ID code: '3EPI' 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' --------------------------------------------------------------------------------- 2917 C1' DA B 7 beta 2913 2918 2916 2938 C1' DG B 8 beta 2934 2939 2937 2960 C1' DG B 9 beta 2956 2961 2959 2982 C1' DA B 10 beta 2978 2983 2981 3003 C1' DC B 11 beta 2999 3004 3002 3022 C1' DC B 12 beta 3018 3023 3021 3039 C1' DOC B 13 beta 3043 3031 3040 3060 C1' 2EG C 840 beta 3056 3061 3059 3084 C1' DG C 841 beta 3080 3085 3083 3106 C1' DG C 842 beta 3102 3107 3105 3128 C1' DG C 843 beta 3124 3129 3127 3150 C1' DT C 844 beta 3146 3151 3149 3170 C1' DC C 845 beta 3166 3171 3169 3189 C1' DC C 846 beta 3185 3190 3188 3208 C1' DT C 847 beta 3204 3209 3207 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2916 C2' DA B 7 2917 2914 2937 C2' DG B 8 2938 2935 2959 C2' DG B 9 2960 2957 2981 C2' DA B 10 2982 2979 3002 C2' DC B 11 3003 3000 3021 C2' DC B 12 3022 3019 3040 C2' DOC B 13 3039 3041 3059 C2' 2EG C 840 3060 3057 3083 C2' DG C 841 3084 3081 3105 C2' DG C 842 3106 3103 3127 C2' DG C 843 3128 3125 3149 C2' DT C 844 3150 3147 3169 C2' DC C 845 3170 3167 3188 C2' DC C 846 3189 3186 3207 C2' DT C 847 3208 3205 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2914 C3' DA B 7 OK 2912 2915 2916 2935 C3' DG B 8 OK 2933 2936 2937 2957 C3' DG B 9 OK 2955 2958 2959 2979 C3' DA B 10 OK 2977 2980 2981 3000 C3' DC B 11 OK 2998 3001 3002 3019 C3' DC B 12 OK 3017 3020 3021 3041 C3' DOC B 13 3042 3040 3057 C3' 2EG C 840 OK 3055 3058 3059 3081 C3' DG C 841 OK 3079 3082 3083 3103 C3' DG C 842 OK 3101 3104 3105 3125 C3' DG C 843 OK 3123 3126 3127 3147 C3' DT C 844 OK 3145 3148 3149 3167 C3' DC C 845 OK 3165 3168 3169 3186 C3' DC C 846 OK 3184 3187 3188 3205 C3' DT C 847 OK 3203 3206 3207 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2912 C4' DA B 7 OK 2914 2911 2913 2933 C4' DG B 8 OK 2935 2932 2934 2955 C4' DG B 9 OK 2957 2954 2956 2977 C4' DA B 10 OK 2979 2976 2978 2998 C4' DC B 11 OK 3000 2997 2999 3017 C4' DC B 12 OK 3019 3016 3018 3042 C4' DOC B 13 OK 3041 3044 3043 3055 C4' 2EG C 840 OK 3057 3054 3056 3079 C4' DG C 841 OK 3081 3078 3080 3101 C4' DG C 842 OK 3103 3100 3102 3123 C4' DG C 843 OK 3125 3122 3124 3145 C4' DT C 844 OK 3147 3144 3146 3165 C4' DC C 845 OK 3167 3164 3166 3184 C4' DC C 846 OK 3186 3183 3185 3203 C4' DT C 847 OK 3205 3202 3204 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2911 C5' DA B 7 2910 2912 2932 C5' DG B 8 2931 2933 2954 C5' DG B 9 2953 2955 2976 C5' DA B 10 2975 2977 2997 C5' DC B 11 2996 2998 3016 C5' DC B 12 3015 3017 3044 C5' DOC B 13 3045 3042 3054 C5' 2EG C 840 3053 3055 3078 C5' DG C 841 3077 3079 3100 C5' DG C 842 3099 3101 3122 C5' DG C 843 3121 3123 3144 C5' DT C 844 3143 3145 3164 C5' DC C 845 3163 3165 3183 C5' DC C 846 3182 3184 3202 C5' DT C 847 3201 3203 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2907 P DA B 7 OK OK 2908 2909 2910 2928 P DG B 8 distorted distorted 2915 2929 2930 2931 2950 P DG B 9 distorted distorted 2936 2951 2952 2953 2972 P DA B 10 distorted distorted 2958 2973 2974 2975 2993 P DC B 11 distorted distorted 2980 2994 2995 2996 3012 P DC B 12 distorted distorted 3001 3013 3014 3015 3046 P DOC B 13 distorted distorted 3020 3047 3048 3045 3051 P 2EG C 840 OK OK 3050 3052 3053 3074 P DG C 841 distorted distorted 3058 3075 3076 3077 3096 P DG C 842 distorted distorted 3082 3097 3098 3099 3118 P DG C 843 distorted distorted 3104 3119 3120 3121 3140 P DT C 844 distorted distorted 3126 3141 3142 3143 3160 P DC C 845 distorted distorted 3148 3161 3162 3163 3179 P DC C 846 distorted distorted 3168 3180 3181 3182 3198 P DT C 847 distorted distorted 3187 3199 3200 3201 3220 P PO4 A 422 ---------------------------------------------------------------------------------