ID code: '4QM6' 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' --------------------------------------------------------------------------------- 2814 C1' C C 1 beta 2809 2815 2812 2834 C1' C C 2 beta 2829 2835 2832 2854 C1' U C 3 beta 2849 2855 2852 2874 C1' G C 4 beta 2869 2875 2872 2900 C1' C D 1 beta 2895 2901 2898 2920 C1' C D 2 beta 2915 2921 2918 2940 C1' U D 3 beta 2935 2941 2938 2960 C1' G D 4 beta 2955 2961 2958 2997 C1' GTP A1001 beta 2992 2998 2995 3036 C1' GTP B1001 beta 3031 3037 3034 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2812 C2' C C 1 OK 2814 2810 2813 2832 C2' C C 2 OK 2834 2830 2833 2852 C2' U C 3 OK 2854 2850 2853 2872 C2' G C 4 OK 2874 2870 2873 2898 C2' C D 1 OK 2900 2896 2899 2918 C2' C D 2 OK 2920 2916 2919 2938 C2' U D 3 OK 2940 2936 2939 2958 C2' G D 4 OK 2960 2956 2959 2995 C2' GTP A1001 OK 2997 2993 2996 3034 C2' GTP B1001 OK 3036 3032 3035 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2810 C3' C C 1 OK 2808 2811 2812 2830 C3' C C 2 OK 2828 2831 2832 2850 C3' U C 3 OK 2848 2851 2852 2870 C3' G C 4 OK 2868 2871 2872 2896 C3' C D 1 OK 2894 2897 2898 2916 C3' C D 2 OK 2914 2917 2918 2936 C3' U D 3 OK 2934 2937 2938 2956 C3' G D 4 OK 2954 2957 2958 2993 C3' GTP A1001 OK 2991 2994 2995 3032 C3' GTP B1001 OK 3030 3033 3034 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2808 C4' C C 1 OK 2810 2807 2809 2828 C4' C C 2 OK 2830 2827 2829 2848 C4' U C 3 OK 2850 2847 2849 2868 C4' G C 4 OK 2870 2867 2869 2894 C4' C D 1 OK 2896 2893 2895 2914 C4' C D 2 OK 2916 2913 2915 2934 C4' U D 3 OK 2936 2933 2935 2954 C4' G D 4 OK 2956 2953 2955 2991 C4' GTP A1001 OK 2993 2990 2992 3030 C4' GTP B1001 OK 3032 3029 3031 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2807 C5' C C 1 2808 2827 C5' C C 2 2826 2828 2847 C5' U C 3 2846 2848 2867 C5' G C 4 2866 2868 2893 C5' C D 1 2894 2913 C5' C D 2 2912 2914 2933 C5' U D 3 2932 2934 2953 C5' G D 4 2952 2954 2990 C5' GTP A1001 2989 2991 3029 C5' GTP B1001 3028 3030 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2823 P C C 2 distorted distorted 2811 2824 2825 2826 2843 P U C 3 distorted distorted 2831 2844 2845 2846 2863 P G C 4 distorted distorted 2851 2864 2865 2866 2886 P U C 5 distorted distorted 2871 2887 2888 2889 2909 P C D 2 distorted distorted 2897 2910 2911 2912 2929 P U D 3 distorted distorted 2917 2930 2931 2932 2949 P G D 4 distorted distorted 2937 2950 2951 2952 2972 P U D 5 distorted distorted 2957 2973 2974 2975 3010 P PO4 A1003 ---------------------------------------------------------------------------------