ID code: '3RBD' 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 3001 C1' DOC D 814 beta 3005 2993 3002 3019 C1' DC E 901 beta 3015 3020 3018 3038 C1' DT E 902 beta 3034 3039 3037 3058 C1' DA E 903 beta 3054 3059 3057 3079 C1' DA E 904 beta 3075 3080 3078 3100 C1' DC E 905 beta 3096 3101 3099 3118 C1' ME6 E 906 beta 3119 3117 3120 3139 C1' DC E 907 beta 3135 3140 3138 3158 C1' DT E 908 beta 3154 3159 3157 3178 C1' DA E 909 beta 3174 3179 3177 3199 C1' DC E 910 beta 3195 3200 3198 3218 C1' DC E 911 beta 3214 3219 3217 3237 C1' DA E 912 beta 3233 3238 3236 3258 C1' DT E 913 beta 3254 3259 3257 3278 C1' DC E 914 beta 3274 3279 3277 3297 C1' DC E 915 beta 3293 3298 3296 3316 C1' DA E 916 beta 3312 3317 3315 3337 C1' DA E 917 beta 3333 3338 3336 3358 C1' DC E 918 beta 3354 3359 3357 3377 C1' DC E 919 beta 3373 3378 3376 6138 C1' DT H1804 beta 6134 6139 6137 6158 C1' DG H1805 beta 6154 6159 6157 6180 C1' DG H1806 beta 6176 6181 6179 6202 C1' DA H1807 beta 6198 6203 6201 6223 C1' DT H1808 beta 6219 6224 6222 6243 C1' DG H1809 beta 6239 6244 6242 6265 C1' DG H1810 beta 6261 6266 6264 6287 C1' DT H1811 beta 6283 6288 6286 6307 C1' DA H1812 beta 6303 6308 6306 6328 C1' DG H1813 beta 6324 6329 6327 6348 C1' DOC H1814 beta 6352 6340 6349 6369 C1' DC J1905 beta 6365 6370 6368 6387 C1' ME6 J1906 beta 6388 6386 6389 6408 C1' DC J1907 beta 6404 6409 6407 6427 C1' DT J1908 beta 6423 6428 6426 6447 C1' DA J1909 beta 6443 6448 6446 6468 C1' DC J1910 beta 6464 6469 6467 6487 C1' DC J1911 beta 6483 6488 6486 6506 C1' DA J1912 beta 6502 6507 6505 6527 C1' DT J1913 beta 6523 6528 6526 6547 C1' DC J1914 beta 6543 6548 6546 6566 C1' DC J1915 beta 6562 6567 6565 6595 C1' DGT A 414 beta 6591 6596 6594 6644 C1' DGT B1414 beta 6640 6645 6643 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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 3002 C2' DOC D 814 3001 3003 3018 C2' DC E 901 3019 3016 3037 C2' DT E 902 3038 3035 3057 C2' DA E 903 3058 3055 3078 C2' DA E 904 3079 3076 3099 C2' DC E 905 3100 3097 3120 C2' ME6 E 906 3118 3121 3138 C2' DC E 907 3139 3136 3157 C2' DT E 908 3158 3155 3177 C2' DA E 909 3178 3175 3198 C2' DC E 910 3199 3196 3217 C2' DC E 911 3218 3215 3236 C2' DA E 912 3237 3234 3257 C2' DT E 913 3258 3255 3277 C2' DC E 914 3278 3275 3296 C2' DC E 915 3297 3294 3315 C2' DA E 916 3316 3313 3336 C2' DA E 917 3337 3334 3357 C2' DC E 918 3358 3355 3376 C2' DC E 919 3377 3374 6137 C2' DT H1804 6138 6135 6157 C2' DG H1805 6158 6155 6179 C2' DG H1806 6180 6177 6201 C2' DA H1807 6202 6199 6222 C2' DT H1808 6223 6220 6242 C2' DG H1809 6243 6240 6264 C2' DG H1810 6265 6262 6286 C2' DT H1811 6287 6284 6306 C2' DA H1812 6307 6304 6327 C2' DG H1813 6328 6325 6349 C2' DOC H1814 6348 6350 6368 C2' DC J1905 6369 6366 6389 C2' ME6 J1906 6387 6390 6407 C2' DC J1907 6408 6405 6426 C2' DT J1908 6427 6424 6446 C2' DA J1909 6447 6444 6467 C2' DC J1910 6468 6465 6486 C2' DC J1911 6487 6484 6505 C2' DA J1912 6506 6503 6526 C2' DT J1913 6527 6524 6546 C2' DC J1914 6547 6544 6565 C2' DC J1915 6566 6563 6594 C2' DGT A 414 6595 6592 6643 C2' DGT B1414 6644 6641 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3003 C3' DOC D 814 3004 3002 3016 C3' DC E 901 OK 3014 3017 3018 3035 C3' DT E 902 OK 3033 3036 3037 3055 C3' DA E 903 OK 3053 3056 3057 3076 C3' DA E 904 OK 3074 3077 3078 3097 C3' DC E 905 OK 3095 3098 3099 3121 