ID code: '2MXY' 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' --------------------------------------------------------------------------------- 1609 C1' A B 1 alpha beta 1604 1626 1610 1607 1642 C1' U B 2 alpha beta 1637 1657 1643 1640 1672 C1' U B 3 alpha beta 1667 1687 1673 1670 1702 C1' U B 4 alpha beta 1697 1717 1703 1700 1732 C1' U B 5 alpha beta 1727 1747 1733 1730 1762 C1' U B 6 alpha beta 1757 1777 1763 1760 1792 C1' C B 7 alpha beta 1787 1807 1793 1790 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1607 C2' A B 1 OK OK 1609 1605 1624 1608 1640 C2' U B 2 OK OK 1642 1638 1655 1641 1670 C2' U B 3 OK OK 1672 1668 1685 1671 1700 C2' U B 4 OK OK 1702 1698 1715 1701 1730 C2' U B 5 OK OK 1732 1728 1745 1731 1760 C2' U B 6 OK OK 1762 1758 1775 1761 1790 C2' C B 7 OK OK 1792 1788 1805 1791 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1605 C3' A B 1 OK OK 1603 1623 1606 1607 1638 C3' U B 2 OK OK 1636 1654 1639 1640 1668 C3' U B 3 OK OK 1666 1684 1669 1670 1698 C3' U B 4 OK OK 1696 1714 1699 1700 1728 C3' U B 5 OK OK 1726 1744 1729 1730 1758 C3' U B 6 OK OK 1756 1774 1759 1760 1788 C3' C B 7 OK OK 1786 1804 1789 1790 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1603 C4' A B 1 OK OK 1605 1622 1602 1604 1636 C4' U B 2 OK OK 1638 1653 1635 1637 1666 C4' U B 3 OK OK 1668 1683 1665 1667 1696 C4' U B 4 OK OK 1698 1713 1695 1697 1726 C4' U B 5 OK OK 1728 1743 1725 1727 1756 C4' U B 6 OK OK 1758 1773 1755 1757 1786 C4' C B 7 OK OK 1788 1803 1785 1787 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1602 C5' A B 1 OK OK 1601 1620 1621 1603 1635 C5' U B 2 OK OK 1634 1651 1652 1636 1665 C5' U B 3 OK OK 1664 1681 1682 1666 1695 C5' U B 4 OK OK 1694 1711 1712 1696 1725 C5' U B 5 OK OK 1724 1741 1742 1726 1755 C5' U B 6 OK OK 1754 1771 1772 1756 1785 C5' C B 7 OK OK 1784 1801 1802 1786 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1631 P U B 2 distorted distorted 1606 1632 1633 1634 1661 P U B 3 distorted distorted 1639 1662 1663 1664 1691 P U B 4 distorted distorted 1669 1692 1693 1694 1721 P U B 5 distorted distorted 1699 1722 1723 1724 1751 P U B 6 distorted distorted 1729 1752 1753 1754 1781 P C B 7 distorted distorted 1759 1782 1783 1784 ---------------------------------------------------------------------------------