ID code: '2MQO' 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' --------------------------------------------------------------------------------- 1581 C1' C B 1 alpha beta 1576 1596 1582 1579 1612 C1' A B 2 alpha beta 1607 1629 1613 1610 1645 C1' C B 3 alpha beta 1640 1660 1646 1643 1676 C1' A B 4 alpha beta 1671 1693 1677 1674 1709 C1' C B 5 alpha beta 1704 1724 1710 1707 1740 C1' A B 6 alpha beta 1735 1757 1741 1738 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1579 C2' C B 1 OK OK 1581 1577 1594 1580 1610 C2' A B 2 OK OK 1612 1608 1627 1611 1643 C2' C B 3 OK OK 1645 1641 1658 1644 1674 C2' A B 4 OK OK 1676 1672 1691 1675 1707 C2' C B 5 OK OK 1709 1705 1722 1708 1738 C2' A B 6 OK OK 1740 1736 1755 1739 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1577 C3' C B 1 OK OK 1575 1593 1578 1579 1608 C3' A B 2 OK OK 1606 1626 1609 1610 1641 C3' C B 3 OK OK 1639 1657 1642 1643 1672 C3' A B 4 OK OK 1670 1690 1673 1674 1705 C3' C B 5 OK OK 1703 1721 1706 1707 1736 C3' A B 6 OK OK 1734 1754 1737 1738 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1575 C4' C B 1 OK OK 1577 1592 1574 1576 1606 C4' A B 2 OK OK 1608 1625 1605 1607 1639 C4' C B 3 OK OK 1641 1656 1638 1640 1670 C4' A B 4 OK OK 1672 1689 1669 1671 1703 C4' C B 5 OK OK 1705 1720 1702 1704 1734 C4' A B 6 OK OK 1736 1753 1733 1735 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1574 C5' C B 1 OK OK 1573 1590 1591 1575 1605 C5' A B 2 OK OK 1604 1623 1624 1606 1638 C5' C B 3 OK OK 1637 1654 1655 1639 1669 C5' A B 4 OK OK 1668 1687 1688 1670 1702 C5' C B 5 OK OK 1701 1718 1719 1703 1733 C5' A B 6 OK OK 1732 1751 1752 1734 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1601 P A B 2 distorted distorted 1578 1602 1603 1604 1634 P C B 3 distorted distorted 1609 1635 1636 1637 1665 P A B 4 distorted distorted 1642 1666 1667 1668 1698 P C B 5 distorted distorted 1673 1699 1700 1701 1729 P A B 6 distorted distorted 1706 1730 1731 1732 ---------------------------------------------------------------------------------