ID code: '2N8M' 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' --------------------------------------------------------------------------------- 2939 C1' U B 1 alpha beta 2934 2954 2940 2937 2969 C1' C B 2 alpha beta 2964 2984 2970 2967 3000 C1' G B 3 alpha beta 2995 3018 3001 2998 3034 C1' G B 4 alpha beta 3029 3052 3035 3032 3068 C1' A B 5 alpha beta 3063 3085 3069 3066 3101 C1' C B 6 alpha beta 3096 3116 3102 3099 3132 C1' U B 7 alpha beta 3127 3148 3133 3130 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2937 C2' U B 1 OK OK 2939 2935 2952 2938 2967 C2' C B 2 OK OK 2969 2965 2982 2968 2998 C2' G B 3 OK OK 3000 2996 3016 2999 3032 C2' G B 4 OK OK 3034 3030 3050 3033 3066 C2' A B 5 OK OK 3068 3064 3083 3067 3099 C2' C B 6 OK OK 3101 3097 3114 3100 3130 C2' U B 7 OK OK 3132 3128 3146 3131 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2935 C3' U B 1 OK OK 2933 2951 2936 2937 2965 C3' C B 2 OK OK 2963 2981 2966 2967 2996 C3' G B 3 OK OK 2994 3015 2997 2998 3030 C3' G B 4 OK OK 3028 3049 3031 3032 3064 C3' A B 5 OK OK 3062 3082 3065 3066 3097 C3' C B 6 OK OK 3095 3113 3098 3099 3128 C3' U B 7 OK OK 3126 3144 3129 3130 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2933 C4' U B 1 OK OK 2935 2950 2932 2934 2963 C4' C B 2 OK OK 2965 2980 2962 2964 2994 C4' G B 3 OK OK 2996 3014 2993 2995 3028 C4' G B 4 OK OK 3030 3048 3027 3029 3062 C4' A B 5 OK OK 3064 3081 3061 3063 3095 C4' C B 6 OK OK 3097 3112 3094 3096 3126 C4' U B 7 OK OK 3128 3143 3125 3127 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2932 C5' U B 1 OK OK 2931 2948 2949 2933 2962 C5' C B 2 OK OK 2961 2978 2979 2963 2993 C5' G B 3 OK OK 2992 3012 3013 2994 3027 C5' G B 4 OK OK 3026 3046 3047 3028 3061 C5' A B 5 OK OK 3060 3079 3080 3062 3094 C5' C B 6 OK OK 3093 3110 3111 3095 3125 C5' U B 7 OK OK 3124 3141 3142 3126 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2928 P U B 1 OK OK 2929 2930 2931 2958 P C B 2 distorted distorted 2936 2959 2960 2961 2989 P G B 3 distorted distorted 2966 2990 2991 2992 3023 P G B 4 distorted distorted 2997 3024 3025 3026 3057 P A B 5 distorted distorted 3031 3058 3059 3060 3090 P C B 6 distorted distorted 3065 3091 3092 3093 3121 P U B 7 distorted distorted 3098 3122 3123 3124 ---------------------------------------------------------------------------------