ID code: '5JB2' 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' GTP X 1 beta 5632 5638 5635 5660 C1' G X 2 beta 5655 5661 5658 5683 C1' U X 3 beta 5678 5684 5681 5703 C1' A X 4 beta 5698 5704 5701 5725 C1' C X 5 beta 5720 5726 5723 5745 C1' G X 6 beta 5740 5746 5743 5768 C1' U X 7 beta 5763 5769 5766 5788 C1' A X 8 beta 5783 5789 5786 5810 C1' C X 9 beta 5805 5811 5808 5830 C1' C X 10 beta 5825 5831 5828 5850 C1' C X 11 beta 5845 5851 5848 5880 C1' GTP Y 1 beta 5875 5881 5878 5903 C1' G Y 2 beta 5898 5904 5901 5926 C1' U Y 3 beta 5921 5927 5924 5946 C1' A Y 4 beta 5941 5947 5944 5968 C1' C Y 5 beta 5963 5969 5966 5988 C1' G Y 6 beta 5983 5989 5986 6011 C1' U Y 7 beta 6006 6012 6009 6031 C1' A Y 8 beta 6026 6032 6029 6053 C1' C Y 9 beta 6048 6054 6051 6073 C1' C Y 10 beta 6068 6074 6071 6100 C1' ADP A 702 beta 6095 6101 6098 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5635 C2' GTP X 1 OK 5637 5633 5636 5658 C2' G X 2 OK 5660 5656 5659 5681 C2' U X 3 OK 5683 5679 5682 5701 C2' A X 4 OK 5703 5699 5702 5723 C2' C X 5 OK 5725 5721 5724 5743 C2' G X 6 OK 5745 5741 5744 5766 C2' U X 7 OK 5768 5764 5767 5786 C2' A X 8 OK 5788 5784 5787 5808 C2' C X 9 OK 5810 5806 5809 5828 C2' C X 10 OK 5830 5826 5829 5848 C2' C X 11 OK 5850 5846 5849 5878 C2' GTP Y 1 OK 5880 5876 5879 5901 C2' G Y 2 OK 5903 5899 5902 5924 C2' U Y 3 OK 5926 5922 5925 5944 C2' A Y 4 OK 5946 5942 5945 5966 C2' C Y 5 OK 5968 5964 5967 5986 C2' G Y 6 OK 5988 5984 5987 6009 C2' U Y 7 OK 6011 6007 6010 6029 C2' A Y 8 OK 6031 6027 6030 6051 C2' C Y 9 OK 6053 6049 6052 6071 C2' C Y 10 OK 6073 6069 6072 6098 C2' ADP A 702 OK 6100 6096 6099 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5633 C3' GTP X 1 OK 5631 5634 5635 5656 C3' G X 2 OK 5654 5657 5658 5679 C3' U X 3 OK 5677 5680 5681 5699 C3' A X 4 OK 5697 5700 5701 5721 C3' C X 5 OK 5719 5722 5723 5741 C3' G X 6 OK 5739 5742 5743 5764 C3' U X 7 OK 5762 5765 5766 5784 C3' A X 8 OK 5782 5785 5786 5806 C3' C X 9 OK 5804 5807 5808 5826 C3' C X 10 OK 5824 5827 5828 5846 C3' C X 11 OK 5844 5847 5848 5876 C3' GTP Y 1 OK 5874 5877 5878 5899 C3' G Y 2 OK 5897 5900 5901 5922 C3' U Y 3 OK 5920 5923 5924 5942 C3' A Y 4 OK 5940 5943 5944 5964 C3' C Y 5 OK 5962 5965 5966 5984 C3' G Y 6 OK 5982 5985 5986 6007 C3' U Y 7 OK 6005 6008 6009 6027 C3' A Y 8 OK 6025 6028 6029 6049 C3' C Y 9 OK 6047 6050 6051 6069 C3' C Y 10 OK 6067 6070 6071 6096 C3' ADP A 702 OK 6094 6097 6098 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 5631 C4' GTP X 1 OK 5633 5630 5632 5654 C4' G X 2 OK 5656 5653 5655 5677 C4' U X 3 OK 5679 5676 5678 5697 C4' A X 4 OK 5699 5696 5698 5719 C4' C X 5 OK 5721 5718 5720 5739 C4' G X 6 OK 5741 5738 5740 5762 C4' U X 7 OK 5764 5761 5763 5782 C4' A X 8 OK 5784 5781 5783 5804 C4' C X 9 OK 5806 5803 5805 5824 C4' C X 10 OK 5826 5823 5825 5844 C4' C X 11 OK 5846 5843 5845 5874 C4' GTP Y 1 OK 5876 5873 5875 5897 C4' G Y 2 OK 5899 5896 5898 5920 C4' U Y 3 OK 5922 5919 5921 5940 C4' A Y 4 OK 5942 5939 5941 5962 C4' C Y 5 OK 5964 5961 5963 5982 C4' G Y 6 OK 5984 5981 5983 6005 C4' U Y 7 OK 6007 6004 6006 6025 C4' A Y 8 OK 6027 6024 6026 6047 C4' C Y 9 OK 6049 6046 6048 6067 C4' C Y 10 OK 6069 6066 6068 6094 C4' ADP A 702 OK 6096 6093 6095 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5630 C5' GTP X 1 5629 5631 5653 C5' G X 2 5652 5654 5676 C5' U X 3 5675 5677 5696 C5' A X 4 5695 5697 5718 C5' C X 5 5717 5719 5738 C5' G X 6 5737 5739 5761 C5' U X 7 5760 5762 5781 C5' A X 8 5780 5782 5803 C5' C X 9 5802 5804 5823 C5' C X 10 5822 5824 5843 C5' C X 11 5842 5844 5873 C5' GTP Y 1 5872 5874 5896 C5' G Y 2 5895 5897 5919 C5' U Y 3 5918 5920 5939 C5' A Y 4 5938 5940 5961 C5' C Y 5 5960 5962 5981 C5' G Y 6 5980 5982 6004 C5' U Y 7 6003 6005 6024 C5' A Y 8 6023 6025 6046 C5' C Y 9 6045 6047 6066 C5' C Y 10 6065 6067 6093 C5' ADP A 702 6092 6094 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 5649 P G X 2 distorted distorted 5634 5650 5651 5652 5672 P U X 3 distorted distorted 5657 5673 5674 5675 5692 P A X 4 distorted distorted 5680 5693 5694 5695 5714 P C X 5 distorted distorted 5700 5715 5716 5717 5734 P G X 6 distorted distorted 5722 5735 5736 5737 5757 P U X 7 distorted distorted 5742 5758 5759 5760 5777 P A X 8 distorted distorted 5765 5778 5779 5780 5799 P C X 9 distorted distorted 5785 5800 5801 5802 5819 P C X 10 distorted distorted 5807 5820 5821 5822 5839 P C X 11 distorted distorted 5827 5840 5841 5842 5892 P G Y 2 distorted distorted 5877 5893 5894 5895 5915 P U Y 3 distorted distorted 5900 5916 5917 5918 5935 P A Y 4 distorted distorted 5923 5936 5937 5938 5957 P C Y 5 distorted distorted 5943 5958 5959 5960 5977 P G Y 6 distorted distorted 5965 5978 5979 5980 6000 P U Y 7 distorted distorted 5985 6001 6002 6003 6020 P A Y 8 distorted distorted 6008 6021 6022 6023 6042 P C Y 9 distorted distorted 6028 6043 6044 6045 6062 P C Y 10 distorted distorted 6050 6063 6064 6065 ---------------------------------------------------------------------------------