ID code: '2JEF' 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' --------------------------------------------------------------------------------- 2794 C1' DG P 1 beta 2790 2795 2793 2816 C1' DG P 2 beta 2812 2817 2815 2838 C1' DG P 3 beta 2834 2839 2837 2860 C1' DG P 4 beta 2856 2861 2859 2882 C1' DG P 5 beta 2878 2883 2881 2904 C1' DA P 6 beta 2900 2905 2903 2925 C1' DA P 7 beta 2921 2926 2924 2946 C1' DG P 8 beta 2942 2947 2945 2968 C1' DG P 9 beta 2964 2969 2967 2990 C1' DA P 10 beta 2986 2991 2989 3011 C1' DT P 11 beta 3007 3012 3010 3031 C1' DT P 12 beta 3027 3032 3030 3051 C1' DC P 13 beta 3047 3052 3050 3068 C1' DOC P 14 beta 3072 3060 3069 3086 C1' DA T 3 beta 3082 3087 3085 3107 C1' DC T 4 beta 3103 3108 3106 3155 C1' DG T 6 beta 3151 3156 3154 3177 C1' DA T 7 beta 3173 3178 3176 3198 C1' DA T 8 beta 3194 3199 3197 3219 C1' DT T 9 beta 3215 3220 3218 3239 C1' DC T 10 beta 3235 3240 3238 3258 C1' DC T 11 beta 3254 3259 3257 3277 C1' DT T 12 beta 3273 3278 3276 3297 C1' DT T 13 beta 3293 3298 3296 3317 C1' DC T 14 beta 3313 3318 3316 3336 C1' DC T 15 beta 3332 3337 3335 3355 C1' DC T 16 beta 3351 3356 3354 3374 C1' DC T 17 beta 3370 3375 3373 3393 C1' DC T 18 beta 3389 3394 3392 3422 C1' DGT A1343 beta 3418 3423 3421 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2793 C2' DG P 1 2794 2791 2815 C2' DG P 2 2816 2813 2837 C2' DG P 3 2838 2835 2859 C2' DG P 4 2860 2857 2881 C2' DG P 5 2882 2879 2903 C2' DA P 6 2904 2901 2924 C2' DA P 7 2925 2922 2945 C2' DG P 8 2946 2943 2967 C2' DG P 9 2968 2965 2989 C2' DA P 10 2990 2987 3010 C2' DT P 11 3011 3008 3030 C2' DT P 12 3031 3028 3050 C2' DC P 13 3051 3048 3069 C2' DOC P 14 3068 3070 3085 C2' DA T 3 3086 3083 3106 C2' DC T 4 3107 3104 3154 C2' DG T 6 3155 3152 3176 C2' DA T 7 3177 3174 3197 C2' DA T 8 3198 3195 3218 C2' DT T 9 3219 3216 3238 C2' DC T 10 3239 3236 3257 C2' DC T 11 3258 3255 3276 C2' DT T 12 3277 3274 3296 C2' DT T 13 3297 3294 3316 C2' DC T 14 3317 3314 3335 C2' DC T 15 3336 3333 3354 C2' DC T 16 3355 3352 3373 C2' DC T 17 3374 3371 3392 C2' DC T 18 3393 3390 3421 C2' DGT A1343 3422 3419 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2791 C3' DG P 1 OK 2789 2792 2793 2813 C3' DG P 2 OK 2811 2814 2815 2835 C3' DG P 3 OK 2833 2836 2837 2857 C3' DG P 4 OK 2855 2858 2859 2879 C3' DG P 5 OK 2877 2880 2881 2901 C3' DA P 6 OK 2899 2902 2903 2922 C3' DA P 7 OK 2920 2923 2924 2943 C3' DG P 8 OK 2941 2944 2945 2965 C3' DG P 9 OK 2963 2966 2967 2987 C3' DA P 10 OK 2985 2988 2989 3008 C3' DT P 11 OK 3006 3009 3010 3028 C3' DT P 12 OK 3026 3029 3030 3048 C3' DC P 13 OK 3046 3049 3050 3070 C3' DOC P 14 3071 3069 3083 C3' DA T 3 OK 3081 3084 3085 3104 C3' DC T 4 OK 3102 3105 3106 3143 C3' BZG T 5 3142 3144 3152 C3' DG T 6 OK 3150 3153 3154 3174 C3' DA T 7 OK 3172 3175 3176 3195 C3' DA T 8 OK 3193 3196 3197 3216 C3' DT T 9 OK 3214 3217 3218 3236 C3' DC T 10 OK 3234 3237 3238 3255 C3' DC T 11 OK 3253 3256 3257 3274 C3' DT T 12 OK 3272 3275 3276 3294 C3' DT T 13 OK 3292 3295 3296 3314 C3' DC T 14 OK 3312 3315 3316 3333 C3' DC T 15 OK 3331 3334 3335 3352 C3' DC T 16 OK 3350 3353 3354 3371 C3' DC T 17 OK 3369 3372 3373 3390 C3' DC T 18 OK 3388 3391 3392 3419 C3' DGT A1343 OK 3417 3420 3421 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2789 C4' DG P 1 OK 2791 2788 2790 2811 C4' DG P 2 OK 2813 2810 2812 2833 C4' DG P 3 OK 2835 2832 2834 2855 C4' DG P 4 OK 2857 2854 2856 2877 C4' DG P 5 OK 2879 2876 