ID code: '4MDX' 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' --------------------------------------------------------------------------------- 1854 C1' U C 1 beta 1849 1855 1852 1874 C1' U C 2 beta 1869 1875 1872 1893 C1' DU C 3 beta 1889 1894 1892 1913 C1' A C 4 beta 1908 1914 1911 1935 C1' C C 5 beta 1930 1936 1933 1955 C1' A C 6 beta 1950 1956 1953 1977 C1' U C 7 beta 1972 1978 1975 1997 C1' A C 8 beta 1992 1998 1995 2019 C1' A C 9 beta 2014 2020 2017 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1852 C2' U C 1 OK 1854 1850 1853 1872 C2' U C 2 OK 1874 1870 1873 1892 C2' DU C 3 1893 1890 1911 C2' A C 4 OK 1913 1909 1912 1933 C2' C C 5 OK 1935 1931 1934 1953 C2' A C 6 OK 1955 1951 1954 1975 C2' U C 7 OK 1977 1973 1976 1995 C2' A C 8 OK 1997 1993 1996 2017 C2' A C 9 OK 2019 2015 2018 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1850 C3' U C 1 OK 1848 1851 1852 1870 C3' U C 2 OK 1868 1871 1872 1890 C3' DU C 3 OK 1888 1891 1892 1909 C3' A C 4 OK 1907 1910 1911 1931 C3' C C 5 OK 1929 1932 1933 1951 C3' A C 6 OK 1949 1952 1953 1973 C3' U C 7 OK 1971 1974 1975 1993 C3' A C 8 OK 1991 1994 1995 2015 C3' A C 9 OK 2013 2016 2017 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1848 C4' U C 1 OK 1850 1847 1849 1868 C4' U C 2 OK 1870 1867 1869 1888 C4' DU C 3 OK 1890 1887 1889 1907 C4' A C 4 OK 1909 1906 1908 1929 C4' C C 5 OK 1931 1928 1930 1949 C4' A C 6 OK 1951 1948 1950 1971 C4' U C 7 OK 1973 1970 1972 1991 C4' A C 8 OK 1993 1990 1992 2013 C4' A C 9 OK 2015 2012 2014 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1847 C5' U C 1 1846 1848 1867 C5' U C 2 1866 1868 1887 C5' DU C 3 1886 1888 1906 C5' A C 4 1905 1907 1928 C5' C C 5 1927 1929 1948 C5' A C 6 1947 1949 1970 C5' U C 7 1969 1971 1990 C5' A C 8 1989 1991 2012 C5' A C 9 2011 2013 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1863 P U C 2 distorted distorted 1851 1864 1865 1866 1883 P DU C 3 distorted distorted 1871 1884 1885 1886 1902 P A C 4 distorted distorted 1891 1903 1904 1905 1924 P C C 5 distorted distorted 1910 1925 1926 1927 1944 P A C 6 distorted distorted 1932 1945 1946 1947 1966 P U C 7 distorted distorted 1952 1967 1968 1969 1986 P A C 8 distorted distorted 1974 1987 1988 1989 2008 P A C 9 distorted distorted 1994 2009 2010 2011 ---------------------------------------------------------------------------------