ID code: '2IZN' 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' --------------------------------------------------------------------------------- 2907 C1' A R 3 beta 2902 2908 2905 2929 C1' U R 4 beta 2924 2930 2927 2949 C1' C R 5 beta 2944 2950 2947 2969 C1' G R 6 beta 2964 2970 2967 2992 C1' C R 7 beta 2987 2993 2990 3012 C1' G R 8 beta 3007 3013 3010 3035 C1' A R 9 beta 3030 3036 3033 3057 C1' U R 10 beta 3052 3058 3055 3077 C1' U R 11 beta 3072 3078 3075 3097 C1' A R 12 beta 3092 3098 3095 3119 C1' C R 13 beta 3114 3120 3117 3139 C1' G R 14 beta 3134 3140 3137 3162 C1' G R 15 beta 3157 3163 3160 3185 C1' A R 16 beta 3180 3186 3183 3207 C1' U R 17 beta 3202 3208 3205 3225 C1' C S 5 beta 3220 3226 3223 3245 C1' G S 6 beta 3240 3246 3243 3268 C1' C S 7 beta 3263 3269 3266 3288 C1' G S 8 beta 3283 3289 3286 3311 C1' A S 9 beta 3306 3312 3309 3333 C1' U S 10 beta 3328 3334 3331 3353 C1' U S 11 beta 3348 3354 3351 3373 C1' A S 12 beta 3368 3374 3371 3395 C1' C S 13 beta 3390 3396 3393 3415 C1' G S 14 beta 3410 3416 3413 3438 C1' G S 15 beta 3433 3439 3436 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2905 C2' A R 3 OK 2907 2903 2906 2927 C2' U R 4 OK 2929 2925 2928 2947 C2' C R 5 OK 2949 2945 2948 2967 C2' G R 6 OK 2969 2965 2968 2990 C2' C R 7 OK 2992 2988 2991 3010 C2' G R 8 OK 3012 3008 3011 3033 C2' A R 9 OK 3035 3031 3034 3055 C2' U R 10 OK 3057 3053 3056 3075 C2' U R 11 OK 3077 3073 3076 3095 C2' A R 12 OK 3097 3093 3096 3117 C2' C R 13 OK 3119 3115 3118 3137 C2' G R 14 OK 3139 3135 3138 3160 C2' G R 15 OK 3162 3158 3161 3183 C2' A R 16 OK 3185 3181 3184 3205 C2' U R 17 OK 3207 3203 3206 3223 C2' C S 5 OK 3225 3221 3224 3243 C2' G S 6 OK 3245 3241 3244 3266 C2' C S 7 OK 3268 3264 3267 3286 C2' G S 8 OK 3288 3284 3287 3309 C2' A S 9 OK 3311 3307 3310 3331 C2' U S 10 OK 3333 3329 3332 3351 C2' U S 11 OK 3353 3349 3352 3371 C2' A S 12 OK 3373 3369 3372 3393 C2' C S 13 OK 3395 3391 3394 3413 C2' G S 14 OK 3415 3411 3414 3436 C2' G S 15 OK 3438 3434 3437 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2903 C3' A R 3 OK 2901 2904 2905 2925 C3' U R 4 OK 2923 2926 2927 2945 C3' C R 5 OK 2943 2946 2947 2965 C3' G R 6 OK 2963 2966 2967 2988 C3' C R 7 OK 2986 2989 2990 3008 C3' G R 8 OK 3006 3009 3010 3031 C3' A R 9 OK 3029 3032 3033 3053 C3' U R 10 OK 3051 3054 3055 3073 C3' U R 11 OK 3071 3074 3075 3093 C3' A R 12 OK 3091 3094 3095 3115 C3' C R 13 OK 3113 3116 3117 3135 C3' G R 14 OK 3133 3136 3137 3158 C3' G R 15 OK 3156 3159 3160 3181 C3' A R 16 OK 3179 3182 3183 3203 C3' U R 17 OK 3201 3204 3205 3221 C3' C S 5 OK 3219 3222 3223 3241 C3' G S 6 OK 3239 3242 3243 3264 C3' C S 7 OK 3262 3265 3266 3284 C3' G S 8 OK 3282 3285 3286 3307 C3' A S 9 OK 3305 3308 3309 3329 C3' U S 10 OK 3327 3330 3331 3349 C3' U S 11 OK 3347 3350 3351 3369 C3' A S 12 OK 3367 3370 3371 3391 C3' C S 13 OK 3389 3392 3393 3411 C3' G S 14 OK 3409 3412 3413 3434 C3' G S 15 OK 3432 3435 3436 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2901 C4' A R 3 