ID code: '2ZKO' 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' --------------------------------------------------------------------------------- 1138 C1' A C 1 beta 1133 1139 1136 1160 C1' G C 2 beta 1155 1161 1158 1183 C1' A C 3 beta 1178 1184 1181 1205 C1' C C 4 beta 1200 1206 1203 1225 C1' A C 5 beta 1220 1226 1223 1247 C1' G C 6 beta 1242 1248 1245 1270 C1' C C 7 beta 1265 1271 1268 1290 C1' A C 8 beta 1285 1291 1288 1312 C1' U C 9 beta 1307 1313 1310 1332 C1' U C 10 beta 1327 1333 1330 1352 C1' A C 11 beta 1347 1353 1350 1374 C1' U C 12 beta 1369 1375 1372 1394 C1' G C 13 beta 1389 1395 1392 1417 C1' C C 14 beta 1412 1418 1415 1437 C1' U C 15 beta 1432 1438 1435 1457 C1' G C 16 beta 1452 1458 1455 1480 C1' U C 17 beta 1475 1481 1478 1500 C1' C C 18 beta 1495 1501 1498 1520 C1' U C 19 beta 1515 1521 1518 1540 C1' U C 20 beta 1535 1541 1538 1560 C1' U C 21 beta 1555 1561 1558 1581 C1' A D 1 beta 1576 1582 1579 1603 C1' G D 2 beta 1598 1604 1601 1626 C1' A D 3 beta 1621 1627 1624 1648 C1' C D 4 beta 1643 1649 1646 1668 C1' A D 5 beta 1663 1669 1666 1690 C1' G D 6 beta 1685 1691 1688 1713 C1' C D 7 beta 1708 1714 1711 1733 C1' A D 8 beta 1728 1734 1731 1755 C1' U D 9 beta 1750 1756 1753 1775 C1' U D 10 beta 1770 1776 1773 1795 C1' A D 11 beta 1790 1796 1793 1817 C1' U D 12 beta 1812 1818 1815 1837 C1' G D 13 beta 1832 1838 1835 1860 C1' C D 14 beta 1855 1861 1858 1880 C1' U D 15 beta 1875 1881 1878 1900 C1' G D 16 beta 1895 1901 1898 1923 C1' U D 17 beta 1918 1924 1921 1943 C1' C D 18 beta 1938 1944 1941 1963 C1' U D 19 beta 1958 1964 1961 1983 C1' U D 20 beta 1978 1984 1981 2003 C1' U D 21 beta 1998 2004 2001 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1136 C2' A C 1 OK 1138 1134 1137 1158 C2' G C 2 OK 1160 1156 1159 1181 C2' A C 3 OK 1183 1179 1182 1203 C2' C C 4 OK 1205 1201 1204 1223 C2' A C 5 OK 1225 1221 1224 1245 C2' G C 6 OK 1247 1243 1246 1268 C2' C C 7 OK 1270 1266 1269 1288 C2' A C 8 OK 1290 1286 1289 1310 C2' U C 9 OK 1312 1308 1311 1330 C2' U C 10 OK 1332 1328 1331 1350 C2' A C 11 OK 1352 1348 1351 1372 C2' U C 12 OK 1374 1370 1373 1392 C2' G C 13 OK 1394 1390 1393 1415 C2' C C 14 OK 1417 1413 1416 1435 C2' U C 15 OK 1437 1433 1436 1455 C2' G C 16 OK 1457 1453 1456 1478 C2' U C 17 OK 1480 1476 1479 1498 C2' C C 18 OK 1500 1496 1499 1518 C2' U C 19 OK 1520 1516 1519 1538 C2' U C 20 OK 1540 1536 1539 1558 C2' U C 21 OK 1560 1556 1559 1579 C2' A D 1 OK 1581 1577 1580 1601 C2' G D 2 OK 1603 1599 1602 1624 C2' A D 3 OK 1626 1622 1625 1646 C2' C D 4 OK 1648 1644 1647 1666 C2' A D 5 OK 1668 1664 1667 1688 C2' G D 6 OK 1690 1686 1689 1711 C2' C D 7 OK 1713 1709 1712 1731 C2' A D 8 OK 1733 1729 1732 1753 C2' U D 9 OK 1755 1751 1754 1773 C2' U D 10 OK 1775 1771 1774 1793 C2' A D 11 OK 1795 1791 1794 1815 C2' U D 12 OK 1817 1813 1816 1835 C2' G D 13 OK 1837 1833 1836 1858 C2' C D 14 OK 1860 1856 1859 1878 C2' U D 15 OK 1880 1876 1879 1898 C2' G D 16 OK 1900 1896 1899 1921 C2' U D 17 OK 1923 1919 1922 1941 C2' C D 18 OK 1943 1939 1942 1961 C2' U D 19 OK 1963 1959 1962 1981 C2' U D 20 OK 1983 1979 1982 2001 C2' U D 21 OK 2003 1999 2002 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1134 C3' A C 1 OK 1132 1135 1136 1156 C3' G C 2 OK 1154 1157 1158 1179 C3' A C 3 OK 1177 1180 1181 1201 C3' C C 4 OK 1199 1202 1203 1221 C3' A C 5 OK 1219 1222 1223 1243 C3' G C 6 OK 1241 