ID code: '3RBE' 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' --------------------------------------------------------------------------------- 2749 C1' DG D 802 beta 2745 2750 2748 2771 C1' DT D 803 beta 2767 2772 2770 2791 C1' DT D 804 beta 2787 2792 2790 2811 C1' DG D 805 beta 2807 2812 2810 2833 C1' DG D 806 beta 2829 2834 2832 2855 C1' DA D 807 beta 2851 2856 2854 2876 C1' DT D 808 beta 2872 2877 2875 2896 C1' DG D 809 beta 2892 2897 2895 2918 C1' DG D 810 beta 2914 2919 2917 2940 C1' DT D 811 beta 2936 2941 2939 2960 C1' DA D 812 beta 2956 2961 2959 2981 C1' DG D 813 beta 2977 2982 2980 3010 C1' 2DT D 814 beta 3009 2997 3006 3020 C1' DC E 901 beta 3016 3021 3019 3039 C1' DT E 902 beta 3035 3040 3038 3059 C1' DA E 903 beta 3055 3060 3058 3080 C1' DA E 904 beta 3076 3081 3079 3101 C1' DC E 905 beta 3097 3102 3100 3119 C1' ME6 E 906 beta 3120 3118 3121 3140 C1' DC E 907 beta 3136 3141 3139 3159 C1' DT E 908 beta 3155 3160 3158 3179 C1' DA E 909 beta 3175 3180 3178 3200 C1' DC E 910 beta 3196 3201 3199 3219 C1' DC E 911 beta 3215 3220 3218 3238 C1' DA E 912 beta 3234 3239 3237 3259 C1' DT E 913 beta 3255 3260 3258 3279 C1' DC E 914 beta 3275 3280 3278 3298 C1' DC E 915 beta 3294 3299 3297 3317 C1' DA E 916 beta 3313 3318 3316 3338 C1' DA E 917 beta 3334 3339 3337 3359 C1' DC E 918 beta 3355 3360 3358 3378 C1' DC E 919 beta 3374 3379 3377 6139 C1' DG H1805 beta 6135 6140 6138 6161 C1' DG H1806 beta 6157 6162 6160 6183 C1' DA H1807 beta 6179 6184 6182 6204 C1' DT H1808 beta 6200 6205 6203 6224 C1' DG H1809 beta 6220 6225 6223 6246 C1' DG H1810 beta 6242 6247 6245 6268 C1' DT H1811 beta 6264 6269 6267 6288 C1' DA H1812 beta 6284 6289 6287 6309 C1' DG H1813 beta 6305 6310 6308 6338 C1' 2DT H1814 beta 6337 6325 6334 6351 C1' DC J1905 beta 6347 6352 6350 6369 C1' ME6 J1906 beta 6370 6368 6371 6390 C1' DC J1907 beta 6386 6391 6389 6409 C1' DT J1908 beta 6405 6410 6408 6429 C1' DA J1909 beta 6425 6430 6428 6450 C1' DC J1910 beta 6446 6451 6449 6469 C1' DC J1911 beta 6465 6470 6468 6488 C1' DA J1912 beta 6484 6489 6487 6509 C1' DT J1913 beta 6505 6510 6508 6529 C1' DC J1914 beta 6525 6530 6528 6558 C1' DGT A 414 beta 6554 6559 6557 6592 C1' DGT B1414 beta 6588 6593 6591 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 2748 C2' DG D 802 2749 2746 2770 C2' DT D 803 2771 2768 2790 C2' DT D 804 2791 2788 2810 C2' DG D 805 2811 2808 2832 C2' DG D 806 2833 2830 2854 C2' DA D 807 2855 2852 2875 C2' DT D 808 2876 2873 2895 C2' DG D 809 2896 2893 2917 C2' DG D 810 2918 2915 2939 C2' DT D 811 2940 2937 2959 C2' DA D 812 2960 2957 2980 C2' DG D 813 2981 2978 3006 C2' 2DT D 814 3010 3011 3019 C2' DC E 901 3020 3017 3038 C2' DT E 902 3039 3036 3058 C2' DA E 903 3059 3056 3079 C2' DA E 904 3080 3077 3100 C2' DC E 905 3101 3098 3121 C2' ME6 E 906 3119 3122 3139 C2' DC E 907 3140 3137 3158 C2' DT E 908 3159 3156 3178 C2' DA E 909 3179 3176 3199 C2' DC E 910 3200 3197 3218 C2' DC E 911 3219 3216 3237 C2' DA E 912 3238 3235 3258 C2' DT E 913 3259 3256 3278 C2' DC E 914 3279 3276 3297 C2' DC E 915 3298 3295 3316 C2' DA E 916 