ID code: '2MZ1' 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' --------------------------------------------------------------------------------- 1610 C1' U B 1 alpha beta 1605 1625 1611 1608 1640 C1' U B 2 alpha beta 1635 1655 1641 1638 1670 C1' U B 3 alpha beta 1665 1685 1671 1668 1700 C1' U B 4 alpha beta 1695 1715 1701 1698 1730 C1' C B 5 alpha beta 1725 1745 1731 1728 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1608 C2' U B 1 OK OK 1610 1606 1623 1609 1638 C2' U B 2 OK OK 1640 1636 1653 1639 1668 C2' U B 3 OK OK 1670 1666 1683 1669 1698 C2' U B 4 OK OK 1700 1696 1713 1699 1728 C2' C B 5 OK OK 1730 1726 1743 1729 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1606 C3' U B 1 OK OK 1604 1622 1607 1608 1636 C3' U B 2 OK OK 1634 1652 1637 1638 1666 C3' U B 3 OK OK 1664 1682 1667 1668 1696 C3' U B 4 OK OK 1694 1712 1697 1698 1726 C3' C B 5 OK OK 1724 1742 1727 1728 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1604 C4' U B 1 OK OK 1606 1621 1603 1605 1634 C4' U B 2 OK OK 1636 1651 1633 1635 1664 C4' U B 3 OK OK 1666 1681 1663 1665 1694 C4' U B 4 OK OK 1696 1711 1693 1695 1724 C4' C B 5 OK OK 1726 1741 1723 1725 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1603 C5' U B 1 OK OK 1602 1619 1620 1604 1633 C5' U B 2 OK OK 1632 1649 1650 1634 1663 C5' U B 3 OK OK 1662 1679 1680 1664 1693 C5' U B 4 OK OK 1692 1709 1710 1694 1723 C5' C B 5 OK OK 1722 1739 1740 1724 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1629 P U B 2 distorted distorted 1607 1630 1631 1632 1659 P U B 3 distorted distorted 1637 1660 1661 1662 1689 P U B 4 distorted distorted 1667 1690 1691 1692 1719 P C B 5 distorted distorted 1697 1720 1721 1722 ---------------------------------------------------------------------------------