ID code: '4J7L' 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' --------------------------------------------------------------------------------- 2955 C1' U B 2 beta 2950 2956 2953 2975 C1' U B 3 beta 2970 2976 2973 2995 C1' U B 4 beta 2990 2996 2993 3015 C1' U B 5 beta 3010 3016 3013 3035 C1' U B 6 beta 3030 3036 3033 3063 C1' UBD A 401 beta 3058 3049 3061 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2953 C2' U B 2 OK 2955 2951 2954 2973 C2' U B 3 OK 2975 2971 2974 2993 C2' U B 4 OK 2995 2991 2994 3013 C2' U B 5 OK 3015 3011 3014 3033 C2' U B 6 OK 3035 3031 3034 3061 C2' UBD A 401 OK 3063 3059 3062 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2951 C3' U B 2 OK 2949 2952 2953 2971 C3' U B 3 OK 2969 2972 2973 2991 C3' U B 4 OK 2989 2992 2993 3011 C3' U B 5 OK 3009 3012 3013 3031 C3' U B 6 OK 3029 3032 3033 3059 C3' UBD A 401 OK 3057 3060 3061 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2949 C4' U B 2 OK 2951 2948 2950 2969 C4' U B 3 OK 2971 2968 2970 2989 C4' U B 4 OK 2991 2988 2990 3009 C4' U B 5 OK 3011 3008 3010 3029 C4' U B 6 OK 3031 3028 3030 3057 C4' UBD A 401 OK 3059 3056 3058 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2948 C5' U B 2 2947 2949 2968 C5' U B 3 2967 2969 2988 C5' U B 4 2987 2989 3008 C5' U B 5 3007 3009 3028 C5' U B 6 3027 3029 3056 C5' UBD A 401 3055 3057 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2944 P U B 2 OK OK 2945 2946 2947 2964 P U B 3 distorted distorted 2952 2965 2966 2967 2984 P U B 4 distorted distorted 2972 2985 2986 2987 3004 P U B 5 distorted distorted 2992 3005 3006 3007 3024 P U B 6 distorted distorted 3012 3025 3026 3027 ---------------------------------------------------------------------------------