ID code: '3KJV' 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' --------------------------------------------------------------------------------- 7760 C1' DG P 805 beta 7756 7761 7759 7782 C1' DT P 806 beta 7778 7783 7781 7802 C1' DC P 807 beta 7798 7803 7801 7821 C1' DC P 808 beta 7817 7822 7820 7840 C1' DC P 809 beta 7836 7841 7839 7859 C1' DT P 810 beta 7855 7860 7858 7879 C1' DG P 811 beta 7875 7880 7878 7901 C1' DT P 812 beta 7897 7902 7900 7921 C1' DT P 813 beta 7917 7922 7920 7941 C1' DC P 814 beta 7937 7942 7940 7960 C1' DG P 815 beta 7956 7961 7959 7982 C1' DG P 816 beta 7978 7983 7981 8004 C1' DG P 817 beta 8000 8005 8003 8026 C1' DC P 818 beta 8022 8027 8025 8045 C1' DG P 819 beta 8041 8046 8044 8067 C1' DC P 820 beta 8063 8068 8066 8086 C1' DC P 821 beta 8082 8087 8085 8103 C1' DOC P 822 beta 8107 8095 8104 8124 C1' DG T 703 beta 8120 8125 8123 8146 C1' DG T 704 beta 8142 8147 8145 8168 C1' DT T 705 beta 8164 8169 8167 8188 C1' DG T 706 beta 8184 8189 8187 8210 C1' DG T 707 beta 8206 8211 8209 8232 C1' DG T 708 beta 8228 8233 8231 8254 C1' DC T 709 beta 8250 8255 8253 8273 C1' DG T 710 beta 8269 8274 8272 8295 C1' DC T 711 beta 8291 8296 8294 8314 C1' DC T 712 beta 8310 8315 8313 8333 C1' DC T 713 beta 8329 8334 8332 8352 C1' DG T 714 beta 8348 8353 8351 8374 C1' DA T 715 beta 8370 8375 8373 8395 C1' DA T 716 beta 8391 8396 8394 8416 C1' DC T 717 beta 8412 8417 8415 8435 C1' DA T 718 beta 8431 8436 8434 8456 C1' DG T 719 beta 8452 8457 8455 8478 C1' DG T 720 beta 8474 8479 8477 8500 C1' DG T 721 beta 8496 8501 8499 8522 C1' DA T 722 beta 8518 8523 8521 8543 C1' DC T 723 beta 8539 8544 8542 8562 C1' DT T 724 beta 8558 8563 8561 8582 C1' DG T 725 beta 8578 8583 8581 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7759 C2' DG P 805 7760 7757 7781 C2' DT P 806 7782 7779 7801 C2' DC P 807 7802 7799 7820 C2' DC P 808 7821 7818 7839 C2' DC P 809 7840 7837 7858 C2' DT P 810 7859 7856 7878 C2' DG P 811 7879 7876 7900 C2' DT P 812 7901 7898 7920 C2' DT P 813 7921 7918 7940 C2' DC P 814 7941 7938 7959 C2' DG P 815 7960 7957 7981 C2' DG P 816 7982 7979 8003 C2' DG P 817 8004 8001 8025 C2' DC P 818 8026 8023 8044 C2' DG P 819 8045 8042 8066 C2' DC P 820 8067 8064 8085 C2' DC P 821 8086 8083 8104 C2' DOC P 822 8103 8105 8123 C2' DG T 703 8124 8121 8145 C2' DG T 704 8146 8143 8167 C2' DT T 705 8168 8165 8187 C2' DG T 706 8188 8185 8209 C2' DG T 707 8210 8207 8231 C2' DG T 708 8232 8229 8253 C2' DC T 709 8254 8251 8272 C2' DG T 710 8273 8270 8294 C2' DC T 711 8295 8292 8313 C2' DC T 712 8314 8311 8332 C2' DC T 713 8333 8330 8351 C2' DG T 714 8352 8349 8373 C2' DA T 715 8374 8371 8394 C2' DA T 716 8395 8392 8415 C2' DC T 717 8416 8413 8434 C2' DA T 718 8435 8432 8455 C2' DG T 719 8456 8453 8477 C2' DG T 720 8478 8475 8499 C2' DG T 721 8500 8497 8521 C2' DA T 722 8522 8519 8542 C2' DC T 723 8543 8540 8561 C2' DT T 724 8562 8559 8581 C2' DG T 725 8582 8579 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7757 C3' DG P 805 OK 7755 7758 7759 7779 C3' DT P 806 OK 7777 7780 7781 7799 C3' DC P 807 OK 7797 7800 7801 7818 C3' DC P 808 OK 7816 7819 7820 7837 C3' DC P 809 OK 7835 7838 7839 7856 C3' DT P 810 OK 7854 7857 7858 7876 C3' DG P 