3317 3314 3337 C2' DA E 917 3338 3335 3358 C2' DC E 918 3359 3356 3377 C2' DC E 919 3378 3375 6138 C2' DG H1805 6139 6136 6160 C2' DG H1806 6161 6158 6182 C2' DA H1807 6183 6180 6203 C2' DT H1808 6204 6201 6223 C2' DG H1809 6224 6221 6245 C2' DG H1810 6246 6243 6267 C2' DT H1811 6268 6265 6287 C2' DA H1812 6288 6285 6308 C2' DG H1813 6309 6306 6334 C2' 2DT H1814 6338 6339 6350 C2' DC J1905 6351 6348 6371 C2' ME6 J1906 6369 6372 6389 C2' DC J1907 6390 6387 6408 C2' DT J1908 6409 6406 6428 C2' DA J1909 6429 6426 6449 C2' DC J1910 6450 6447 6468 C2' DC J1911 6469 6466 6487 C2' DA J1912 6488 6485 6508 C2' DT J1913 6509 6506 6528 C2' DC J1914 6529 6526 6557 C2' DGT A 414 6558 6555 6591 C2' DGT B1414 6592 6589 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 2746 C3' DG D 802 OK 2744 2747 2748 2768 C3' DT D 803 OK 2766 2769 2770 2788 C3' DT D 804 OK 2786 2789 2790 2808 C3' DG D 805 OK 2806 2809 2810 2830 C3' DG D 806 OK 2828 2831 2832 2852 C3' DA D 807 OK 2850 2853 2854 2873 C3' DT D 808 OK 2871 2874 2875 2893 C3' DG D 809 OK 2891 2894 2895 2915 C3' DG D 810 OK 2913 2916 2917 2937 C3' DT D 811 OK 2935 2938 2939 2957 C3' DA D 812 OK 2955 2958 2959 2978 C3' DG D 813 OK 2976 2979 2980 3011 C3' 2DT D 814 3008 3006 3017 C3' DC E 901 OK 3015 3018 3019 3036 C3' DT E 902 OK 3034 3037 3038 3056 C3' DA E 903 OK 3054 3057 3058 3077 C3' DA E 904 OK 3075 3078 3079 3098 C3' DC E 905 OK 3096 3099 3100 3122 C3' ME6 E 906 OK 3124 3123 3121 3137 C3' DC E 907 OK 3135 3138 3139 3156 C3' DT E 908 OK 3154 3157 3158 3176 C3' DA E 909 OK 3174 3177 3178 3197 C3' DC E 910 OK 3195 3198 3199 3216 C3' DC E 911 OK 3214 3217 3218 3235 C3' DA E 912 OK 3233 3236 3237 3256 C3' DT E 913 OK 3254 3257 3258 3276 C3' DC E 914 OK 3274 3277 3278 3295 C3' DC E 915 OK 3293 3296 3297 3314 C3' DA E 916 OK 3312 3315 3316 3335 C3' DA E 917 OK 3333 3336 3337 3356 C3' DC E 918 OK 3354 3357 3358 3375 C3' DC E 919 OK 3373 3376 3377 6136 C3' DG H1805 OK 6134 6137 6138 6158 C3' DG H1806 OK 6156 6159 6160 6180 C3' DA H1807 OK 6178 6181 6182 6201 C3' DT H1808 OK 6199 6202 6203 6221 C3' DG H1809 OK 6219 6222 6223 6243 C3' DG H1810 OK 6241 6244 6245 6265 C3' DT H1811 OK 6263 6266 6267 6285 C3' DA H1812 OK 6283 6286 6287 6306 C3' DG H1813 OK 6304 6307 6308 6339 C3' 2DT H1814 6336 6334 6348 C3' DC J1905 OK 6346 6349 6350 6372 C3' ME6 J1906 OK 6374 6373 6371 6387 C3' DC J1907 OK 6385 6388 6389 6406 C3' DT J1908 OK 6404 6407 6408 6426 C3' DA J1909 OK 6424 6427 6428 6447 C3' DC J1910 OK 6445 6448 6449 6466 C3' DC J1911 OK 6464 6467 6468 6485 C3' DA J1912 OK 6483 6486 6487 6506 C3' DT J1913 OK 6504 6507 6508 6526 C3' DC J1914 OK 6524 6527 6528 6555 C3' DGT A 414 OK 6553 6556 6557 6589 C3' DGT B1414 OK 6587 6590 6591 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 2744 C4' DG D 802 OK 2746 2743 2745 2766 C4' DT D 803 OK 2768 2765 2767 2786 C4' DT D 804 OK 2788 2785 2787 2806 C4' DG D 805 OK 2808 2805 2807 2828 C4' DG D 806 OK 2830 2827 2829 2850 C4' DA D 807 OK 2852 2849 2851 2871 C4' DT D 808 OK 2873 2870 2872 2891 C4' DG D 809 OK 2893 2890 2892 2913 C4' DG D 810 OK 2915 