ID code: '2YJY' 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' --------------------------------------------------------------------------------- 5504 C1' A C -1 beta 5499 5505 5502 5526 C1' U C 0 beta 5521 5527 5524 5546 C1' U C 1 beta 5541 5547 5544 5566 C1' G C 2 beta 5561 5567 5564 5589 C1' C C 3 beta 5584 5590 5587 5609 C1' A C 4 beta 5604 5610 5607 5631 C1' U C 5 beta 5626 5632 5629 5651 C1' A C 6 beta 5646 5652 5649 5673 C1' U C 7 beta 5668 5674 5671 5693 C1' A C 8 beta 5688 5694 5691 5716 C1' A D -1 beta 5711 5717 5714 5738 C1' U D 0 beta 5733 5739 5736 5758 C1' U D 1 beta 5753 5759 5756 5778 C1' G D 2 beta 5773 5779 5776 5801 C1' C D 3 beta 5796 5802 5799 5821 C1' A D 4 beta 5816 5822 5819 5843 C1' U D 5 beta 5838 5844 5841 5863 C1' A D 6 beta 5858 5864 5861 5885 C1' U D 7 beta 5880 5886 5883 5905 C1' A D 8 beta 5900 5906 5903 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5502 C2' A C -1 OK 5504 5500 5503 5524 C2' U C 0 OK 5526 5522 5525 5544 C2' U C 1 OK 5546 5542 5545 5564 C2' G C 2 OK 5566 5562 5565 5587 C2' C C 3 OK 5589 5585 5588 5607 C2' A C 4 OK 5609 5605 5608 5629 C2' U C 5 OK 5631 5627 5630 5649 C2' A C 6 OK 5651 5647 5650 5671 C2' U C 7 OK 5673 5669 5672 5691 C2' A C 8 OK 5693 5689 5692 5714 C2' A D -1 OK 5716 5712 5715 5736 C2' U D 0 OK 5738 5734 5737 5756 C2' U D 1 OK 5758 5754 5757 5776 C2' G D 2 OK 5778 5774 5777 5799 C2' C D 3 OK 5801 5797 5800 5819 C2' A D 4 OK 5821 5817 5820 5841 C2' U D 5 OK 5843 5839 5842 5861 C2' A D 6 OK 5863 5859 5862 5883 C2' U D 7 OK 5885 5881 5884 5903 C2' A D 8 OK 5905 5901 5904 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5500 C3' A C -1 OK 5498 5501 5502 5522 C3' U C 0 OK 5520 5523 5524 5542 C3' U C 1 OK 5540 5543 5544 5562 C3' G C 2 OK 5560 5563 5564 5585 C3' C C 3 OK 5583 5586 5587 5605 C3' A C 4 OK 5603 5606 5607 5627 C3' U C 5 OK 5625 5628 5629 5647 C3' A C 6 OK 5645 5648 5649 5669 C3' U C 7 OK 5667 5670 5671 5689 C3' A C 8 OK 5687 5690 5691 5712 C3' A D -1 OK 5710 5713 5714 5734 C3' U D 0 OK 5732 5735 5736 5754 C3' U D 1 OK 5752 5755 5756 5774 C3' G D 2 OK 5772 5775 5776 5797 C3' C D 3 OK 5795 5798 5799 5817 C3' A D 4 OK 5815 5818 5819 5839 C3' U D 5 OK 5837 5840 5841 5859 C3' A D 6 OK 5857 5860 5861 5881 C3' U D 7 OK 5879 5882 5883 5901 C3' A D 8 OK 5899 5902 5903 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5498 C4' A C -1 OK 5500 5497 5499 5520 C4' U C 0 OK 5522 5519 5521 5540 C4' U C 1 OK 5542 5539 5541 5560 C4' G C 2 OK 5562 5559 5561 5583 C4' C C 3 OK 5585 5582 5584 5603 C4' A C 4 OK 5605 5602 5604 5625 C4' U C 5 OK 5627 5624 5626 5645 C4' A C 6 OK 5647 5644 5646 5667 C4' U C 7 OK 5669 5666 5668 5687 C4' A C 8 OK 5689 5686 5688 5710 C4' A D -1 OK 5712 5709 5711 5732 C4' U D 0 OK 5734 5731 5733 5752 C4' U D 1 OK 5754 5751 5753 5772 C4' G D 2 OK 5774 5771 5773 5795 C4' C D 3 OK 5797 5794 5796 5815 C4' A D 4 OK 5817 5814 5816 5837 C4' U D 5 OK 5839 5836 5838 5857 C4' A D 6 OK 5859 5856 5858 5879 C4' U D 7 OK 5881 5878 5880 5899 C4' A D 8 OK 5901 5898 5900 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5497 C5' A C -1 5496 5498 5519 C5' U C 0 5518 5520 5539 C5' U C 1 5538 5540 5559 C5' G C 2 5558 5560 5582 C5' C C 3 5581 5583 5602 C5' A C 4 5601 5603 5624 C5' U C 5 5623 5625 5644 C5' A C 6 5643 5645 5666 C5' U C 7 5665 5667 5686 C5' A C 8 5685 5687 5709 C5' A D -1 5708 5710 5731 C5' U D 0 5730 5732 5751 C5' U D 1 5750 5752 5771 C5' G D 2 5770 5772 5794 C5' C D 3 5793 5795 5814 C5' A D 4 5813 5815 5836 C5' U D 5 5835 5837 5856 C5' A D 6 5855 5857 5878 C5' U D 7 5877 5879 5898 C5' A D 8 5897 5899 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5493 P A C -1 distorted distorted 5494 5495 5496 5515 P U C 0 distorted distorted 5501 5516 5517 5518 5535 P U C 1 distorted distorted 5523 5536 5537 5538 5555 P G C 2 distorted distorted 5543 5556 5557 5558 5578 P C C 3 distorted distorted 5563 5579 5580 5581 5598 P A C 4 distorted distorted 5586 5599 5600 5601 5620 P U C 5 OK OK 5606 5621 5622 5623 5640 P A C 6 distorted distorted 5628 5641 5642 5643 5662 P U C 7 distorted distorted 5648 5663 5664 5665 5682 P A C 8 distorted distorted 5670 5683 5684 5685 5705 P A D -1 distorted distorted 5706 5707 5708 5727 P U D 0 distorted distorted 5713 5728 5729 5730 5747 P U D 1 distorted distorted 5735 5748 5749 5750 5767 P G D 2 OK OK 5755 5768 5769 5770 5790 P C D 3 OK OK 5775 5791 5792 5793 5810 P A D 4 distorted distorted 5798 5811 5812 5813 5832 P U D 5 distorted distorted 5818 5833 5834 5835 5852 P A D 6 OK OK 5840 5853 5854 5855 5874 P U D 7 distorted distorted 5860 5875 5876 5877 5894 P A D 8 distorted distorted 5882 5895 5896 5897 ---------------------------------------------------------------------------------