ID code: '5BZV' 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' --------------------------------------------------------------------------------- 2946 C1' U B 1 beta 2941 2947 2944 2966 C1' G B 2 beta 2961 2967 2964 2989 C1' U B 3 beta 2984 2990 2987 3009 C1' A B 4 beta 3004 3010 3007 3031 C1' C B 5 beta 3026 3032 3029 3051 C1' U B 6 beta 3046 3052 3049 3071 C1' A B 7 beta 3066 3072 3069 3093 C1' U B 8 beta 3088 3094 3091 3113 C1' A B 9 beta 3108 3114 3111 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2944 C2' U B 1 OK 2946 2942 2945 2964 C2' G B 2 OK 2966 2962 2965 2987 C2' U B 3 OK 2989 2985 2988 3007 C2' A B 4 OK 3009 3005 3008 3029 C2' C B 5 OK 3031 3027 3030 3049 C2' U B 6 OK 3051 3047 3050 3069 C2' A B 7 OK 3071 3067 3070 3091 C2' U B 8 OK 3093 3089 3092 3111 C2' A B 9 OK 3113 3109 3112 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2942 C3' U B 1 OK 2940 2943 2944 2962 C3' G B 2 OK 2960 2963 2964 2985 C3' U B 3 OK 2983 2986 2987 3005 C3' A B 4 OK 3003 3006 3007 3027 C3' C B 5 OK 3025 3028 3029 3047 C3' U B 6 OK 3045 3048 3049 3067 C3' A B 7 OK 3065 3068 3069 3089 C3' U B 8 OK 3087 3090 3091 3109 C3' A B 9 OK 3107 3110 3111 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2940 C4' U B 1 OK 2942 2939 2941 2960 C4' G B 2 OK 2962 2959 2961 2983 C4' U B 3 OK 2985 2982 2984 3003 C4' A B 4 OK 3005 3002 3004 3025 C4' C B 5 OK 3027 3024 3026 3045 C4' U B 6 OK 3047 3044 3046 3065 C4' A B 7 OK 3067 3064 3066 3087 C4' U B 8 OK 3089 3086 3088 3107 C4' A B 9 OK 3109 3106 3108 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2939 C5' U B 1 2938 2940 2959 C5' G B 2 2958 2960 2982 C5' U B 3 2981 2983 3002 C5' A B 4 3001 3003 3024 C5' C B 5 3023 3025 3044 C5' U B 6 3043 3045 3064 C5' A B 7 3063 3065 3086 C5' U B 8 3085 3087 3106 C5' A B 9 3105 3107 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2955 P G B 2 distorted distorted 2943 2956 2957 2958 2978 P U B 3 distorted distorted 2963 2979 2980 2981 2998 P A B 4 distorted distorted 2986 2999 3000 3001 3020 P C B 5 distorted distorted 3006 3021 3022 3023 3040 P U B 6 distorted distorted 3028 3041 3042 3043 3060 P A B 7 distorted distorted 3048 3061 3062 3063 3082 P U B 8 distorted distorted 3068 3083 3084 3085 3102 P A B 9 distorted distorted 3090 3103 3104 3105 ---------------------------------------------------------------------------------