ID code: '2MB0' 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' --------------------------------------------------------------------------------- 1477 C1' A A 96 alpha beta 1472 1494 1478 1475 1511 C1' U A 97 alpha beta 1506 1526 1512 1509 1541 C1' C A 98 alpha beta 1536 1556 1542 1539 1572 C1' A A 99 alpha beta 1567 1589 1573 1570 1605 C1' A A 100 alpha beta 1600 1622 1606 1603 1638 C1' A A 101 alpha beta 1633 1656 1639 1636 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1475 C2' A A 96 OK OK 1477 1473 1492 1476 1509 C2' U A 97 OK OK 1511 1507 1524 1510 1539 C2' C A 98 OK OK 1541 1537 1554 1540 1570 C2' A A 99 OK OK 1572 1568 1587 1571 1603 C2' A A 100 OK OK 1605 1601 1620 1604 1636 C2' A A 101 OK OK 1638 1634 1654 1637 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1473 C3' A A 96 OK OK 1471 1491 1474 1475 1507 C3' U A 97 OK OK 1505 1523 1508 1509 1537 C3' C A 98 OK OK 1535 1553 1538 1539 1568 C3' A A 99 OK OK 1566 1586 1569 1570 1601 C3' A A 100 OK OK 1599 1619 1602 1603 1634 C3' A A 101 OK OK 1632 1652 1635 1636 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1471 C4' A A 96 OK OK 1473 1490 1470 1472 1505 C4' U A 97 OK OK 1507 1522 1504 1506 1535 C4' C A 98 OK OK 1537 1552 1534 1536 1566 C4' A A 99 OK OK 1568 1585 1565 1567 1599 C4' A A 100 OK OK 1601 1618 1598 1600 1632 C4' A A 101 OK OK 1634 1651 1631 1633 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1470 C5' A A 96 OK OK 1469 1488 1489 1471 1504 C5' U A 97 OK OK 1503 1520 1521 1505 1534 C5' C A 98 OK OK 1533 1550 1551 1535 1565 C5' A A 99 OK OK 1564 1583 1584 1566 1598 C5' A A 100 OK OK 1597 1616 1617 1599 1631 C5' A A 101 OK OK 1630 1649 1650 1632 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1500 P U A 97 distorted distorted 1474 1501 1502 1503 1530 P C A 98 distorted distorted 1508 1531 1532 1533 1561 P A A 99 distorted distorted 1538 1562 1563 1564 1594 P A A 100 distorted distorted 1569 1595 1596 1597 1627 P A A 101 distorted distorted 1602 1628 1629 1630 ---------------------------------------------------------------------------------