ID code: '3QRP' 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' --------------------------------------------------------------------------------- 1719 C1' G B 4 beta 1714 1720 1717 1742 C1' U B 5 beta 1737 1743 1740 1762 C1' C B 6 beta 1757 1763 1760 1782 C1' C B 7 beta 1777 1783 1780 1802 C1' C B 8 beta 1797 1803 1800 1822 C1' C B 9 beta 1817 1823 1820 1842 C1' A B 10 beta 1837 1843 1840 1864 C1' C B 11 beta 1859 1865 1862 1888 C1' PGP B 12 beta 1883 1889 1886 1909 C1' U5P C 15 beta 1915 1901 1910 1933 C1' G C 16 beta 1928 1934 1931 1956 C1' U C 17 beta 1951 1957 1954 1976 C1' G C 18 beta 1971 1977 1974 1999 C1' G C 19 beta 1994 2000 1997 2022 C1' G C 20 beta 2017 2023 2020 2045 C1' G C 21 beta 2040 2046 2043 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1717 C2' G B 4 OK 1719 1715 1718 1740 C2' U B 5 OK 1742 1738 1741 1760 C2' C B 6 OK 1762 1758 1761 1780 C2' C B 7 OK 1782 1778 1781 1800 C2' C B 8 OK 1802 1798 1801 1820 C2' C B 9 OK 1822 1818 1821 1840 C2' A B 10 OK 1842 1838 1841 1862 C2' C B 11 OK 1864 1860 1863 1886 C2' PGP B 12 OK 1888 1884 1887 1910 C2' U5P C 15 OK 1909 1912 1911 1931 C2' G C 16 OK 1933 1929 1932 1954 C2' U C 17 OK 1956 1952 1955 1974 C2' G C 18 OK 1976 1972 1975 1997 C2' G C 19 OK 1999 1995 1998 2020 C2' G C 20 OK 2022 2018 2021 2043 C2' G C 21 OK 2045 2041 2044 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1715 C3' G B 4 OK 1713 1716 1717 1738 C3' U B 5 OK 1736 1739 1740 1758 C3' C B 6 OK 1756 1759 1760 1778 C3' C B 7 OK 1776 1779 1780 1798 C3' C B 8 OK 1796 1799 1800 1818 C3' C B 9 OK 1816 1819 1820 1838 C3' A B 10 OK 1836 1839 1840 1860 C3' C B 11 OK 1858 1861 1862 1884 C3' PGP B 12 OK 1882 1885 1886 1912 C3' U5P C 15 OK 1913 1914 1910 1929 C3' G C 16 OK 1927 1930 1931 1952 C3' U C 17 OK 1950 1953 1954 1972 C3' G C 18 OK 1970 1973 1974 1995 C3' G C 19 OK 1993 1996 1997 2018 C3' G C 20 OK 2016 2019 2020 2041 C3' G C 21 OK 2039 2042 2043 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1713 C4' G B 4 OK 1715 1712 1714 1736 C4' U B 5 OK 1738 1735 1737 1756 C4' C B 6 OK 1758 1755 1757 1776 C4' C B 7 OK 1778 1775 1777 1796 C4' C B 8 OK 1798 1795 1797 1816 C4' C B 9 OK 1818 1815 1817 1836 C4' A B 10 OK 1838 1835 1837 1858 C4' C B 11 OK 1860 1857 1859 1882 C4' PGP B 12 OK 1884 1881 1883 1913 C4' U5P C 15 OK 1912 1916 1915 1927 C4' G C 16 OK 1929 1926 1928 1950 C4' U C 17 OK 1952 1949 1951 1970 C4' G C 18 OK 1972 1969 1971 1993 C4' G C 19 OK 1995 1992 1994 2016 C4' G C 20 OK 2018 2015 2017 2039 C4' G C 21 OK 2041 2038 2040 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1712 C5' G B 4 1711 1713 1735 C5' U B 5 1734 1736 1755 C5' C B 6 1754 1756 1775 C5' C B 7 1774 1776 1795 C5' C B 8 1794 1796 1815 C5' C B 9 1814 1816 1835 C5' A B 10 1834 1836 1857 C5' C B 11 1856 1858 1881 C5' PGP B 12 1880 1882 1916 C5' U5P C 15 1917 1913 1926 C5' G C 16 1925 1927 1949 C5' U C 17 1948 1950 1969 C5' G C 18 1968 1970 1992 C5' G C 19 1991 1993 2015 C5' G C 20 2014 2016 2038 C5' G C 21 2037 2039 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1731 P U B 5 distorted distorted 1716 1732 1733 1734 1751 P C B 6 distorted distorted 1739 1752 1753 1754 1771 P C B 7 distorted distorted 1759 1772 1773 1774 1791 P C B 8 distorted distorted 1779 1792 1793 1794 1811 P C B 9 distorted distorted 1799 1812 1813 1814 1831 P A B 10 distorted distorted 1819 1832 1833 1834 1853 P C B 11 distorted distorted 1839 1854 1855 1856 1877 P PGP B 12 OK OK 1861 1878 1879 1880 1918 P U5P C 15 OK OK 1919 1920 1917 1922 P G C 16 distorted distorted 1914 1923 1924 1925 1945 P U C 17 distorted distorted 1930 1946 1947 1948 1965 P G C 18 distorted distorted 1953 1966 1967 1968 1988 P G C 19 distorted distorted 1973 1989 1990 1991 2011 P G C 20 distorted distorted 1996 2012 2013 2014 2034 P G C 21 distorted distorted 2019 2035 2036 2037 ---------------------------------------------------------------------------------