ID code: '2MQP' 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' --------------------------------------------------------------------------------- 1834 C1' A B 1 alpha beta 1829 1851 1835 1832 1867 C1' C B 2 alpha beta 1862 1882 1868 1865 1898 C1' A B 3 alpha beta 1893 1915 1899 1896 1931 C1' C B 4 alpha beta 1926 1946 1932 1929 1962 C1' A B 5 alpha beta 1957 1979 1963 1960 1995 C1' C B 6 alpha beta 1990 2010 1996 1993 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1832 C2' A B 1 OK OK 1834 1830 1849 1833 1865 C2' C B 2 OK OK 1867 1863 1880 1866 1896 C2' A B 3 OK OK 1898 1894 1913 1897 1929 C2' C B 4 OK OK 1931 1927 1944 1930 1960 C2' A B 5 OK OK 1962 1958 1977 1961 1993 C2' C B 6 OK OK 1995 1991 2008 1994 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1830 C3' A B 1 OK OK 1828 1848 1831 1832 1863 C3' C B 2 OK OK 1861 1879 1864 1865 1894 C3' A B 3 OK OK 1892 1912 1895 1896 1927 C3' C B 4 OK OK 1925 1943 1928 1929 1958 C3' A B 5 OK OK 1956 1976 1959 1960 1991 C3' C B 6 OK OK 1989 2007 1992 1993 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1828 C4' A B 1 OK OK 1830 1847 1827 1829 1861 C4' C B 2 OK OK 1863 1878 1860 1862 1892 C4' A B 3 OK OK 1894 1911 1891 1893 1925 C4' C B 4 OK OK 1927 1942 1924 1926 1956 C4' A B 5 OK OK 1958 1975 1955 1957 1989 C4' C B 6 OK OK 1991 2006 1988 1990 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1827 C5' A B 1 OK OK 1826 1845 1846 1828 1860 C5' C B 2 OK OK 1859 1876 1877 1861 1891 C5' A B 3 OK OK 1890 1909 1910 1892 1924 C5' C B 4 OK OK 1923 1940 1941 1925 1955 C5' A B 5 OK OK 1954 1973 1974 1956 1988 C5' C B 6 OK OK 1987 2004 2005 1989 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1856 P C B 2 distorted distorted 1831 1857 1858 1859 1887 P A B 3 distorted distorted 1864 1888 1889 1890 1920 P C B 4 distorted distorted 1895 1921 1922 1923 1951 P A B 5 distorted distorted 1928 1952 1953 1954 1984 P C B 6 distorted distorted 1959 1985 1986 1987 ---------------------------------------------------------------------------------