ID code: '3O8R' 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' --------------------------------------------------------------------------------- 4821 C1' U C 3 beta 4816 4822 4819 4841 C1' 5BU C 4 beta 4836 4842 4839 4862 C1' U C 5 beta 4857 4863 4860 4882 C1' U C 6 beta 4877 4883 4880 4902 C1' U C 7 beta 4897 4903 4900 4922 C1' U C 8 beta 4917 4923 4920 9758 C1' ADP A 875 beta 9753 9759 9756 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 4819 C2' U C 3 OK 4821 4817 4820 4839 C2' 5BU C 4 OK 4841 4837 4840 4860 C2' U C 5 OK 4862 4858 4861 4880 C2' U C 6 OK 4882 4878 4881 4900 C2' U C 7 OK 4902 4898 4901 4920 C2' U C 8 OK 4922 4918 4921 9756 C2' ADP A 875 OK 9758 9754 9757 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 4817 C3' U C 3 OK 4815 4818 4819 4837 C3' 5BU C 4 OK 4835 4838 4839 4858 C3' U C 5 OK 4856 4859 4860 4878 C3' U C 6 OK 4876 4879 4880 4898 C3' U C 7