ID code: '4J7M' 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' --------------------------------------------------------------------------------- 2984 C1' U B 1 beta 2979 2985 2982 3004 C1' U37 B 2 beta 2999 3005 3002 3024 C1' U37 B 3 beta 3019 3025 3022 3044 C1' U B 4 beta 3039 3045 3042 3076 C1' UBD A 401 beta 3071 3062 3074 3101 C1' UBD A 402 beta 3096 3087 3099 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2982 C2' U B 1 OK 2984 2980 2983 3002 C2' U37 B 2 OK 3004 3000 3003 3022 C2' U37 B 3 OK 3024 3020 3023 3042 C2' U B 4 OK 3044 3040 3043 3074 C2' UBD A 401 OK 3076 3072 3075 3099 C2' UBD A 402 OK 3101 3097 3100 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2980 C3' U B 1 OK 2978 2981 2982 3000 C3' U37 B 2 OK 2998 3001 3002 3020 C3' U37 B 3 OK 3018 3021 3022 3040 C3' U B 4 OK 3038 3041 3042 3072 C3' UBD A 401 OK 3070 3073 3074 3097 C3' UBD A 402 OK 3095 3098 3099 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2978 C4' U B 1 OK 2980 2977 2979 2998 C4' U37 B 2 OK 3000 2997 2999 3018 C4' U37 B 3 OK 3020 3017 3019 3038 C4' U B 4 OK 3040 3037 3039 3070 C4' UBD A 401 OK 3072 3069 3071 3095 C4' UBD A 402 OK 3097 3094 3096 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2977 C5' U B 1 2976 2978 2997 C5' U37 B 2 2996 2998 3017 C5' U37 B 3 3016 3018 3037 C5' U B 4 3036 3038 3069 C5' UBD A 401 3068 3070 3094 C5' UBD A 402 3093 3095 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2973 P U B 1 distorted distorted 2974 2975 2976 2993 P U37 B 2 2981 2995 2996 3013 P U37 B 3 3001 3015 3016 3033 P U B 4 distorted distorted 3021 3034 3035 3036 3053 P U B 5 distorted distorted 3041 3054 3055 3056 ---------------------------------------------------------------------------------