ID code: '3MAQ' 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' --------------------------------------------------------------------------------- 6315 C1' DT T 802 beta 6311 6316 6314 6335 C1' DA T 803 beta 6331 6336 6334 6356 C1' DC T 804 beta 6352 6357 6355 6375 C1' DG T 805 beta 6371 6376 6374 6397 C1' DT T 806 beta 6393 6398 6396 6417 C1' DA T 807 beta 6413 6418 6416 6438 C1' DC T 808 beta 6434 6439 6437 6457 C1' DG T 809 beta 6453 6458 6456 6479 C1' DC T 810 beta 6475 6480 6478 6498 C1' DT T 811 beta 6494 6499 6497 6518 C1' DA T 812 beta 6514 6519 6517 6539 C1' DG T 813 beta 6535 6540 6538 6561 C1' DG T 814 beta 6557 6562 6560 6583 C1' DC T 815 beta 6579 6584 6582 6602 C1' DA T 816 beta 6598 6603 6601 6623 C1' DC T 817 beta 6619 6624 6622 6642 C1' DA T 818 beta 6638 6643 6641 6661 C1' DG P 901 beta 6657 6662 6660 6683 C1' DT P 902 beta 6679 6684 6682 6703 C1' DG P 903 beta 6699 6704 6702 6725 C1' DC P 904 beta 6721 6726 6724 6744 C1' DC P 905 beta 6740 6745 6743 6763 C1' DT P 906 beta 6759 6764 6762 6783 C1' DA P 907 beta 6779 6784 6782 6804 C1' DG P 908 beta 6800 6805 6803 6826 C1' DC P 909 beta 6822 6827 6825 6845 C1' DG P 910 beta 6841 6846 6844 6867 C1' DT P 911 beta 6863 6868 6866 6887 C1' DA P 912 beta 6883 6888 6886 6906 C1' DOC P 913 beta 6910 6898 6907 6936 C1' DGT A 914 beta 6932 6937 6935 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 6314 C2' DT T 802 6315 6312 6334 C2' DA T 803 6335 6332 6355 C2' DC T 804 6356 6353 6374 C2' DG T 805 6375 6372 6396 C2' DT T 806 6397 6394 6416 C2' DA T 807 6417 6414 6437 C2' DC T 808 6438 6435 6456 C2' DG T 809 6457 6454 6478 C2' DC T 810 6479 6476 6497 C2' DT T 811 6498 6495 6517 C2' DA T 812 6518 6515 6538 C2' DG T 813 6539 6536 6560 C2' DG T 814 6561 6558 6582 C2' DC T 815 6583 6580 6601 C2' DA T 816 6602 6599 6622 C2' DC T 817 6623 6620 6641 C2' DA T 818 6642 6639 6660 C2' DG P 901 6661 6658 6682 C2' DT P 902 6683 6680 6702 C2' DG P 903 6703 6700 6724 C2' DC P 904 6725 6722 6743 C2' DC P 905 6744 6741 6762 C2' DT P 906 6763 6760 6782 C2' DA P 907 6783 6780 6803 C2' DG P 908 6804 6801 6825 C2' DC P 909 6826 6823 6844 C2' DG P 910 6845 6842 6866 C2' DT P 911 6867 6864 6886 C2' DA P 912 6887 6884 6907 C2' DOC P 913 6906 6908 6935 C2' DGT A 914 6936 6933 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 6312 C3' DT T 802 OK 6310 6313 6314 6332 C3' DA T 803 OK 6330 6333 6334 6353 C3' DC T 804 OK 6351 6354 6355 6372 C3' DG T 805 OK 6370 6373 6374 6394 C3' DT T 806 OK 6392 6395 6396 6414 C3' DA T 807 OK 6412 6415 6416 6435 C3' DC T 808 OK 6433 6436 6437 6454 C3' DG T 809 OK 6452 6455 6456 6476 C3' DC T 810 OK 6474 6477 6478 6495 C3' DT T 811 OK 6493 6496 6497 6515 C3' DA T 812 OK 6513 6516 6517 6536 C3' DG T 813 OK 6534 6537 6538 6558 C3' DG T 814 OK 6556 6559 6560 6580 C3' DC T 815 OK 6578 6581 6582 6599 C3' DA T 816 OK 6597 6600 6601 6620 C3' DC T 817 OK 6618 6621 6622 6639 C3' DA T 818 OK 6637 6640 6641 6658 C3' DG P 901 OK 6656 6659 6660 6680 C3' DT P 902 OK 6678 6681 6682 6700 C3' DG P 903 OK 6698 6701 6702 6722 C3' DC P 904 OK 6720 6723 6724 6741 C3' DC P 905 OK 6739 6742 6743 6760 C3' DT P 906 OK 6758 6761 6762 6780 C3' DA P 907 OK 6778 6781 6782 6801 C3' DG P 908 OK 6799 6802 6803 6823 C3' DC P 909 OK 6821 6824 6825 6842 C3' DG P 910 OK 6840 6843 6844 6864 C3' DT P 911 OK 6862 6865 6866 6884 C3' DA P 912 OK 6882 6885 6886 6908 C3' DOC P 913 6909 6907 6933 C3' DGT A 914 OK 6931 6934 6935 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6310 C4' DT T 802 OK 6312 6309 6311 6330 C4' DA T 803 OK 6332 6329 6331 6351 C4' DC T 804 OK 6353 6350 6352 6370 C4' DG T 