OK 2903 2900 2902 2923 C4' U R 4 OK 2925 2922 2924 2943 C4' C R 5 OK 2945 2942 2944 2963 C4' G R 6 OK 2965 2962 2964 2986 C4' C R 7 OK 2988 2985 2987 3006 C4' G R 8 OK 3008 3005 3007 3029 C4' A R 9 OK 3031 3028 3030 3051 C4' U R 10 OK 3053 3050 3052 3071 C4' U R 11 OK 3073 3070 3072 3091 C4' A R 12 OK 3093 3090 3092 3113 C4' C R 13 OK 3115 3112 3114 3133 C4' G R 14 OK 3135 3132 3134 3156 C4' G R 15 OK 3158 3155 3157 3179 C4' A R 16 OK 3181 3178 3180 3201 C4' U R 17 OK 3203 3200 3202 3219 C4' C S 5 OK 3221 3218 3220 3239 C4' G S 6 OK 3241 3238 3240 3262 C4' C S 7 OK 3264 3261 3263 3282 C4' G S 8 OK 3284 3281 3283 3305 C4' A S 9 OK 3307 3304 3306 3327 C4' U S 10 OK 3329 3326 3328 3347 C4' U S 11 OK 3349 3346 3348 3367 C4' A S 12 OK 3369 3366 3368 3389 C4' C S 13 OK 3391 3388 3390 3409 C4' G S 14 OK 3411 3408 3410 3432 C4' G S 15 OK 3434 3431 3433 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2900 C5' A R 3 2899 2901 2922 C5' U R 4 2921 2923 2942 C5' C R 5 2941 2943 2962 C5' G R 6 2961 2963 2985 C5' C R 7 2984 2986 3005 C5' G R 8 3004 3006 3028 C5' A R 9 3027 3029 3050 C5' U R 10 3049 3051 3070 C5' U R 11 3069 3071 3090 C5' A R 12 3089 3091 3112 C5' C R 13 3111 3113 3132 C5' G R 14 3131 3133 3155 C5' G R 15 3154 3156 3178 C5' A R 16 3177 3179 3200 C5' U R 17 3199 3201 3218 C5' C S 5 3217 3219 3238 C5' G S 6 3237 3239 3261 C5' C S 7 3260 3262 3281 C5' G S 8 3280 3282 3304 C5' A S 9 3303 3305 3326 C5' U S 10 3325 3327 3346 C5' U S 11 3345 3347 3366 C5' A S 12 3365 3367 3388 C5' C S 13 3387 3389 3408 C5' G S 14 3407 3409 3431 C5' G S 15 3430 3432 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2918 P U R 4 distorted distorted 2904 2919 2920 2921 2938 P C R 5 distorted distorted 2926 2939 2940 2941 2958 P G R 6 distorted distorted 2946 2959 2960 2961 2981 P C R 7 distorted distorted 2966 2982 2983 2984 3001 P G R 8 distorted distorted 2989 3002 3003 3004 3024 P A R 9 distorted distorted 3009 3025 3026 3027 3046 P U R 10 distorted distorted 3032 3047 3048 3049 3066 P U R 11 distorted distorted 3054 3067 3068 3069 3086 P A R 12 distorted distorted 3074 3087 3088 3089 3108 P C R 13 distorted distorted 3094 3109 3110 3111 3128 P G R 14 distorted distorted 3116 3129 3130 3131 3151 P G R 15 distorted distorted 3136 3152 3153 3154 3174 P A R 16 distorted distorted 3159 3175 3176 3177 3196 P U R 17 distorted distorted 3182 3197 3198 3199 3234 P G S 6 distorted distorted 3222 3235 3236 3237 3257 P C S 7 distorted distorted 3242 3258 3259 3260 3277 P G S 8 distorted distorted 3265 3278 3279 3280 3300 P A S 9 distorted distorted 3285 3301 3302 3303 3322 P U S 10 distorted distorted 3308 3323 3324 3325 3342 P U S 11 distorted distorted 3330 3343 3344 3345 3362 P A S 12 distorted distorted 3350 3363 3364 3365 3384 P C S 13 distorted distorted 3370 3385 3386 3387 3404 P G S 14 distorted distorted 3392 3405 3406 3407 3427 P G S 15 distorted distorted 3412 3428 3429 3430 ---------------------------------------------------------------------------------