2912 2914 2935 C4' DT D 811 OK 2937 2934 2936 2955 C4' DA D 812 OK 2957 2954 2956 2976 C4' DG D 813 OK 2978 2975 2977 3008 C4' 2DT D 814 OK 3011 3007 3009 3015 C4' DC E 901 OK 3017 3014 3016 3034 C4' DT E 902 OK 3036 3033 3035 3054 C4' DA E 903 OK 3056 3053 3055 3075 C4' DA E 904 OK 3077 3074 3076 3096 C4' DC E 905 OK 3098 3095 3097 3124 C4' ME6 E 906 OK 3122 3125 3120 3135 C4' DC E 907 OK 3137 3134 3136 3154 C4' DT E 908 OK 3156 3153 3155 3174 C4' DA E 909 OK 3176 3173 3175 3195 C4' DC E 910 OK 3197 3194 3196 3214 C4' DC E 911 OK 3216 3213 3215 3233 C4' DA E 912 OK 3235 3232 3234 3254 C4' DT E 913 OK 3256 3253 3255 3274 C4' DC E 914 OK 3276 3273 3275 3293 C4' DC E 915 OK 3295 3292 3294 3312 C4' DA E 916 OK 3314 3311 3313 3333 C4' DA E 917 OK 3335 3332 3334 3354 C4' DC E 918 OK 3356 3353 3355 3373 C4' DC E 919 OK 3375 3372 3374 6134 C4' DG H1805 OK 6136 6133 6135 6156 C4' DG H1806 OK 6158 6155 6157 6178 C4' DA H1807 OK 6180 6177 6179 6199 C4' DT H1808 OK 6201 6198 6200 6219 C4' DG H1809 OK 6221 6218 6220 6241 C4' DG H1810 OK 6243 6240 6242 6263 C4' DT H1811 OK 6265 6262 6264 6283 C4' DA H1812 OK 6285 6282 6284 6304 C4' DG H1813 OK 6306 6303 6305 6336 C4' 2DT H1814 OK 6339 6335 6337 6346 C4' DC J1905 OK 6348 6345 6347 6374 C4' ME6 J1906 OK 6372 6375 6370 6385 C4' DC J1907 OK 6387 6384 6386 6404 C4' DT J1908 OK 6406 6403 6405 6424 C4' DA J1909 OK 6426 6423 6425 6445 C4' DC J1910 OK 6447 6444 6446 6464 C4' DC J1911 OK 6466 6463 6465 6483 C4' DA J1912 OK 6485 6482 6484 6504 C4' DT J1913 OK 6506 6503 6505 6524 C4' DC J1914 OK 6526 6523 6525 6553 C4' DGT A 414 OK 6555 6552 6554 6587 C4' DGT B1414 OK 6589 6586 6588 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2743 C5' DG D 802 2742 2744 2765 C5' DT D 803 2764 2766 2785 C5' DT D 804 2784 2786 2805 C5' DG D 805 2804 2806 2827 C5' DG D 806 2826 2828 2849 C5' DA D 807 2848 2850 2870 C5' DT D 808 2869 2871 2890 C5' DG D 809 2889 2891 2912 C5' DG D 810 2911 2913 2934 C5' DT D 811 2933 2935 2954 C5' DA D 812 2953 2955 2975 C5' DG D 813 2974 2976 3007 C5' 2DT D 814 2996 3008 3014 C5' DC E 901 3013 3015 3033 C5' DT E 902 3032 3034 3053 C5' DA E 903 3052 3054 3074 C5' DA E 904 3073 3075 3095 C5' DC E 905 3094 3096 3125 C5' ME6 E 906 3126 3124 3134 C5' DC E 907 3133 3135 3153 C5' DT E 908 3152 3154 3173 C5' DA E 909 3172 3174 3194 C5' DC E 910 3193 3195 3213 C5' DC E 911 3212 3214 3232 C5' DA E 912 3231 3233 3253 C5' DT E 913 3252 3254 3273 C5' DC E 914 3272 3274 3292 C5' DC E 915 3291 3293 3311 C5' DA E 916 3310 3312 3332 C5' DA E 917 3331 3333 3353 C5' DC E 918 3352 3354 3372 C5' DC E 919 3371 3373 6133 C5' DG H1805 6132 6134 6155 C5' DG H1806 6154 6156 6177 C5' DA H1807 6176 6178 6198 C5' DT H1808 6197 6199 6218 C5' DG H1809 6217 6219 6240 C5' DG H1810 6239 6241 6262 C5' DT H1811 6261 6263 6282 C5' DA H1812 6281 6283 6303 C5' DG H1813 6302 6304 6335 C5' 2DT H1814 6324 6336 6345 C5' DC J1905 6344 6346 6375 C5' ME6 J1906 6376 6374 6384 C5' DC J1907 6383 6385 6403 C5' DT J1908 6402 6404 6423 C5' DA J1909 6422 6424 6444 C5' DC J1910 6443 6445 6463 C5' DC J1911 6462 6464 