805 OK 6372 6369 6371 6392 C4' DT T 806 OK 6394 6391 6393 6412 C4' DA T 807 OK 6414 6411 6413 6433 C4' DC T 808 OK 6435 6432 6434 6452 C4' DG T 809 OK 6454 6451 6453 6474 C4' DC T 810 OK 6476 6473 6475 6493 C4' DT T 811 OK 6495 6492 6494 6513 C4' DA T 812 OK 6515 6512 6514 6534 C4' DG T 813 OK 6536 6533 6535 6556 C4' DG T 814 OK 6558 6555 6557 6578 C4' DC T 815 OK 6580 6577 6579 6597 C4' DA T 816 OK 6599 6596 6598 6618 C4' DC T 817 OK 6620 6617 6619 6637 C4' DA T 818 OK 6639 6636 6638 6656 C4' DG P 901 OK 6658 6655 6657 6678 C4' DT P 902 OK 6680 6677 6679 6698 C4' DG P 903 OK 6700 6697 6699 6720 C4' DC P 904 OK 6722 6719 6721 6739 C4' DC P 905 OK 6741 6738 6740 6758 C4' DT P 906 OK 6760 6757 6759 6778 C4' DA P 907 OK 6780 6777 6779 6799 C4' DG P 908 OK 6801 6798 6800 6821 C4' DC P 909 OK 6823 6820 6822 6840 C4' DG P 910 OK 6842 6839 6841 6862 C4' DT P 911 OK 6864 6861 6863 6882 C4' DA P 912 OK 6884 6881 6883 6909 C4' DOC P 913 OK 6908 6911 6910 6931 C4' DGT A 914 OK 6933 6930 6932 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6309 C5' DT T 802 6308 6310 6329 C5' DA T 803 6328 6330 6350 C5' DC T 804 6349 6351 6369 C5' DG T 805 6368 6370 6391 C5' DT T 806 6390 6392 6411 C5' DA T 807 6410 6412 6432 C5' DC T 808 6431 6433 6451 C5' DG T 809 6450 6452 6473 C5' DC T 810 6472 6474 6492 C5' DT T 811 6491 6493 6512 C5' DA T 812 6511 6513 6533 C5' DG T 813 6532 6534 6555 C5' DG T 814 6554 6556 6577 C5' DC T 815 6576 6578 6596 C5' DA T 816 6595 6597 6617 C5' DC T 817 6616 6618 6636 C5' DA T 818 6635 6637 6655 C5' DG P 901 6654 6656 6677 C5' DT P 902 6676 6678 6697 C5' DG P 903 6696 6698 6719 C5' DC P 904 6718 6720 6738 C5' DC P 905 6737 6739 6757 C5' DT P 906 6756 6758 6777 C5' DA P 907 6776 6778 6798 C5' DG P 908 6797 6799 6820 C5' DC P 909 6819 6821 6839 C5' DG P 910 6838 6840 6861 C5' DT P 911 6860 6862 6881 C5' DA P 912 6880 6882 6911 C5' DOC P 913 6912 6909 6930 C5' DGT A 914 6929 6931 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 6325 P DA T 803 distorted distorted 6313 6326 6327 6328 6346 P DC T 804 distorted distorted 6333 6347 6348 6349 6365 P DG T 805 distorted distorted 6354 6366 6367 6368 6387 P DT T 806 distorted distorted 6373 6388 6389 6390 6407 P DA T 807 distorted distorted 6395 6408 6409 6410 6428 P DC T 808 distorted distorted 6415 6429 6430 6431 6447 P DG T 809 distorted distorted 6436 6448 6449 6450 6469 P DC T 810 distorted distorted 6455 6470 6471 6472 6488 P DT T 811 distorted distorted 6477 6489 6490 6491 6508 P DA T 812 distorted distorted 6496 6509 6510 6511 6529 P DG T 813 distorted distorted 6516 6530 6531 6532 6551 P DG T 814 distorted distorted 6537 6552 6553 6554 6573 P DC T 815 distorted distorted 6559 6574 6575 6576 6592 P DA T 816 distorted distorted 6581 6593 6594 6595 6613 P DC T 817 distorted distorted 6600 6614 6615 6616 6632 P DA T 818 distorted distorted 6621 6633 6634 6635 6673 P DT P 902 distorted distorted 6659 6674 6675 6676 6693 P DG P 903 distorted distorted 6681 6694 6695 6696 6715 P DC P 904 distorted distorted 6701 6716 6717 6718 6734 P DC P 905 distorted distorted 6723 6735 6736 6737 6753 P DT P 906 distorted distorted 6742 6754 6755 6756 6773 P DA P 907 distorted distorted 6761 6774 6775 6776 6794 P DG P 908 distorted distorted 6781 6795 6796 6797 6816 P DC P 909 distorted distorted 6802 6817 6818 6819 6835 P DG P 910 distorted distorted 6824 6836 6837 6838 6857 P DT P 911 distorted distorted 6843 6858 6859 6860 6877 P DA P 912 distorted distorted 6865 6878 6879 6880 6913 P DOC P 913 distorted distorted 6885 6914 6915 6912 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