ID code: '2KG0' 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' --------------------------------------------------------------------------------- 1439 C1' A B 1 alpha beta 1434 1456 1440 1437 1473 C1' G B 2 alpha beta 1468 1491 1474 1471 1507 C1' G B 3 alpha beta 1502 1525 1508 1505 1541 C1' G B 4 alpha beta 1536 1559 1542 1539 1575 C1' A B 5 alpha beta 1570 1592 1576 1573 1608 C1' U B 6 alpha beta 1603 1624 1609 1606 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1437 C2' A B 1 OK OK 1439 1435 1454 1438 1471 C2' G B 2 OK OK 1473 1469 1489 1472 1505 C2' G B 3 OK OK 1507 1503 1523 1506 1539 C2' G B 4 OK OK 1541 1537 1557 1540 1573 C2' A B 5 OK OK 1575 1571 1590 1574 1606 C2' U B 6 OK OK 1608 1604 1622 1607 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1435 C3' A B 1 OK OK 1433 1453 1436 1437 1469 C3' G B 2 OK OK 1467 1488 1470 1471 1503 C3' G B 3 OK OK 1501 1522 1504 1505 1537 C3' G B 4 OK OK 1535 1556 1538 1539 1571 C3' A B 5 OK OK 1569 1589 1572 1573 1604 C3' U B 6 OK OK 1602 1620 1605 1606 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1433 C4' A B 1 OK OK 1435 1452 1432 1434 1467 C4' G B 2 OK OK 1469 1487 1466 1468 1501 C4' G B 3 OK OK 1503 1521 1500 1502 1535 C4' G B 4 OK OK 1537 1555 1534 1536 1569 C4' A B 5 OK OK 1571 1588 1568 1570 1602 C4' U B 6 OK OK 1604 1619 1601 1603 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1432 C5' A B 1 OK OK 1431 1450 1451 1433 1466 C5' G B 2 OK OK 1465 1485 1486 1467 1500 C5' G B 3 OK OK 1499 1519 1520 1501 1534 C5' G B 4 OK OK 1533 1553 1554 1535 1568 C5' A B 5 OK OK 1567 1586 1587 1569 1601 C5' U B 6 OK OK 1600 1617 1618 1602 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1462 P G B 2 distorted distorted 1436 1463 1464 1465 1496 P G B 3 distorted distorted 1470 1497 1498 1499 1530 P G B 4 distorted distorted 1504 1531 1532 1533 1564 P A B 5 distorted distorted 1538 1565 1566 1567 1597 P U B 6 distorted distorted 1572 1598 1599 1600 ---------------------------------------------------------------------------------