C3' ME6 E 906 OK 3123 3122 3120 3136 C3' DC E 907 OK 3134 3137 3138 3155 C3' DT E 908 OK 3153 3156 3157 3175 C3' DA E 909 OK 3173 3176 3177 3196 C3' DC E 910 OK 3194 3197 3198 3215 C3' DC E 911 OK 3213 3216 3217 3234 C3' DA E 912 OK 3232 3235 3236 3255 C3' DT E 913 OK 3253 3256 3257 3275 C3' DC E 914 OK 3273 3276 3277 3294 C3' DC E 915 OK 3292 3295 3296 3313 C3' DA E 916 OK 3311 3314 3315 3334 C3' DA E 917 OK 3332 3335 3336 3355 C3' DC E 918 OK 3353 3356 3357 3374 C3' DC E 919 OK 3372 3375 3376 6135 C3' DT H1804 OK 6133 6136 6137 6155 C3' DG H1805 OK 6153 6156 6157 6177 C3' DG H1806 OK 6175 6178 6179 6199 C3' DA H1807 OK 6197 6200 6201 6220 C3' DT H1808 OK 6218 6221 6222 6240 C3' DG H1809 OK 6238 6241 6242 6262 C3' DG H1810 OK 6260 6263 6264 6284 C3' DT H1811 OK 6282 6285 6286 6304 C3' DA H1812 OK 6302 6305 6306 6325 C3' DG H1813 OK 6323 6326 6327 6350 C3' DOC H1814 6351 6349 6366 C3' DC J1905 OK 6364 6367 6368 6390 C3' ME6 J1906 OK 6392 6391 6389 6405 C3' DC J1907 OK 6403 6406 6407 6424 C3' DT J1908 OK 6422 6425 6426 6444 C3' DA J1909 OK 6442 6445 6446 6465 C3' DC J1910 OK 6463 6466 6467 6484 C3' DC J1911 OK 6482 6485 6486 6503 C3' DA J1912 OK 6501 6504 6505 6524 C3' DT J1913 OK 6522 6525 6526 6544 C3' DC J1914 OK 6542 6545 6546 6563 C3' DC J1915 OK 6561 6564 6565 6592 C3' DGT A 414 OK 6590 6593 6594 6641 C3' DGT B1414 OK 6639 6642 6643 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3004 C4' DOC D 814 OK 3003 3006 3005 3014 C4' DC E 901 OK 3016 3013 3015 3033 C4' DT E 902 OK 3035 3032 3034 3053 C4' DA E 903 OK 3055 3052 3054 3074 C4' DA E 904 OK 3076 3073 3075 3095 C4' DC E 905 OK 3097 3094 3096 3123 C4' ME6 E 906 OK 3121 3124 3119 3134 C4' DC E 907 OK 3136 3133 3135 3153 C4' DT E 908 OK 3155 3152 3154 3173 C4' DA E 909 OK 3175 3172 3174 3194 C4' DC E 910 OK 3196 3193 3195 3213 C4' DC E 911 OK 3215 3212 3214 3232 C4' DA E 912 OK 3234 3231 3233 3253 C4' DT E 913 OK 3255 3252 3254 3273 C4' DC E 914 OK 3275 3272 3274 3292 C4' DC E 915 OK 3294 3291 3293 3311 C4' DA E 916 OK 3313 3310 3312 3332 C4' DA E 917 OK 3334 3331 3333 3353 C4' DC E 918 OK 3355 3352 3354 3372 C4' DC E 919 OK 3374 3371 3373 6133 C4' DT H1804 OK 6135 6132 6134 6153 C4' DG H1805 OK 6155 6152 6154 6175 C4' DG H1806 OK 6177 6174 6176 6197 C4' DA H1807 OK 6199 6196 6198 6218 C4' DT H1808 OK 6220 6217 6219 6238 C4' DG H1809 OK 6240 6237 6239 6260 C4' DG H1810 OK 6262 6259 6261 6282 C4' DT H1811 OK 6284 6281 6283 6302 C4' DA H1812 OK 6304 6301 6303 6323 C4' DG H1813 OK 6325 6322 6324 6351 C4' DOC H1814 OK 6350 6353 6352 6364 C4' DC J1905 OK 6366 6363 6365 6392 C4' ME6 J1906 OK 6390 6393 6388 6403 C4' DC J1907 OK 6405 6402 6404 6422 C4' DT J1908 OK 6424 6421 6423 6442 C4' DA J1909 OK 6444 6441 6443 6463 C4' DC J1910 OK 6465 6462 6464 6482 C4' DC J1911 OK 6484 6481 6483 6501 C4' DA J1912 OK 6503 6500 6502 6522 C4' DT J1913 OK 6524 6521 6523 6542 C4' DC J1914 OK 6544 6541 6543 6561 C4' DC J1915 OK 6563 6560 6562 6590 C4' DGT A 414 OK 6592 6589 6591 6639 C4' DGT B1414 OK 6641 6638 6640 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3006 C5' DOC D 814 3007 3004 3013 C5' DC E 901 3012 3014 3032 C5' DT E 902 3031 3033 3052 C5' DA E 903 3051 3053 3073 C5' DA E 904 3072 3074 3094 C5' DC E 905 3093 3095 3124 C5' ME6 E 906 3125 3123 3133 C5' DC E 907 3132 3134 3152 C5' DT E 908 3151 3153 3172 C5' DA E 909 3171 3173 3193 C5' DC E 910 3192 