ID code: '5BZ1' 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' --------------------------------------------------------------------------------- 3000 C1' U B 1 beta 2995 3001 2998 3020 C1' G B 2 beta 3015 3021 3018 3043 C1' U B 3 beta 3038 3044 3041 3063 C1' A B 4 beta 3058 3064 3061 3085 C1' U B 5 beta 3080 3086 3083 3105 C1' U B 6 beta 3100 3106 3103 3125 C1' U B 7 beta 3120 3126 3123 3191 C1' U B 9 beta 3186 3192 3189 3211 C1' A B 10 beta 3206 3212 3209 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2998 C2' U B 1 OK 3000 2996 2999 3018 C2' G B 2 OK 3020 3016 3019 3041 C2' U B 3 OK 3043 3039 3042 3061 C2' A B 4 OK 3063 3059 3062 3083 C2' U B 5 OK 3085 3081 3084 3103 C2' U B 6 OK 3105 3101 3104 3123 C2' U B 7 OK 3125 3121 3124 3189 C2' U B 9 OK 3191 3187 3190 3209 C2' A B 10 OK 3211 3207 3210 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2996 C3' U B 1 OK 2994 2997 2998 3016 C3' G B 2 OK 3014 3017 3018 3039 C3' U B 3 OK 3037 3040 3041 3059 C3' A B 4 OK 3057 3060 3061 3081 C3' U B 5 OK 3079 3082 3083 3101 C3' U B 6 OK 3099 3102 3103 3121 C3' U B 7 OK 3119 3122 3123 3187 C3' U B 9 OK 3185 3188 3189 3207 C3' A B 10 OK 3205 3208 3209 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2994 C4' U B 1 OK 2996 2993 2995 3014 C4' G B 2 OK 3016 3013 3015 3037 C4' U B 3 OK 3039 3036 3038 3057 C4' A B 4 OK 3059 3056 3058 3079 C4' U B 5 OK 3081 3078 3080 3099 C4' U B 6 OK 3101 3098 3100 3119 C4' U B 7 OK 3121 3118 3120 3185 C4' U B 9 OK 3187 3184 3186 3205 C4' A B 10 OK 3207 3204 3206 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2993 C5' U B 1 2992 2994 3013 C5' G B 2 3012 3014 3036 C5' U B 3 3035 3037 3056 C5' A B 4 3055 3057 3078 C5' U B 5 3077 3079 3098 C5' U B 6 3097 3099 3118 C5' U B 7 3117 3119 3184 C5' U B 9 3183 3185 3204 C5' A B 10 3203 3205 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 3009 P G B 2 distorted distorted 2997 3010 3011 3012 3032 P U B 3 distorted distorted 3017 3033 3034 3035 3052 P A B 4 distorted distorted 3040 3053 3054 3055 3074 P U B 5 distorted distorted 3060 3075 3076 3077 3094 P U B 6 distorted distorted 3082 3095 3096 3097 3114 P U B 7 distorted distorted 3102 3115 3116 3117 3134 P G B 8 3122 3135 P G B 8 3122 3180 P U B 9 distorted distorted 3181 3182 3183 3200 P A B 10 distorted distorted 3188 3201 3202 3203 ---------------------------------------------------------------------------------