3190 3195 3193 3215 C1' DG T 15 beta 3211 3216 3214 3237 C1' DC T 16 beta 3233 3238 3236 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2626 C2' DG D 1 2627 2624 2648 C2' DT D 2 2649 2646 2668 C2' DC D 3 2669 2666 2687 C2' DG D 4 2688 2685 2709 C2' DG D 5 2710 2707 2729 C2' DG P 1 2730 2727 2751 C2' DC P 2 2752 2749 2770 C2' DT P 3 2771 2768 2790 C2' DG P 4 2791 2788 2812 C2' DA P 5 2813 2810 2833 C2' DT P 6 2834 2831 2853 C2' DG P 7 2854 2851 2875 C2' DC P 8 2876 2873 2894 C2' DG P 9 2895 2892 2916 C2' DOC P 10 2915 2917 2932 C2' DC T 1 2933 2930 2951 C2' DC T 2 2952 2949 2970 C2' DG T 3 2971 2968 2992 C2' DA T 4 2993 2990 3013 C2' DC T 5 3014 3011 3032 C2' DC T 6 3033 3030 3051 C2' DG T 7 3052 3049 3073 C2' DC T 8 3074 3071 3092 C2' DG T 9 3093 3090 3114 C2' DC T 10 3115 3112 3133 C2' DA T 11 3134 3131 3154 C2' DT T 12 3155 3152 3174 C2' DC T 13 3175 3172 3193 C2' DA T 14 3194 3191 3214 C2' DG T 15 3215 3212 3236 C2' DC T 16 3237 3234 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2624 C3' DG D 1 OK 2622 2625 2626 2646 C3' DT D 2 OK 2644 2647 2648 2666 C3' DC D 3 OK 2664 2667 2668 2685 C3' DG D 4 OK 2683 2686 2687 2707 C3' DG D 5 OK 2705 2708 2709 2727 C3' DG P 1 OK 2725 2728 2729 2749 C3' DC P 2 OK 2747 2750 2751 2768 C3' DT P 3 OK 2766 2769 2770 2788 C3' DG P 4 OK 2786 2789 2790 2810 C3' DA P 5 OK 2808 2811 2812 2831 C3' DT P 6 OK 2829 2832 2833 2851 C3' DG P 7 OK 2849 2852 2853 2873 C3' DC P 8 OK 2871 2874 2875 2892 C3' DG P 9 OK 2890 2893 2894 2917 C3' DOC P 10 2918 2916 2930 C3' DC T 1 OK 2928 2931 2932 2949 C3' DC T 2 OK 2947 2950 2951 2968 C3' DG T 3 OK 2966 2969 2970 2990 C3' DA T 4 OK 2988 2991 2992 3011 C3' DC T 5 OK 3009 3012 3013 3030 C3' DC T 6 OK 3028 3031 3032 3049 C3' DG T 7 OK 3047 3050 3051 3071 C3' DC T 8 OK 3069 3072 3073 3090 C3' DG T 9 OK 3088 3091 3092 3112 C3' DC T 10 OK 3110 3113 3114 3131 C3' DA T 11 OK 3129 3132 3133 3152 C3' DT T 12 OK 3150 3153 3154 3172 C3' DC T 13 OK 3170 3173 3174 3191 C3' DA T 14 OK 3189 3192 3193 3212 C3' DG T 15 OK 3210 3213 3214 3234 C3' DC T 16 OK 3232 3235 3236 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2622 C4' DG D 1 OK 2624 2621 2623 2644 C4' DT D 2 OK 2646 2643 2645 2664 C4' DC D 3 OK 2666 2663 2665 2683 C4' DG D 4 OK 2685 2682 2684 2705 C4' DG D 5 OK 2707 2704 2706 2725 C4' DG P 1 OK 2727 2724 2726 2747 C4' DC P 2 OK 2749 2746 2748 2766 C4' DT P 3 OK 2768 2765 2767 2786 C4' DG P 4 OK 2788 2785 2787 2808 C4' DA P 5 OK 2810 2807 2809 2829 C4' DT P 6 OK 2831 2828 2830 2849 C4' DG P 7 OK 2851 2848 2850 2871 C4' DC P 8 OK 2873 2870 2872 2890 C4' DG P 9 OK 2892 2889 2891 2918 C4' DOC P 10 OK 2917 2920 2919 2928 C4' DC T 1 OK 2930 2927 2929 2947 C4' DC T 2 OK 2949 2946 2948 2966 C4' DG T 3 OK 2968 2965 2967 2988 C4' DA T 4 OK 2990 2987 2989 3009 C4' DC T 5 OK 3011 3008 3010 3028 C4' DC T 6 OK 3030 3027 3029 3047 C4' DG T 7 OK 3049 3046 3048 