ID code: '3UZT' 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' --------------------------------------------------------------------------------- 4819 C1' C B 47 beta 4814 4820 4817 4839 C1' C B 48 beta 4834 4840 4837 4859 C1' A B 49 beta 4854 4860 4857 4881 C1' U B 50 beta 4876 4882 4879 4901 C1' A B 51 beta 4896 4902 4899 4923 C1' C B 52 beta 4918 4924 4921 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4817 C2' C B 47 OK 4819 4815 4818 4837 C2' C B 48 OK 4839 4835 4838 4857 C2' A B 49 OK 4859 4855 4858 4879 C2' U B 50 OK 4881 4877 4880 4899 C2' A B 51 OK 4901 4897 4900 4921 C2' C B 52 OK 4923 4919 4922 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4815 C3' C B 47 OK 4813 4816 4817 4835 C3' C B 48 OK 4833 4836 4837 4855 C3' A B 49 OK 4853 4856 4857 4877 C3' U B 50 OK 4875 4878 4879 4897 C3' A B 51 OK 4895 4898 4899 4919 C3' C B 52 OK 4917 4920 4921 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 4813 C4' C B 47 OK 4815 4812 4814 4833 C4' C B 48 OK 4835 4832 4834 4853 C4' A B 49 OK 4855 4852 4854 4875 C4' U B 50 OK 4877 4874 4876 4895 C4' A B 51 OK 4897 4894 4896 4917 C4' C B 52 OK 4919 4916 4918 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 4812 C5' C B 47 4811 4813 4832 C5' C B 48 4831 4833 4852 C5' A B 49 4851 4853 4874 C5' U B 50 4873 4875 4894 C5' A B 51 4893 4895 4916 C5' C B 52 4915 4917 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 4828 P C B 48 distorted distorted 4816 4829 4830 4831 4848 P A B 49 distorted distorted 4836 4849 4850 4851 4870 P U B 50 distorted distorted 4856 4871 4872 4873 4890 P A B 51 distorted distorted 4878 4891 4892 4893 4912 P C B 52 distorted distorted 4898 4913 4914 4915 4932 P G B 53 distorted distorted 4920 4933 4934 4935 ---------------------------------------------------------------------------------