ID code: '2W8L' 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' --------------------------------------------------------------------------------- 2763 C1' DG P 1 beta 2759 2764 2762 2785 C1' DG P 2 beta 2781 2786 2784 2807 C1' DG P 3 beta 2803 2808 2806 2829 C1' DG P 4 beta 2825 2830 2828 2851 C1' DG P 5 beta 2847 2852 2850 2873 C1' DA P 6 beta 2869 2874 2872 2894 C1' DA P 7 beta 2890 2895 2893 2915 C1' DG P 8 beta 2911 2916 2914 2937 C1' DG P 9 beta 2933 2938 2936 2959 C1' DA P 10 beta 2955 2960 2958 2980 C1' DT P 11 beta 2976 2981 2979 3000 C1' DT P 12 beta 2996 3001 2999 3020 C1' DC P 13 beta 3016 3021 3019 3037 C1' DOC P 14 beta 3041 3029 3038 3164 C1' DG T 6 beta 3160 3165 3163 3186 C1' DA T 7 beta 3182 3187 3185 3207 C1' DA T 8 beta 3203 3208 3206 3228 C1' DT T 9 beta 3224 3229 3227 3248 C1' DC T 10 beta 3244 3249 3247 3267 C1' DC T 11 beta 3263 3268 3266 3286 C1' DT T 12 beta 3282 3287 3285 3306 C1' DT T 13 beta 3302 3307 3305 3326 C1' DC T 14 beta 3322 3327 3325 3345 C1' DC T 15 beta 3341 3346 3344 3364 C1' DC T 16 beta 3360 3365 3363 3383 C1' DC T 17 beta 3379 3384 3382 3402 C1' DC T 18 beta 3398 3403 3401 3431 C1' DGT A1343 beta 3427 3432 3430 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2762 C2' DG P 1 2763 2760 2784 C2' DG P 2 2785 2782 2806 C2' DG P 3 2807 2804 2828 C2' DG P 4 2829 2826 2850 C2' DG P 5 2851 2848 2872 C2' DA P 6 2873 2870 2893 C2' DA P 7 2894 2891 2914 C2' DG P 8 2915 2912 2936 C2' DG P 9 2937 2934 2958 C2' DA P 10 2959 2956 2979 C2' DT P 11 2980 2977 2999 C2' DT P 12 3000 2997 3019 C2' DC P 13 3020 3017 3038 C2' DOC P 14 3037 3039 3163 C2' DG T 6 3164 3161 3185 C2' DA T 7 3186 3183 3206 C2' DA T 8 3207 3204 3227 C2' DT T 9 3228 3225 3247 C2' DC T 10 3248 3245 3266 C2' DC T 11 3267 3264 3285 C2' DT T 12 3286 3283 3305 C2' DT T 13 3306 3303 3325 C2' DC T 14 3326 3323 3344 C2' DC T 15 3345 3342 3363 C2' DC T 16 3364 3361 3382 C2' DC T 17 3383 3380 3401 C2' DC T 18 3402 3399 3430 C2' DGT A1343 3431 3428 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2760 C3' DG P 1 OK 2758 2761 2762 2782 C3' DG P 2 OK 2780 2783 2784 2804 C3' DG P 3 OK 2802 2805 2806 2826 C3' DG P 4 OK 2824 2827 2828 2848 C3' DG P 5 OK 2846 2849 2850 2870 C3' DA P 6 OK 2868 2871 2872 2891 C3' DA P 7 OK 2889 2892 2893 2912 C3' DG P 8 OK 2910 2913 2914 2934 C3' DG P 9 OK 2932 2935 2936 2956 C3' DA P 10 OK 2954 2957 2958 2977 C3' DT P 11 OK 2975 2978 2979 2997 C3' DT P 12 OK 2995 2998 2999 3017 C3' DC P 13 OK 3015 3018 3019 3039 C3' DOC P 14 3040 3038 3161 C3' DG T 6 OK 3159 3162 3163 3183 C3' DA T 7 OK 3181 3184 3185 3204 C3' DA T 8 OK 3202 3205 3206 3225 C3' DT T 9 OK 3223 3226 3227 3245 C3' DC T 10 OK 3243 3246 3247 3264 C3' DC T 11 OK 3262 3265 3266 3283 C3' DT T 12 OK 3281 3284 3285 3303 C3' DT T 13 OK 3301 3304 3305 3323 C3' DC T 14 OK 3321 3324 3325 3342 C3' DC T 15 OK 3340 3343 3344 3361 C3' DC T 16 OK 3359 3362 3363 3380 C3' DC T 17 OK 3378 3381 3382 3399 C3' DC T 18 OK 3397 3400 3401 3428 C3' DGT A1343 OK 3426 3429 3430 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2758 C4' DG P 1 OK 2760 2757 2759 2780 C4' DG P 2 OK 2782 2779 2781 2802 C4' DG P 3 OK 2804 2801 2803 2824 C4' DG P 4 OK 2826 2823 2825 2846 C4' DG