ID code: '3QRR' 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' --------------------------------------------------------------------------------- 1641 C1' G B 4 beta 1636 1642 1639 1664 C1' U B 5 beta 1659 1665 1662 1684 C1' C B 6 beta 1679 1685 1682 1704 C1' C B 7 beta 1699 1705 1702 1724 C1' C B 8 beta 1719 1725 1722 1744 C1' C B 9 beta 1739 1745 1742 1764 C1' A B 10 beta 1759 1765 1762 1786 C1' C B 11 beta 1781 1787 1784 1806 C1' G B 12 beta 1801 1807 1804 1829 C1' C B 13 beta 1824 1830 1827 1849 C1' G B 14 beta 1844 1850 1847 1872 C1' U B 15 beta 1867 1873 1870 1892 C1' G B 16 beta 1887 1893 1890 1915 C1' U B 17 beta 1910 1916 1913 1935 C1' G B 18 beta 1930 1936 1933 1958 C1' G B 19 beta 1953 1959 1956 1981 C1' G B 20 beta 1976 1982 1979 2006 C1' 23G B 21 beta 2012 2004 2007 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1639 C2' G B 4 OK 1641 1637 1640 1662 C2' U B 5 OK 1664 1660 1663 1682 C2' C B 6 OK 1684 1680 1683 1702 C2' C B 7 OK 1704 1700 1703 1722 C2' C B 8 OK 1724 1720 1723 1742 C2' C B 9 OK 1744 1740 1743 1762 C2' A B 10 OK 1764 1760 1763 1784 C2' C B 11 OK 1786 1782 1785 1804 C2' G B 12 OK 1806 1802 1805 1827 C2' C B 13 OK 1829 1825 1828 1847 C2' G B 14 OK 1849 1845 1848 1870 C2' U B 15 OK 1872 1868 1871 1890 C2' G B 16 OK 1892 1888 1891 1913 C2' U B 17 OK 1915 1911 1914 1933 C2' G B 18 OK 1935 1931 1934 1956 C2' G B 19 OK 1958 1954 1957 1979 C2' G B 20 OK 1981 1977 1980 2007 C2' 23G B 21 OK 2006 2009 2008 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1637 C3' G B 4 OK 1635 1638 1639 1660 C3' U B 5 OK 1658 1661 1662 1680 C3' C B 6 OK 1678 1681 1682 1700 C3' C B 7 OK 1698 1701 1702 1720 C3' C B 8 OK 1718 1721 1722 1740 C3' C B 9 OK 1738 1741 1742 1760 C3' A B 10 OK 1758 1761 1762 1782 C3' C B 11 OK 1780 1783 1784 1802 C3' G B 12 OK 1800 1803 1804 1825 C3' C B 13 OK 1823 1826 1827 1845 C3' G B 14 OK 1843 1846 1847 1868 C3' U B 15 OK 1866 1869 1870 1888 C3' G B 16 OK 1886 1889 1890 1911 C3' U B 17 OK 1909 1912 1913 1931 C3' G B 18 OK 1929 1932 1933 1954 C3' G B 19 OK 1952 1955 1956 1977 C3' G B 20 OK 1975 1978 1979 2009 C3' 23G B 21 OK 2011 2010 2007 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1635 C4' G B 4 OK 1637 1634 1636 1658 C4' U B 5 OK 1660 1657 1659 1678 C4' C B 6 OK 1680 1677 1679 1698 C4' C B 7 OK 1700 1697 1699 1718 C4' C B 8 OK 1720 1717 1719 1738 C4' C B 9 OK 1740 1737 1739 1758 C4' A B 10 OK 1760 1757 1759 1780 C4' C B 11 OK 1782 1779 1781 1800 C4' G B 12 OK 1802 1799 1801 1823 C4' C B 13 OK 1825 1822 1824 1843 C4' G B 14 OK 1845 1842 1844 1866 C4' U B 15 OK 1868 1865 1867 1886 C4' G B 16 OK 1888 1885 1887 1909 C4' U B 17 OK 1911 1908 1910 1929 C4' G B 18 OK 1931 1928 1930 1952 C4' G B 19 OK 1954 1951 1953 1975 C4' G B 20 OK 1977 1974 1976 2011 C4' 23G B 21 OK 2009 2013 2012 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1634 C5' G B 4 1633 1635 1657 C5' U B 5 1656 1658 1677 C5' C B 6 1676 1678 1697 C5' C B 7 1696 1698 1717 C5' C B 8 1716 1718 1737 C5' C B 9 1736 1738 1757 C5' A B 10 1756 1758 1779 C5' C B 11 1778 1780 1799 C5' G B 12 1798 1800 1822 C5' C B 13 1821 1823 1842 C5' G B 14 1841 1843 1865 C5' U B 15 1864 1866 1885 C5' G B 16 1884 1886 1908 C5' U B 17 1907 1909 1928 C5' G B 18 1927 1929 1951 C5' G B 19 1950 1952 1974 C5' G B 20 1973 1975 2013 C5' 23G B 21 2014 2011 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1653 P U B 5 distorted distorted 1638 1654 1655 1656 1673 P C B 6 distorted distorted 1661 1674 1675 1676 1693 P C B 7 distorted distorted 1681 1694 1695 1696 1713 P C B 8 distorted distorted 1701 1714 1715 1716 1733 P C B 9 distorted distorted 1721 1734 1735 1736 1753 P A B 10 distorted distorted 1741 1754 1755 1756 1775 P C B 11 distorted distorted 1761 1776 1777 1778 1795 P G B 12 distorted distorted 1783 1796 1797 1798 1818 P C B 13 distorted distorted 1803 1819 1820 1821 1838 P G B 14 distorted distorted 1826 1839 1840 1841 1861 P U B 15 distorted distorted 1846 1862 1863 1864 1881 P G B 16 distorted distorted 1869 1882 1883 1884 1904 P U B 17 distorted distorted 1889 1905 1906 1907 1924 P G B 18 distorted distorted 1912 1925 1926 1927 1947 P G B 19 distorted distorted 1932 1948 1949 1950 1970 P G B 20 distorted distorted 1955 1971 1972 1973 1993 P 23G B 21 distorted distorted 1978 2017 2018 2014 ---------------------------------------------------------------------------------