2878 2899 C4' DA P 6 OK 2901 2898 2900 2920 C4' DA P 7 OK 2922 2919 2921 2941 C4' DG P 8 OK 2943 2940 2942 2963 C4' DG P 9 OK 2965 2962 2964 2985 C4' DA P 10 OK 2987 2984 2986 3006 C4' DT P 11 OK 3008 3005 3007 3026 C4' DT P 12 OK 3028 3025 3027 3046 C4' DC P 13 OK 3048 3045 3047 3071 C4' DOC P 14 OK 3070 3073 3072 3081 C4' DA T 3 OK 3083 3080 3082 3102 C4' DC T 4 OK 3104 3101 3103 3142 C4' BZG T 5 3143 3141 3150 C4' DG T 6 OK 3152 3149 3151 3172 C4' DA T 7 OK 3174 3171 3173 3193 C4' DA T 8 OK 3195 3192 3194 3214 C4' DT T 9 OK 3216 3213 3215 3234 C4' DC T 10 OK 3236 3233 3235 3253 C4' DC T 11 OK 3255 3252 3254 3272 C4' DT T 12 OK 3274 3271 3273 3292 C4' DT T 13 OK 3294 3291 3293 3312 C4' DC T 14 OK 3314 3311 3313 3331 C4' DC T 15 OK 3333 3330 3332 3350 C4' DC T 16 OK 3352 3349 3351 3369 C4' DC T 17 OK 3371 3368 3370 3388 C4' DC T 18 OK 3390 3387 3389 3417 C4' DGT A1343 OK 3419 3416 3418 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2788 C5' DG P 1 2787 2789 2810 C5' DG P 2 2809 2811 2832 C5' DG P 3 2831 2833 2854 C5' DG P 4 2853 2855 2876 C5' DG P 5 2875 2877 2898 C5' DA P 6 2897 2899 2919 C5' DA P 7 2918 2920 2940 C5' DG P 8 2939 2941 2962 C5' DG P 9 2961 2963 2984 C5' DA P 10 2983 2985 3005 C5' DT P 11 3004 3006 3025 C5' DT P 12 3024 3026 3045 C5' DC P 13 3044 3046 3073 C5' DOC P 14 3074 3071 3080 C5' DA T 3 3079 3081 3101 C5' DC T 4 3100 3102 3141 C5' BZG T 5 3119 3142 3149 C5' DG T 6 3148 3150 3171 C5' DA T 7 3170 3172 3192 C5' DA T 8 3191 3193 3213 C5' DT T 9 3212 3214 3233 C5' DC T 10 3232 3234 3252 C5' DC T 11 3251 3253 3271 C5' DT T 12 3270 3272 3291 C5' DT T 13 3290 3292 3311 C5' DC T 14 3310 3312 3330 C5' DC T 15 3329 3331 3349 C5' DC T 16 3348 3350 3368 C5' DC T 17 3367 3369 3387 C5' DC T 18 3386 3388 3416 C5' DGT A1343 3415 3417 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2806 P DG P 2 distorted distorted 2792 2807 2808 2809 2828 P DG P 3 distorted distorted 2814 2829 2830 2831 2850 P DG P 4 distorted distorted 2836 2851 2852 2853 2872 P DG P 5 distorted distorted 2858 2873 2874 2875 2894 P DA P 6 distorted distorted 2880 2895 2896 2897 2915 P DA P 7 distorted distorted 2902 2916 2917 2918 2936 P DG P 8 distorted distorted 2923 2937 2938 2939 2958 P DG P 9 distorted distorted 2944 2959 2960 2961 2980 P DA P 10 distorted distorted 2966 2981 2982 2983 3001 P DT P 11 distorted distorted 2988 3002 3003 3004 3021 P DT P 12 distorted distorted 3009 3022 3023 3024 3041 P DC P 13 distorted distorted 3029 3042 3043 3044 3075 P DOC P 14 distorted distorted 3049 3076 3077 3074 3097 P DC T 4 distorted distorted 3084 3098 3099 3100 3116 P BZG T 5 OK OK 3105 3117 3118 3119 3145 P DG T 6 distorted distorted 3144 3146 3147 3148 3167 P DA T 7 distorted distorted 3153 3168 3169 3170 3188 P DA T 8 distorted distorted 3175 3189 3190 3191 3209 P DT T 9 distorted distorted 3196 3210 3211 3212 3229 P DC T 10 distorted distorted 3217 3230 3231 3232 3248 P DC T 11 distorted distorted 3237 3249 3250 3251 3267 P DT T 12 distorted distorted 3256 3268 3269 3270 3287 P DT T 13 distorted distorted 3275 3288 3289 3290 3307 P DC T 14 distorted distorted 3295 3308 3309 3310 3326 P DC T 15 distorted distorted 3315 3327 3328 3329 3345 P DC T 16 distorted distorted 3334 3346 3347 3348 3364 P DC T 17 distorted distorted 3353 3365 3366 3367 3383 P DC T 18 distorted distorted 3372 3384 3385 3386 ---------------------------------------------------------------------------------