P 5 OK 2848 2845 2847 2868 C4' DA P 6 OK 2870 2867 2869 2889 C4' DA P 7 OK 2891 2888 2890 2910 C4' DG P 8 OK 2912 2909 2911 2932 C4' DG P 9 OK 2934 2931 2933 2954 C4' DA P 10 OK 2956 2953 2955 2975 C4' DT P 11 OK 2977 2974 2976 2995 C4' DT P 12 OK 2997 2994 2996 3015 C4' DC P 13 OK 3017 3014 3016 3040 C4' DOC P 14 OK 3039 3042 3041 3159 C4' DG T 6 OK 3161 3158 3160 3181 C4' DA T 7 OK 3183 3180 3182 3202 C4' DA T 8 OK 3204 3201 3203 3223 C4' DT T 9 OK 3225 3222 3224 3243 C4' DC T 10 OK 3245 3242 3244 3262 C4' DC T 11 OK 3264 3261 3263 3281 C4' DT T 12 OK 3283 3280 3282 3301 C4' DT T 13 OK 3303 3300 3302 3321 C4' DC T 14 OK 3323 3320 3322 3340 C4' DC T 15 OK 3342 3339 3341 3359 C4' DC T 16 OK 3361 3358 3360 3378 C4' DC T 17 OK 3380 3377 3379 3397 C4' DC T 18 OK 3399 3396 3398 3426 C4' DGT A1343 OK 3428 3425 3427 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2757 C5' DG P 1 2756 2758 2779 C5' DG P 2 2778 2780 2801 C5' DG P 3 2800 2802 2823 C5' DG P 4 2822 2824 2845 C5' DG P 5 2844 2846 2867 C5' DA P 6 2866 2868 2888 C5' DA P 7 2887 2889 2909 C5' DG P 8 2908 2910 2931 C5' DG P 9 2930 2932 2953 C5' DA P 10 2952 2954 2974 C5' DT P 11 2973 2975 2994 C5' DT P 12 2993 2995 3014 C5' DC P 13 3013 3015 3042 C5' DOC P 14 3043 3040 3158 C5' DG T 6 3157 3159 3180 C5' DA T 7 3179 3181 3201 C5' DA T 8 3200 3202 3222 C5' DT T 9 3221 3223 3242 C5' DC T 10 3241 3243 3261 C5' DC T 11 3260 3262 3280 C5' DT T 12 3279 3281 3300 C5' DT T 13 3299 3301 3320 C5' DC T 14 3319 3321 3339 C5' DC T 15 3338 3340 3358 C5' DC T 16 3357 3359 3377 C5' DC T 17 3376 3378 3396 C5' DC T 18 3395 3397 3425 C5' DGT A1343 3424 3426 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2775 P DG P 2 distorted distorted 2761 2776 2777 2778 2797 P DG P 3 distorted distorted 2783 2798 2799 2800 2819 P DG P 4 distorted distorted 2805 2820 2821 2822 2841 P DG P 5 distorted distorted 2827 2842 2843 2844 2863 P DA P 6 distorted distorted 2849 2864 2865 2866 2884 P DA P 7 distorted distorted 2871 2885 2886 2887 2905 P DG P 8 distorted distorted 2892 2906 2907 2908 2927 P DG P 9 distorted distorted 2913 2928 2929 2930 2949 P DA P 10 distorted distorted 2935 2950 2951 2952 2970 P DT P 11 distorted distorted 2957 2971 2972 2973 2990 P DT P 12 distorted distorted 2978 2991 2992 2993 3010 P DC P 13 distorted distorted 2998 3011 3012 3013 3044 P DOC P 14 distorted distorted 3018 3045 3046 3043 3085 P DC T 4 3103 P DC T 4 3121 P N2G T 5 OK OK 3123 3122 3124 3154 P DG T 6 OK OK 3153 3155 3156 3157 3176 P DA T 7 distorted distorted 3162 3177 3178 3179 3197 P DA T 8 distorted distorted 3184 3198 3199 3200 3218 P DT T 9 distorted distorted 3205 3219 3220 3221 3238 P DC T 10 distorted distorted 3226 3239 3240 3241 3257 P DC T 11 distorted distorted 3246 3258 3259 3260 3276 P DT T 12 distorted distorted 3265 3277 3278 3279 3296 P DT T 13 distorted distorted 3284 3297 3298 3299 3316 P DC T 14 distorted distorted 3304 3317 3318 3319 3335 P DC T 15 distorted distorted 3324 3336 3337 3338 3354 P DC T 16 distorted distorted 3343 3355 3356 3357 3373 P DC T 17 distorted distorted 3362 3374 3375 3376 3392 P DC T 18 distorted distorted 3381 3393 3394 3395 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