6482 C5' DA J1912 6481 6483 6503 C5' DT J1913 6502 6504 6523 C5' DC J1914 6522 6524 6552 C5' DGT A 414 6551 6553 6586 C5' DGT B1414 6585 6587 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2761 P DT D 803 distorted distorted 2747 2762 2763 2764 2781 P DT D 804 distorted distorted 2769 2782 2783 2784 2801 P DG D 805 distorted distorted 2789 2802 2803 2804 2823 P DG D 806 distorted distorted 2809 2824 2825 2826 2845 P DA D 807 distorted distorted 2831 2846 2847 2848 2866 P DT D 808 distorted distorted 2853 2867 2868 2869 2886 P DG D 809 distorted distorted 2874 2887 2888 2889 2908 P DG D 810 distorted distorted 2894 2909 2910 2911 2930 P DT D 811 distorted distorted 2916 2931 2932 2933 2950 P DA D 812 distorted distorted 2938 2951 2952 2953 2971 P DG D 813 distorted distorted 2958 2972 2973 2974 2993 P 2DT D 814 distorted distorted 2979 2994 2995 2996 3029 P DT E 902 distorted distorted 3018 3030 3031 3032 3049 P DA E 903 distorted distorted 3037 3050 3051 3052 3070 P DA E 904 distorted distorted 3057 3071 3072 3073 3091 P DC E 905 distorted distorted 3078 3092 3093 3094 3127 P ME6 E 906 distorted distorted 3099 3129 3128 3126 3130 P DC E 907 distorted distorted 3123 3131 3132 3133 3149 P DT E 908 distorted distorted 3138 3150 3151 3152 3169 P DA E 909 distorted distorted 3157 3170 3171 3172 3190 P DC E 910 distorted distorted 3177 3191 3192 3193 3209 P DC E 911 distorted distorted 3198 3210 3211 3212 3228 P DA E 912 distorted distorted 3217 3229 3230 3231 3249 P DT E 913 distorted distorted 3236 3250 3251 3252 3269 P DC E 914 distorted distorted 3257 3270 3271 3272 3288 P DC E 915 distorted distorted 3277 3289 3290 3291 3307 P DA E 916 distorted distorted 3296 3308 3309 3310 3328 P DA E 917 distorted distorted 3315 3329 3330 3331 3349 P DC E 918 distorted distorted 3336 3350 3351 3352 3368 P DC E 919 distorted distorted 3357 3369 3370 3371 6129 P DG H1805 distorted distorted 6130 6131 6132 6151 P DG H1806 distorted distorted 6137 6152 6153 6154 6173 P DA H1807 distorted distorted 6159 6174 6175 6176 6194 P DT H1808 distorted distorted 6181 6195 6196 6197 6214 P DG H1809 distorted distorted 6202 6215 6216 6217 6236 P DG H1810 distorted distorted 6222 6237 6238 6239 6258 P DT H1811 distorted distorted 6244 6259 6260 6261 6278 P DA H1812 distorted distorted 6266 6279 6280 6281 6299 P DG H1813 distorted distorted 6286 6300 6301 6302 6321 P 2DT H1814 distorted distorted 6307 6322 6323 6324 6341 P DC J1905 distorted distorted 6342 6343 6344 6377 P ME6 J1906 distorted distorted 6349 6379 6378 6376 6380 P DC J1907 distorted distorted 6373 6381 6382 6383 6399 P DT J1908 distorted distorted 6388 6400 6401 6402 6419 P DA J1909 distorted distorted 6407 6420 6421 6422 6440 P DC J1910 distorted distorted 6427 6441 6442 6443 6459 P DC J1911 distorted distorted 6448 6460 6461 6462 6478 P DA J1912 distorted distorted 6467 6479 6480 6481 6499 P DT J1913 distorted distorted 6486 6500 6501 6502 6519 P DC J1914 distorted distorted 6507 6520 6521 6522 ---------------------------------------------------------------------------------