ID code: '2BNY' 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' --------------------------------------------------------------------------------- 2898 C1' A R 3 beta 2893 2899 2896 2920 C1' U R 4 beta 2915 2921 2918 2940 C1' G R 5 beta 2935 2941 2938 2963 C1' A R 6 beta 2958 2964 2961 2985 C1' G R 7 beta 2980 2986 2983 3008 C1' G R 8 beta 3003 3009 3006 3031 C1' A R 9 beta 3026 3032 3029 3053 C1' U R 10 beta 3048 3054 3051 3073 C1' U R 11 beta 3068 3074 3071 3093 C1' A R 12 beta 3088 3094 3091 3115 C1' C R 13 beta 3110 3116 3113 3135 C1' C R 14 beta 3130 3136 3133 3155 C1' C R 15 beta 3150 3156 3153 3175 C1' A R 16 beta 3170 3176 3173 3197 C1' U R 17 beta 3192 3198 3195 3215 C1' U S 4 beta 3210 3216 3213 3235 C1' G S 5 beta 3230 3236 3233 3258 C1' A S 6 beta 3253 3259 3256 3280 C1' G S 7 beta 3275 3281 3278 3303 C1' G S 8 beta 3298 3304 3301 3326 C1' A S 9 beta 3321 3327 3324 3348 C1' U S 10 beta 3343 3349 3346 3368 C1' U S 11 beta 3363 3369 3366 3388 C1' A S 12 beta 3383 3389 3386 3410 C1' C S 13 beta 3405 3411 3408 3430 C1' C S 14 beta 3425 3431 3428 3450 C1' C S 15 beta 3445 3451 3448 3470 C1' A S 16 beta 3465 3471 3468 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2896 C2' A R 3 OK 2898 2894 2897 2918 C2' U R 4 OK 2920 2916 2919 2938 C2' G R 5 OK 2940 2936 2939 2961 C2' A R 6 OK 2963 2959 2962 2983 C2' G R 7 OK 2985 2981 2984 3006 C2' G R 8 OK 3008 3004 3007 3029 C2' A R 9 OK 3031 3027 3030 3051 C2' U R 10 OK 3053 3049 3052 3071 C2' U R 11 OK 3073 3069 3072 3091 C2' A R 12 OK 3093 3089 3092 3113 C2' C R 13 OK 3115 3111 3114 3133 C2' C R 14 OK 3135 3131 3134 3153 C2' C R 15 OK 3155 3151 3154 3173 C2' A R 16 OK 3175 3171 3174 3195 C2' U R 17 OK 3197 3193 3196 3213 C2' U S 4 OK 3215 3211 3214 3233 C2' G S 5 OK 3235 3231 3234 3256 C2' A S 6 OK 3258 3254 3257 3278 C2' G S 7 OK 3280 3276 3279 3301 C2' G S 8 OK 3303 3299 3302 3324 C2' A S 9 OK 3326 3322 3325 3346 C2' U S 10 OK 3348 3344 3347 3366 C2' U S 11 OK 3368 3364 3367 3386 C2' A S 12 OK 3388 3384 3387 3408 C2' C S 13 OK 3410 3406 3409 3428 C2' C S 14 OK 3430 3426 3429 3448 C2' C S 15 OK 3450 3446 3449 3468 C2' A S 16 OK 3470 3466 3469 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2894 C3' A R 3 OK 2892 2895 2896 2916 C3' U R 4 OK 2914 2917 2918 2936 C3' G R 5 OK 2934 2937 2938 2959 C3' A R 6 OK 2957 2960 2961 2981 C3' G R 7 OK 2979 2982 2983 3004 C3' G R 8 OK 3002 3005 3006 3027 C3' A R 9 OK 3025 3028 3029 3049 C3' U R 10 OK 3047 3050 3051 3069 C3' U R 11 OK 3067 3070 3071 3089 C3' A R 12 OK 3087 3090 3091 3111 C3' C R 13 OK 3109 3112 3113 3131 C3' C R 14 OK 3129 3132 3133 3151 C3' C R 15 OK 3149 3152 3153 3171 C3' A R 16 OK 3169 3172 3173 3193 C3' U R 17 OK 3191 3194 3195 3211 C3' U S 4 OK 3209 3212 3213 3231 C3' G S 5 OK 3229 3232 3233 3254 C3' A S 6 OK 3252 3255 3256 3276 C3' G S 7 OK 3274 3277 3278 3299 C3' G S 8 OK 3297 3300 3301 3322 C3' A S 9 OK 3320 3323 3324 3344 C3' U S 10 OK 3342 3345 3346 3364 C3' U S 11 OK 3362 3365 3366 3384 C3' A S 12 OK 3382 3385 3386 3406 C3' C S 13 OK 3404 3407 3408 3426 C3' C S 14 OK 3424 3427 3428 3446 C3' C S 15 OK 3444 3447 3448 3466 C3' A S 16 OK 3464 3467 3468 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2892 C4' A