ID code: '5JAJ' 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' --------------------------------------------------------------------------------- 5637 C1' U X 3 beta 5632 5638 5635 5657 C1' A X 4 beta 5652 5658 5655 5679 C1' C X 5 beta 5674 5680 5677 5699 C1' G X 6 beta 5694 5700 5697 5722 C1' U X 7 beta 5717 5723 5720 5742 C1' A X 8 beta 5737 5743 5740 5764 C1' C X 9 beta 5759 5765 5762 5784 C1' C X 10 beta 5779 5785 5782 5804 C1' C X 11 beta 5799 5805 5802 5826 C1' G Y 1 beta 5821 5827 5824 5849 C1' G Y 2 beta 5844 5850 5847 5872 C1' U Y 3 beta 5867 5873 5870 5892 C1' A Y 4 beta 5887 5893 5890 5914 C1' C Y 5 beta 5909 5915 5912 5934 C1' G Y 6 beta 5929 5935 5932 5957 C1' U Y 7 beta 5952 5958 5955 5977 C1' A Y 8 beta 5972 5978 5975 5999 C1' C Y 9 beta 5994 6000 5997 6019 C1' C Y 10 beta 6014 6020 6017 6046 C1' ADP A 702 beta 6041 6047 6044 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5635 C2' U X 3 OK 5637 5633 5636 5655 C2' A X 4 OK 5657 5653 5656 5677 C2' C X 5 OK 5679 5675 5678 5697 C2' G X 6 OK 5699 5695 5698 5720 C2' U X 7 OK 5722 5718 5721 5740 C2' A X 8 OK 5742 5738 5741 5762 C2' C X 9 OK 5764 5760 5763 5782 C2' C X 10 OK 5784 5780 5783 5802 C2' C X 11 OK 5804 5800 5803 5824 C2' G Y 1 OK 5826 5822 5825 5847 C2' G Y 2 OK 5849 5845 5848 5870 C2' U Y 3 OK 5872 5868 5871 5890 C2' A Y 4 OK 5892 5888 5891 5912 C2' C Y 5 OK 5914 5910 5913 5932 C2' G Y 6 OK 5934 5930 5933 5955 C2' U Y 7 OK 5957 5953 5956 5975 C2' A Y 8 OK 5977 5973 5976 5997 C2' C Y 9 OK 5999 5995 5998 6017 C2' C Y 10 OK 6019 6015 6018 6044 C2' ADP A 702 OK 6046 6042 6045 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5633 C3' U X 3 OK 5631 5634 5635 5653 C3' A X 4 OK 5651 5654 5655 5675 C3' C X 5 OK 5673 5676 5677 5695 C3' G X 6 OK 5693 5696 5697 5718 C3' U X 7 OK 5716 5719 5720 5738 C3' A X 8 OK 5736 5739 5740 5760 C3' C X 9 OK 5758 5761 5762 5780 C3' C X 10 OK 5778 5781 5782 5800 C3' C X 11 OK 5798 5801 5802 5822 C3' G Y 1 OK 5820 5823 5824 5845 C3' G Y 2 OK 5843 5846 5847 5868 C3' U Y 3 OK 5866 5869 5870 5888 C3' A Y 4 OK 5886 5889 5890 5910 C3' C Y 5 OK 5908 5911 5912 5930 C3' G Y 6 OK 5928 5931 5932 5953 C3' U Y 7 OK 5951 5954 5955 5973 C3' A Y 8 OK 5971 5974 5975 5995 C3' C Y 9 OK 5993 5996 5997 6015 C3' C Y 10 OK 6013 6016 6017 6042 C3' ADP A 702 OK 6040 6043 6044 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5631 C4' U X 3 OK 5633 5630 5632 5651 C4' A X 4 OK 5653 5650 5652 5673 C4' C X 5 OK 5675 5672 5674 5693 C4' G X 6 OK 5695 5692 5694 5716 C4' U X 7 OK 5718 5715 5717 5736 C4' A X 8 OK 5738 5735 5737 5758 C4' C X 9 OK 5760 5757 5759 5778 C4' C X 10 OK 5780 5777 5779 5798 C4' C X 11 OK 5800 5797 5799 5820 C4' G Y 1 OK 5822 5819 5821 5843 C4' G Y 2 OK 5845 5842 5844 5866 C4' U Y 3 OK 5868 5865 5867 5886 C4' A Y 4 OK 5888 5885 5887 5908 C4' C Y 5 OK 5910 5907 5909 5928 C4' G Y 6 OK 5930 5927 5929 5951 C4' U Y 7 OK 5953 5950 5952 5971 C4' A Y 8 OK 5973 5970 5972 5993 C4' C Y 9 OK 5995 5992 5994 6013 C4' C Y 10 OK 6015 6012 6014 6040 C4' ADP A 702 OK 6042 6039 6041 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5630 C5' U X 3 5629 5631 5650 C5' A X 4 5649 5651 5672 C5' C X 5 5671 5673 5692 C5' G X 6 5691 5693 5715 C5' U X 7 5714 5716 5735 C5' A X 8 5734 5736 5757 C5' C X 9 5756 5758 5777 C5' C X 10 5776 5778 5797 C5' C X 11 5796 5798 5819 C5' G Y 1 5818 5820 5842 C5' G Y 2 5841 5843 5865 C5' U Y 3 5864 5866 5885 C5' A Y 4 5884 5886 5907 C5' C Y 5 5906 5908 5927 C5' G Y 6 5926 5928 5950 C5' U Y 7 5949 5951 5970 C5' A Y 8 5969 5971 5992 C5' C Y 9 5991 5993 6012 C5' C Y 10 6011 6013 6039 C5' ADP A 702 6038 6040 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5534 P G X 1 5535 P G X 1 5580 P G X 2 5581 P G X 2 5626 P U X 3 distorted distorted 5627 5628 5629 5646 P A X 4 distorted distorted 5634 5647 5648 5649 5668 P C X 5 distorted distorted 5654 5669 5670 5671 5688 P G X 6 distorted distorted 5676 5689 5690 5691 5711 P U X 7 distorted distorted 5696 5712 5713 5714 5731 P A X 8 distorted distorted 5719 5732 5733 5734 5753 P C X 9 distorted distorted 5739 5754 5755 5756 5773 P C X 10 distorted distorted 5761 5774 5775 5776 5793 P C X 11 distorted distorted 5781 5794 5795 5796 5815 P G Y 1 distorted distorted 5816 5817 5818 5838 P G Y 2 distorted distorted 5823 5839 5840 5841 5861 P U Y 3 distorted distorted 5846 5862 5863 5864 5881 P A Y 4 distorted distorted 5869 5882 5883 5884 5903 P C Y 5 distorted distorted 5889 5904 5905 5906 5923 P G Y 6 distorted distorted 5911 5924 5925 5926 5946 P U Y 7 distorted distorted 5931 5947 5948 5949 5966 P A Y 8 distorted distorted 5954 5967 5968 5969 5988 P C Y 9 distorted distorted 5974 5989 5990 5991 6008 P C Y 10 distorted distorted 5996 6009 6010 6011 ---------------------------------------------------------------------------------