ID code: '2N8L' 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' --------------------------------------------------------------------------------- 2954 C1' G B 1 alpha beta 2949 2972 2955 2952 2988 C1' C B 2 alpha beta 2983 3003 2989 2986 3019 C1' A B 3 alpha beta 3014 3036 3020 3017 3052 C1' C B 4 alpha beta 3047 3067 3053 3050 3083 C1' A B 5 alpha beta 3078 3100 3084 3081 3116 C1' C B 6 alpha beta 3111 3131 3117 3114 3147 C1' C B 7 alpha beta 3142 3162 3148 3145 3178 C1' C B 8 alpha beta 3173 3194 3179 3176 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2952 C2' G B 1 OK OK 2954 2950 2970 2953 2986 C2' C B 2 OK OK 2988 2984 3001 2987 3017 C2' A B 3 OK OK 3019 3015 3034 3018 3050 C2' C B 4 OK OK 3052 3048 3065 3051 3081 C2' A B 5 OK OK 3083 3079 3098 3082 3114 C2' C B 6 OK OK 3116 3112 3129 3115 3145 C2' C B 7 OK OK 3147 3143 3160 3146 3176 C2' C B 8 OK OK 3178 3174 3192 3177 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2950 C3' G B 1 OK OK 2948 2969 2951 2952 2984 C3' C B 2 OK OK 2982 3000 2985 2986 3015 C3' A B 3 OK OK 3013 3033 3016 3017 3048 C3' C B 4 OK OK 3046 3064 3049 3050 3079 C3' A B 5 OK OK 3077 3097 3080 3081 3112 C3' C B 6 OK OK 3110 3128 3113 3114 3143 C3' C B 7 OK OK 3141 3159 3144 3145 3174 C3' C B 8 OK OK 3172 3190 3175 3176 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2948 C4' G B 1 OK OK 2950 2968 2947 2949 2982 C4' C B 2 OK OK 2984 2999 2981 2983 3013 C4' A B 3 OK OK 3015 3032 3012 3014 3046 C4' C B 4 OK OK 3048 3063 3045 3047 3077 C4' A B 5 OK OK 3079 3096 3076 3078 3110 C4' C B 6 OK OK 3112 3127 3109 3111 3141 C4' C B 7 OK OK 3143 3158 3140 3142 3172 C4' C B 8 OK OK 3174 3189 3171 3173 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2947 C5' G B 1 OK OK 2946 2966 2967 2948 2981 C5' C B 2 OK OK 2980 2997 2998 2982 3012 C5' A B 3 OK OK 3011 3030 3031 3013 3045 C5' C B 4 OK OK 3044 3061 3062 3046 3076 C5' A B 5 OK OK 3075 3094 3095 3077 3109 C5' C B 6 OK OK 3108 3125 3126 3110 3140 C5' C B 7 OK OK 3139 3156 3157 3141 3171 C5' C B 8 OK OK 3170 3187 3188 3172 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2943 P G B 1 OK OK 2944 2945 2946 2977 P C B 2 distorted distorted 2951 2978 2979 2980 3008 P A B 3 distorted distorted 2985 3009 3010 3011 3041 P C B 4 distorted distorted 3016 3042 3043 3044 3072 P A B 5 distorted distorted 3049 3073 3074 3075 3105 P C B 6 distorted distorted 3080 3106 3107 3108 3136 P C B 7 distorted distorted 3113 3137 3138 3139 3167 P C B 8 distorted distorted 3144 3168 3169 3170 ---------------------------------------------------------------------------------