ID code: '4RCJ' 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' --------------------------------------------------------------------------------- 1559 C1' G B 1 beta 1554 1560 1557 1582 C1' G B 2 beta 1577 1583 1580 1611 C1' 6MZ B 3 beta 1610 1599 1612 1628 C1' C B 4 beta 1623 1629 1626 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1557 C2' G B 1 OK 1559 1555 1558 1580 C2' G B 2 OK 1582 1578 1581 1612 C2' 6MZ B 3 OK 1611 1614 1613 1626 C2' C B 4 OK 1628 1624 1627 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1555 C3' G B 1 OK 1553 1556 1557 1578 C3' G B 2 OK 1576 1579 1580 1614 C3' 6MZ B 3 OK 1609 1615 1612 1624 C3' C B 4 OK 1622 1625 1626 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1553 C4' G B 1 OK 1555 1552 1554 1576 C4' G B 2 OK 1578 1575 1577 1609 C4' 6MZ B 3 OK 1614 1608 1610 1622 C4' C B 4 OK 1624 1621 1623 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1552 C5' G B 1 1551 1553 1575 C5' G B 2 1574 1576 1608 C5' 6MZ B 3 1607 1609 1621 C5' C B 4 1620 1622 1641 C5' U B 5 1640 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1571 P G B 2 distorted distorted 1556 1572 1573 1574 1616 P 6MZ B 3 distorted distorted 1579 1597 1598 1607 1617 P C B 4 distorted distorted 1615 1618 1619 1620 1637 P U B 5 distorted distorted 1625 1638 1639 1640 ---------------------------------------------------------------------------------