3194 3212 C5' DC E 911 3211 3213 3231 C5' DA E 912 3230 3232 3252 C5' DT E 913 3251 3253 3272 C5' DC E 914 3271 3273 3291 C5' DC E 915 3290 3292 3310 C5' DA E 916 3309 3311 3331 C5' DA E 917 3330 3332 3352 C5' DC E 918 3351 3353 3371 C5' DC E 919 3370 3372 6132 C5' DT H1804 6131 6133 6152 C5' DG H1805 6151 6153 6174 C5' DG H1806 6173 6175 6196 C5' DA H1807 6195 6197 6217 C5' DT H1808 6216 6218 6237 C5' DG H1809 6236 6238 6259 C5' DG H1810 6258 6260 6281 C5' DT H1811 6280 6282 6301 C5' DA H1812 6300 6302 6322 C5' DG H1813 6321 6323 6353 C5' DOC H1814 6354 6351 6363 C5' DC J1905 6362 6364 6393 C5' ME6 J1906 6394 6392 6402 C5' DC J1907 6401 6403 6421 C5' DT J1908 6420 6422 6441 C5' DA J1909 6440 6442 6462 C5' DC J1910 6461 6463 6481 C5' DC J1911 6480 6482 6500 C5' DA J1912 6499 6501 6521 C5' DT J1913 6520 6522 6541 C5' DC J1914 6540 6542 6560 C5' DC J1915 6559 6561 6589 C5' DGT A 414 6588 6590 6638 C5' DGT B1414 6637 6639 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 3008 P DOC D 814 distorted distorted 2979 3009 3010 3007 3028 P DT E 902 distorted distorted 3017 3029 3030 3031 3048 P DA E 903 distorted distorted 3036 3049 3050 3051 3069 P DA E 904 distorted distorted 3056 3070 3071 3072 3090 P DC E 905 distorted distorted 3077 3091 3092 3093 3126 P ME6 E 906 distorted distorted 3098 3128 3127 3125 3129 P DC E 907 distorted distorted 3122 3130 3131 3132 3148 P DT E 908 distorted distorted 3137 3149 3150 3151 3168 P DA E 909 distorted distorted 3156 3169 3170 3171 3189 P DC E 910 distorted distorted 3176 3190 3191 3192 3208 P DC E 911 distorted distorted 3197 3209 3210 3211 3227 P DA E 912 distorted distorted 3216 3228 3229 3230 3248 P DT E 913 distorted distorted 3235 3249 3250 3251 3268 P DC E 914 distorted distorted 3256 3269 3270 3271 3287 P DC E 915 distorted distorted 3276 3288 3289 3290 3306 P DA E 916 distorted distorted 3295 3307 3308 3309 3327 P DA E 917 distorted distorted 3314 3328 3329 3330 3348 P DC E 918 distorted distorted 3335 3349 3350 3351 3367 P DC E 919 distorted distorted 3356 3368 3369 3370 6128 P DT H1804 distorted distorted 6129 6130 6131 6148 P DG H1805 distorted distorted 6136 6149 6150 6151 6170 P DG H1806 distorted distorted 6156 6171 6172 6173 6192 P DA H1807 distorted distorted 6178 6193 6194 6195 6213 P DT H1808 distorted distorted 6200 6214 6215 6216 6233 P DG H1809 distorted distorted 6221 6234 6235 6236 6255 P DG H1810 distorted distorted 6241 6256 6257 6258 6277 P DT H1811 distorted distorted 6263 6278 6279 6280 6297 P DA H1812 distorted distorted 6285 6298 6299 6300 6318 P DG H1813 distorted distorted 6305 6319 6320 6321 6355 P DOC H1814 distorted distorted 6326 6356 6357 6354 6359 P DC J1905 distorted distorted 6360 6361 6362 6395 P ME6 J1906 distorted distorted 6367 6397 6396 6394 6398 P DC J1907 distorted distorted 6391 6399 6400 6401 6417 P DT J1908 distorted distorted 6406 6418 6419 6420 6437 P DA J1909 distorted distorted 6425 6438 6439 6440 6458 P DC J1910 distorted distorted 6445 6459 6460 6461 6477 P DC J1911 distorted distorted 6466 6478 6479 6480 6496 P DA J1912 distorted distorted 6485 6497 6498 6499 6517 P DT J1913 distorted distorted 6504 6518 6519 6520 6537 P DC J1914 distorted distorted 6525 6538 6539 6540 6556 P DC J1915 distorted distorted 6545 6557 6558 6559 ---------------------------------------------------------------------------------