811 OK 7874 7877 7878 7898 C3' DT P 812 OK 7896 7899 7900 7918 C3' DT P 813 OK 7916 7919 7920 7938 C3' DC P 814 OK 7936 7939 7940 7957 C3' DG P 815 OK 7955 7958 7959 7979 C3' DG P 816 OK 7977 7980 7981 8001 C3' DG P 817 OK 7999 8002 8003 8023 C3' DC P 818 OK 8021 8024 8025 8042 C3' DG P 819 OK 8040 8043 8044 8064 C3' DC P 820 OK 8062 8065 8066 8083 C3' DC P 821 OK 8081 8084 8085 8105 C3' DOC P 822 8106 8104 8121 C3' DG T 703 OK 8119 8122 8123 8143 C3' DG T 704 OK 8141 8144 8145 8165 C3' DT T 705 OK 8163 8166 8167 8185 C3' DG T 706 OK 8183 8186 8187 8207 C3' DG T 707 OK 8205 8208 8209 8229 C3' DG T 708 OK 8227 8230 8231 8251 C3' DC T 709 OK 8249 8252 8253 8270 C3' DG T 710 OK 8268 8271 8272 8292 C3' DC T 711 OK 8290 8293 8294 8311 C3' DC T 712 OK 8309 8312 8313 8330 C3' DC T 713 OK 8328 8331 8332 8349 C3' DG T 714 OK 8347 8350 8351 8371 C3' DA T 715 OK 8369 8372 8373 8392 C3' DA T 716 OK 8390 8393 8394 8413 C3' DC T 717 OK 8411 8414 8415 8432 C3' DA T 718 OK 8430 8433 8434 8453 C3' DG T 719 OK 8451 8454 8455 8475 C3' DG T 720 OK 8473 8476 8477 8497 C3' DG T 721 OK 8495 8498 8499 8519 C3' DA T 722 OK 8517 8520 8521 8540 C3' DC T 723 OK 8538 8541 8542 8559 C3' DT T 724 OK 8557 8560 8561 8579 C3' DG T 725 OK 8577 8580 8581 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7755 C4' DG P 805 OK 7757 7754 7756 7777 C4' DT P 806 OK 7779 7776 7778 7797 C4' DC P 807 OK 7799 7796 7798 7816 C4' DC P 808 OK 7818 7815 7817 7835 C4' DC P 809 OK 7837 7834 7836 7854 C4' DT P 810 OK 7856 7853 7855 7874 C4' DG P 811 OK 7876 7873 7875 7896 C4' DT P 812 OK 7898 7895 7897 7916 C4' DT P 813 OK 7918 7915 7917 7936 C4' DC P 814 OK 7938 7935 7937 7955 C4' DG P 815 OK 7957 7954 7956 7977 C4' DG P 816 OK 7979 7976 7978 7999 C4' DG P 817 OK 8001 7998 8000 8021 C4' DC P 818 OK 8023 8020 8022 8040 C4' DG P 819 OK 8042 8039 8041 8062 C4' DC P 820 OK 8064 8061 8063 8081 C4' DC P 821 OK 8083 8080 8082 8106 C4' DOC P 822 OK 8105 8108 8107 8119 C4' DG T 703 OK 8121 8118 8120 8141 C4' DG T 704 OK 8143 8140 8142 8163 C4' DT T 705 OK 8165 8162 8164 8183 C4' DG T 706 OK 8185 8182 8184 8205 C4' DG T 707 OK 8207 8204 8206 8227 C4' DG T 708 OK 8229 8226 8228 8249 C4' DC T 709 OK 8251 8248 8250 8268 C4' DG T 710 OK 8270 8267 8269 8290 C4' DC T 711 OK 8292 8289 8291 8309 C4' DC T 712 OK 8311 8308 8310 8328 C4' DC T 713 OK 8330 8327 8329 8347 C4' DG T 714 OK 8349 8346 8348 8369 C4' DA T 715 OK 8371 8368 8370 8390 C4' DA T 716 OK 8392 8389 8391 8411 C4' DC T 717 OK 8413 8410 8412 8430 C4' DA T 718 OK 8432 8429 8431 8451 C4' DG T 719 OK 8453 8450 8452 8473 C4' DG T 720 OK 8475 8472 8474 8495 C4' DG T 721 OK 8497 8494 8496 8517 C4' DA T 722 OK 8519 8516 8518 8538 C4' DC T 723 OK 8540 8537 8539 8557 C4' DT T 724 OK 8559 8556 8558 8577 C4' DG T 725 OK 8579 8576 8578 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7754 C5' DG P 805 7753 7755 7776 C5' DT P 806 7775 7777 7796 C5' DC P 807 7795 7797 7815 C5' DC P 808 7814 7816 7834 C5' DC P 809 7833 7835 7853 C5' DT P 810 7852 7854 7873 C5' DG P 811 7872 7874 7895 C5' DT P 812 7894 7896 7915 C5' DT P 813 7914 7916 7935 C5' DC P 814 7934 7936 7954 C5' DG P 815 7953 7955 7976 C5' DG P 816 7975 7977 7998 C5' DG P 817 7997 7999 8020 C5' DC