3069 C4' DC T 8 OK 3071 3068 3070 3088 C4' DG T 9 OK 3090 3087 3089 3110 C4' DC T 10 OK 3112 3109 3111 3129 C4' DA T 11 OK 3131 3128 3130 3150 C4' DT T 12 OK 3152 3149 3151 3170 C4' DC T 13 OK 3172 3169 3171 3189 C4' DA T 14 OK 3191 3188 3190 3210 C4' DG T 15 OK 3212 3209 3211 3232 C4' DC T 16 OK 3234 3231 3233 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2621 C5' DG D 1 2620 2622 2643 C5' DT D 2 2642 2644 2663 C5' DC D 3 2662 2664 2682 C5' DG D 4 2681 2683 2704 C5' DG D 5 2703 2705 2724 C5' DG P 1 2723 2725 2746 C5' DC P 2 2745 2747 2765 C5' DT P 3 2764 2766 2785 C5' DG P 4 2784 2786 2807 C5' DA P 5 2806 2808 2828 C5' DT P 6 2827 2829 2848 C5' DG P 7 2847 2849 2870 C5' DC P 8 2869 2871 2889 C5' DG P 9 2888 2890 2920 C5' DOC P 10 2921 2918 2927 C5' DC T 1 2926 2928 2946 C5' DC T 2 2945 2947 2965 C5' DG T 3 2964 2966 2987 C5' DA T 4 2986 2988 3008 C5' DC T 5 3007 3009 3027 C5' DC T 6 3026 3028 3046 C5' DG T 7 3045 3047 3068 C5' DC T 8 3067 3069 3087 C5' DG T 9 3086 3088 3109 C5' DC T 10 3108 3110 3128 C5' DA T 11 3127 3129 3149 C5' DT T 12 3148 3150 3169 C5' DC T 13 3168 3170 3188 C5' DA T 14 3187 3189 3209 C5' DG T 15 3208 3210 3231 C5' DC T 16 3230 3232 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2617 P DG D 1 OK OK 2618 2619 2620 2639 P DT D 2 distorted distorted 2625 2640 2641 2642 2659 P DC D 3 distorted distorted 2647 2660 2661 2662 2678 P DG D 4 distorted distorted 2667 2679 2680 2681 2700 P DG D 5 distorted distorted 2686 2701 2702 2703 2742 P DC P 2 distorted distorted 2728 2743 2744 2745 2761 P DT P 3 distorted distorted 2750 2762 2763 2764 2781 P DG P 4 distorted distorted 2769 2782 2783 2784 2803 P DA P 5 distorted distorted 2789 2804 2805 2806 2824 P DT P 6 distorted distorted 2811 2825 2826 2827 2844 P DG P 7 distorted distorted 2832 2845 2846 2847 2866 P DC P 8 distorted distorted 2852 2867 2868 2869 2885 P DG P 9 distorted distorted 2874 2886 2887 2888 2922 P DOC P 10 distorted distorted 2893 2923 2924 2921 2942 P DC T 2 distorted distorted 2931 2943 2944 2945 2961 P DG T 3 distorted distorted 2950 2962 2963 2964 2983 P DA T 4 distorted distorted 2969 2984 2985 2986 3004 P DC T 5 distorted distorted 2991 3005 3006 3007 3023 P DC T 6 distorted distorted 3012 3024 3025 3026 3042 P DG T 7 distorted distorted 3031 3043 3044 3045 3064 P DC T 8 distorted distorted 3050 3065 3066 3067 3083 P DG T 9 distorted distorted 3072 3084 3085 3086 3105 P DC T 10 distorted distorted 3091 3106 3107 3108 3124 P DA T 11 distorted distorted 3113 3125 3126 3127 3145 P DT T 12 distorted distorted 3132 3146 3147 3148 3165 P DC T 13 distorted distorted 3153 3166 3167 3168 3184 P DA T 14 distorted distorted 3173 3185 3186 3187 3205 P DG T 15 distorted distorted 3192 3206 3207 3208 3227 P DC T 16 distorted distorted 3213 3228 3229 3230 ---------------------------------------------------------------------------------