ID code: '1MJM' 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' --------------------------------------------------------------------------------- 1700 C1' G C 401 beta 1696 1701 1699 1722 C1' A C 402 beta 1718 1723 1721 1743 C1' G C 403 beta 1739 1744 1742 1765 C1' A C 404 beta 1761 1766 1764 1786 C1' C C 405 beta 1782 1787 1785 1805 C1' G C 406 beta 1801 1806 1804 1827 C1' T C 407 beta 1823 1828 1826 1847 C1' C C 408 beta 1843 1848 1846 1866 C1' T C 409 beta 1862 1867 1865 1886 C1' C C 410 beta 1882 1887 1885 1903 C1' G D 411 beta 1899 1904 1902 1925 C1' A D 412 beta 1921 1926 1924 1946 C1' G D 413 beta 1942 1947 1945 1968 C1' A D 414 beta 1964 1969 1967 1989 C1' C D 415 beta 1985 1990 1988 2008 C1' G D 416 beta 2004 2009 2007 2030 C1' T D 417 beta 2026 2031 2029 2050 C1' C D 418 beta 2046 2051 2049 2069 C1' T D 419 beta 2065 2070 2068 2089 C1' C D 420 beta 2085 2090 2088 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1699 C2' G C 401 1700 1697 1721 C2' A C 402 1722 1719 1742 C2' G C 403 1743 1740 1764 C2' A C 404 1765 1762 1785 C2' C C 405 1786 1783 1804 C2' G C 406 1805 1802 1826 C2' T C 407 1827 1824 1846 C2' C C 408 1847 1844 1865 C2' T C 409 1866 1863 1885 C2' C C 410 1886 1883 1902 C2' G D 411 1903 1900 1924 C2' A D 412 1925 1922 1945 C2' G D 413 1946 1943 1967 C2' A D 414 1968 1965 1988 C2' C D 415 1989 1986 2007 C2' G D 416 2008 2005 2029 C2' T D 417 2030 2027 2049 C2' C D 418 2050 2047 2068 C2' T D 419 2069 2066 2088 C2' C D 420 2089 2086 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1697 C3' G C 401 OK 1695 1698 1699 1719 C3' A C 402 OK 1717 1720 1721 1740 C3' G C 403 OK 1738 1741 1742 1762 C3' A C 404 OK 1760 1763 1764 1783 C3' C C 405 OK 1781 1784 1785 1802 C3' G C 406 OK 1800 1803 1804 1824 C3' T C 407 OK 1822 1825 1826 1844 C3' C C 408 OK 1842 1845 1846 1863 C3' T C 409 OK 1861 1864 1865 1883 C3' C C 410 OK 1881 1884 1885 1900 C3' G D 411 OK 1898 1901 1902 1922 C3' A D 412 OK 1920 1923 1924 1943 C3' G D 413 OK 1941 1944 1945 1965 C3' A D 414 OK 1963 1966 1967 1986 C3' C D 415 OK 1984 1987 1988 2005 C3' G D 416 OK 2003 2006 2007 2027 C3' T D 417 OK 2025 2028 2029 2047 C3' C D 418 OK 2045 2048 2049 2066 C3' T D 419 OK 2064 2067 2068 2086 C3' C D 420 OK 2084 2087 2088 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1695 C4' G C 401 OK 1697 1694 1696 1717 C4' A C 402 OK 1719 1716 1718 1738 C4' G C 403 OK 1740 1737 1739 1760 C4' A C 404 OK 1762 1759 1761 1781 C4' C C 405 OK 1783 1780 1782 1800 C4' G C 406 OK 1802 1799 1801 1822 C4' T C 407 OK 1824 1821 1823 1842 C4' C C 408 OK 1844 1841 1843 1861 C4' T C 409 OK 1863 1860 1862 1881 C4' C C 410 OK 1883 1880 1882 1898 C4' G D 411 OK 1900 1897 1899 1920 C4' A D 412 OK 1922 1919 1921 1941 C4' G D 413 OK 1943 1940 1942 1963 C4' A D 414 OK 1965 1962 1964 1984 C4' C D 415 OK 1986 1983 1985 2003 C4' G D 416 OK 2005 2002 2004 2025 C4' T D 417 OK 2027 2024 2026 2045 C4' C D 418 OK 2047 2044 2046 2064 C4' T D 419 OK 2066 2063 2065 2084 C4' C D 420 OK 2086 2083 2085 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1694 C5' G C 401 1693 1695 1716 C5' A C 402 1715 1717 1737 C5' G C 403 1736 1738 1759 C5' A C 404 1758 1760 1780 C5' C C 405 1779 1781 1799 C5' G C 406 1798 1800 1821 C5' T C 407 1820 1822 1841 C5' C C 408 1840 1842 1860 C5' T C 409 1859 1861 1880 C5' C C 410 1879 1881 1897 C5' G D 411 1896 1898 1919 C5' A D 412 1918 1920 1940 C5' G D 413 1939 1941 1962 C5' A D 414 1961 1963 1983 C5' C D 415 1982 1984 2002 C5' G D 416 2001 2003 2024 C5' T D 417 2023 2025 2044 C5' C D 418 2043 2045 2063 C5' T D 419 2062 2064 2083 C5' C D 420 2082 2084 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1712 P A C 402 distorted distorted 1698 1713 1714 1715 1733 P G C 403 distorted distorted 1720 1734 1735 1736 1755 P A C 404 distorted distorted 1741 1756 1757 1758 1776 P C C 405 distorted distorted 1763 1777 1778 1779 1795 P G C 406 distorted distorted 1784 1796 1797 1798 1817 P T C 407 distorted distorted 1803 1818 1819 1820 1837 P C C 408 distorted distorted 1825 1838 1839 1840 1856 P T C 409 distorted distorted 1845 1857 1858 1859 1876 P C C 410 distorted distorted 1864 1877 1878 1879 1915 P A D 412 distorted distorted 1901 1916 1917 1918 1936 P G D 413 distorted distorted 1923 1937 1938 1939 1958 P A D 414 distorted distorted 1944 1959 1960 1961 1979 P C D 415 distorted distorted 1966 1980 1981 1982 1998 P G D 416 distorted distorted 1987 1999 2000 2001 2020 P T D 417 distorted distorted 2006 2021 2022 2023 2040 P C D 418 distorted distorted 2028 2041 2042 2043 2059 P T D 419 distorted distorted 2048 2060 2061 2062 2079 P C D 420 distorted distorted 2067 2080 2081 2082 ---------------------------------------------------------------------------------