P 818 8019 8021 8039 C5' DG P 819 8038 8040 8061 C5' DC P 820 8060 8062 8080 C5' DC P 821 8079 8081 8108 C5' DOC P 822 8109 8106 8118 C5' DG T 703 8117 8119 8140 C5' DG T 704 8139 8141 8162 C5' DT T 705 8161 8163 8182 C5' DG T 706 8181 8183 8204 C5' DG T 707 8203 8205 8226 C5' DG T 708 8225 8227 8248 C5' DC T 709 8247 8249 8267 C5' DG T 710 8266 8268 8289 C5' DC T 711 8288 8290 8308 C5' DC T 712 8307 8309 8327 C5' DC T 713 8326 8328 8346 C5' DG T 714 8345 8347 8368 C5' DA T 715 8367 8369 8389 C5' DA T 716 8388 8390 8410 C5' DC T 717 8409 8411 8429 C5' DA T 718 8428 8430 8450 C5' DG T 719 8449 8451 8472 C5' DG T 720 8471 8473 8494 C5' DG T 721 8493 8495 8516 C5' DA T 722 8515 8517 8537 C5' DC T 723 8536 8538 8556 C5' DT T 724 8555 8557 8576 C5' DG T 725 8575 8577 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7750 P DG P 805 distorted distorted 7751 7752 7753 7772 P DT P 806 distorted distorted 7758 7773 7774 7775 7792 P DC P 807 distorted distorted 7780 7793 7794 7795 7811 P DC P 808 distorted distorted 7800 7812 7813 7814 7830 P DC P 809 distorted distorted 7819 7831 7832 7833 7849 P DT P 810 distorted distorted 7838 7850 7851 7852 7869 P DG P 811 distorted distorted 7857 7870 7871 7872 7891 P DT P 812 distorted distorted 7877 7892 7893 7894 7911 P DT P 813 distorted distorted 7899 7912 7913 7914 7931 P DC P 814 distorted distorted 7919 7932 7933 7934 7950 P DG P 815 distorted distorted 7939 7951 7952 7953 7972 P DG P 816 distorted distorted 7958 7973 7974 7975 7994 P DG P 817 distorted distorted 7980 7995 7996 7997 8016 P DC P 818 distorted distorted 8002 8017 8018 8019 8035 P DG P 819 distorted distorted 8024 8036 8037 8038 8057 P DC P 820 distorted distorted 8043 8058 8059 8060 8076 P DC P 821 distorted distorted 8065 8077 8078 8079 8110 P DOC P 822 distorted distorted 8084 8111 8112 8109 8114 P DG T 703 distorted distorted 8115 8116 8117 8136 P DG T 704 distorted distorted 8122 8137 8138 8139 8158 P DT T 705 distorted distorted 8144 8159 8160 8161 8178 P DG T 706 distorted distorted 8166 8179 8180 8181 8200 P DG T 707 distorted distorted 8186 8201 8202 8203 8222 P DG T 708 distorted distorted 8208 8223 8224 8225 8244 P DC T 709 distorted distorted 8230 8245 8246 8247 8263 P DG T 710 distorted distorted 8252 8264 8265 8266 8285 P DC T 711 distorted distorted 8271 8286 8287 8288 8304 P DC T 712 distorted distorted 8293 8305 8306 8307 8323 P DC T 713 distorted distorted 8312 8324 8325 8326 8342 P DG T 714 distorted distorted 8331 8343 8344 8345 8364 P DA T 715 distorted distorted 8350 8365 8366 8367 8385 P DA T 716 distorted distorted 8372 8386 8387 8388 8406 P DC T 717 distorted distorted 8393 8407 8408 8409 8425 P DA T 718 distorted distorted 8414 8426 8427 8428 8446 P DG T 719 distorted distorted 8433 8447 8448 8449 8468 P DG T 720 distorted distorted 8454 8469 8470 8471 8490 P DG T 721 distorted distorted 8476 8491 8492 8493 8512 P DA T 722 distorted distorted 8498 8513 8514 8515 8533 P DC T 723 distorted distorted 8520 8534 8535 8536 8552 P DT T 724 distorted distorted 8541 8553 8554 8555 8572 P DG T 725 distorted distorted 8560 8573 8574 8575 ---------------------------------------------------------------------------------