R 3 OK 2894 2891 2893 2914 C4' U R 4 OK 2916 2913 2915 2934 C4' G R 5 OK 2936 2933 2935 2957 C4' A R 6 OK 2959 2956 2958 2979 C4' G R 7 OK 2981 2978 2980 3002 C4' G R 8 OK 3004 3001 3003 3025 C4' A R 9 OK 3027 3024 3026 3047 C4' U R 10 OK 3049 3046 3048 3067 C4' U R 11 OK 3069 3066 3068 3087 C4' A R 12 OK 3089 3086 3088 3109 C4' C R 13 OK 3111 3108 3110 3129 C4' C R 14 OK 3131 3128 3130 3149 C4' C R 15 OK 3151 3148 3150 3169 C4' A R 16 OK 3171 3168 3170 3191 C4' U R 17 OK 3193 3190 3192 3209 C4' U S 4 OK 3211 3208 3210 3229 C4' G S 5 OK 3231 3228 3230 3252 C4' A S 6 OK 3254 3251 3253 3274 C4' G S 7 OK 3276 3273 3275 3297 C4' G S 8 OK 3299 3296 3298 3320 C4' A S 9 OK 3322 3319 3321 3342 C4' U S 10 OK 3344 3341 3343 3362 C4' U S 11 OK 3364 3361 3363 3382 C4' A S 12 OK 3384 3381 3383 3404 C4' C S 13 OK 3406 3403 3405 3424 C4' C S 14 OK 3426 3423 3425 3444 C4' C S 15 OK 3446 3443 3445 3464 C4' A S 16 OK 3466 3463 3465 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2891 C5' A R 3 2890 2892 2913 C5' U R 4 2912 2914 2933 C5' G R 5 2932 2934 2956 C5' A R 6 2955 2957 2978 C5' G R 7 2977 2979 3001 C5' G R 8 3000 3002 3024 C5' A R 9 3023 3025 3046 C5' U R 10 3045 3047 3066 C5' U R 11 3065 3067 3086 C5' A R 12 3085 3087 3108 C5' C R 13 3107 3109 3128 C5' C R 14 3127 3129 3148 C5' C R 15 3147 3149 3168 C5' A R 16 3167 3169 3190 C5' U R 17 3189 3191 3208 C5' U S 4 3207 3209 3228 C5' G S 5 3227 3229 3251 C5' A S 6 3250 3252 3273 C5' G S 7 3272 3274 3296 C5' G S 8 3295 3297 3319 C5' A S 9 3318 3320 3341 C5' U S 10 3340 3342 3361 C5' U S 11 3360 3362 3381 C5' A S 12 3380 3382 3403 C5' C S 13 3402 3404 3423 C5' C S 14 3422 3424 3443 C5' C S 15 3442 3444 3463 C5' A S 16 3462 3464 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2909 P U R 4 distorted distorted 2895 2910 2911 2912 2929 P G R 5 distorted distorted 2917 2930 2931 2932 2952 P A R 6 distorted distorted 2937 2953 2954 2955 2974 P G R 7 distorted distorted 2960 2975 2976 2977 2997 P G R 8 distorted distorted 2982 2998 2999 3000 3020 P A R 9 distorted distorted 3005 3021 3022 3023 3042 P U R 10 distorted distorted 3028 3043 3044 3045 3062 P U R 11 distorted distorted 3050 3063 3064 3065 3082 P A R 12 distorted distorted 3070 3083 3084 3085 3104 P C R 13 distorted distorted 3090 3105 3106 3107 3124 P C R 14 distorted distorted 3112 3125 3126 3127 3144 P C R 15 distorted distorted 3132 3145 3146 3147 3164 P A R 16 distorted distorted 3152 3165 3166 3167 3186 P U R 17 distorted distorted 3172 3187 3188 3189 3224 P G S 5 distorted distorted 3212 3225 3226 3227 3247 P A S 6 distorted distorted 3232 3248 3249 3250 3269 P G S 7 distorted distorted 3255 3270 3271 3272 3292 P G S 8 distorted distorted 3277 3293 3294 3295 3315 P A S 9 distorted distorted 3300 3316 3317 3318 3337 P U S 10 distorted distorted 3323 3338 3339 3340 3357 P U S 11 distorted distorted 3345 3358 3359 3360 3377 P A S 12 distorted distorted 3365 3378 3379 3380 3399 P C S 13 distorted distorted 3385 3400 3401 3402 3419 P C S 14 distorted distorted 3407 3420 3421 3422 3439 P C S 15 distorted distorted 3427 3440 3441 3442 3459 P A S 16 distorted distorted 3447 3460 3461 3462 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