1244 1245 1266 C3' C C 7 OK 1264 1267 1268 1286 C3' A C 8 OK 1284 1287 1288 1308 C3' U C 9 OK 1306 1309 1310 1328 C3' U C 10 OK 1326 1329 1330 1348 C3' A C 11 OK 1346 1349 1350 1370 C3' U C 12 OK 1368 1371 1372 1390 C3' G C 13 OK 1388 1391 1392 1413 C3' C C 14 OK 1411 1414 1415 1433 C3' U C 15 OK 1431 1434 1435 1453 C3' G C 16 OK 1451 1454 1455 1476 C3' U C 17 OK 1474 1477 1478 1496 C3' C C 18 OK 1494 1497 1498 1516 C3' U C 19 OK 1514 1517 1518 1536 C3' U C 20 OK 1534 1537 1538 1556 C3' U C 21 OK 1554 1557 1558 1577 C3' A D 1 OK 1575 1578 1579 1599 C3' G D 2 OK 1597 1600 1601 1622 C3' A D 3 OK 1620 1623 1624 1644 C3' C D 4 OK 1642 1645 1646 1664 C3' A D 5 OK 1662 1665 1666 1686 C3' G D 6 OK 1684 1687 1688 1709 C3' C D 7 OK 1707 1710 1711 1729 C3' A D 8 OK 1727 1730 1731 1751 C3' U D 9 OK 1749 1752 1753 1771 C3' U D 10 OK 1769 1772 1773 1791 C3' A D 11 OK 1789 1792 1793 1813 C3' U D 12 OK 1811 1814 1815 1833 C3' G D 13 OK 1831 1834 1835 1856 C3' C D 14 OK 1854 1857 1858 1876 C3' U D 15 OK 1874 1877 1878 1896 C3' G D 16 OK 1894 1897 1898 1919 C3' U D 17 OK 1917 1920 1921 1939 C3' C D 18 OK 1937 1940 1941 1959 C3' U D 19 OK 1957 1960 1961 1979 C3' U D 20 OK 1977 1980 1981 1999 C3' U D 21 OK 1997 2000 2001 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1132 C4' A C 1 OK 1134 1131 1133 1154 C4' G C 2 OK 1156 1153 1155 1177 C4' A C 3 OK 1179 1176 1178 1199 C4' C C 4 OK 1201 1198 1200 1219 C4' A C 5 OK 1221 1218 1220 1241 C4' G C 6 OK 1243 1240 1242 1264 C4' C C 7 OK 1266 1263 1265 1284 C4' A C 8 OK 1286 1283 1285 1306 C4' U C 9 OK 1308 1305 1307 1326 C4' U C 10 OK 1328 1325 1327 1346 C4' A C 11 OK 1348 1345 1347 1368 C4' U C 12 OK 1370 1367 1369 1388 C4' G C 13 OK 1390 1387 1389 1411 C4' C C 14 OK 1413 1410 1412 1431 C4' U C 15 OK 1433 1430 1432 1451 C4' G C 16 OK 1453 1450 1452 1474 C4' U C 17 OK 1476 1473 1475 1494 C4' C C 18 OK 1496 1493 1495 1514 C4' U C 19 OK 1516 1513 1515 1534 C4' U C 20 OK 1536 1533 1535 1554 C4' U C 21 OK 1556 1553 1555 1575 C4' A D 1 OK 1577 1574 1576 1597 C4' G D 2 OK 1599 1596 1598 1620 C4' A D 3 OK 1622 1619 1621 1642 C4' C D 4 OK 1644 1641 1643 1662 C4' A D 5 OK 1664 1661 1663 1684 C4' G D 6 OK 1686 1683 1685 1707 C4' C D 7 OK 1709 1706 1708 1727 C4' A D 8 OK 1729 1726 1728 1749 C4' U D 9 OK 1751 1748 1750 1769 C4' U D 10 OK 1771 1768 1770 1789 C4' A D 11 OK 1791 1788 1790 1811 C4' U D 12 OK 1813 1810 1812 1831 C4' G D 13 OK 1833 1830 1832 1854 C4' C D 14 OK 1856 1853 1855 1874 C4' U D 15 OK 1876 1873 1875 1894 C4' G D 16 OK 1896 1893 1895 1917 C4' U D 17 OK 1919 1916 1918 1937 C4' C D 18 OK 1939 1936 1938 1957 C4' U D 19 OK 1959 1956 1958 1977 C4' U D 20 OK 1979 1976 1978 1997 C4' U D 21 OK 1999 1996 1998 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1131 C5' A C 1 1130 1132 1153 C5' G C 2 1152 1154 1176 C5' A C 3 1175 1177 1198 C5' C C 4 1197 1199 1218 C5' A C 5 1217 1219 1240 C5' G C 6 1239 1241 1263 C5' C C 7 1262 1264 1283 C5' A C 8 1282 1284 1305 C5' U C 9 1304 1306 1325 C5' U C 10 1324 1326 1345 C5' A C 11 1344 1346 1367 C5' U C 12 1366 1368 1387 C5' G C 13 1386 1388 1410 C5' C C 14 1409 1411 1430 C5' U C 15 1429 1431 1450 C5' G C 16 1449 1451 1473 C5' U C 17 1472 1474 1493 C5' C C 18 1492 1494 1513 C5' U C 19 1512 1514 1533 C5' U C 20 1532 1534 1553 C5' U C 21 1552 1554 1574 C5' A D 1 1573 1575 1596 C5' G D 2 1595 1597 1619 C5' A D 3 1618 1620 1641 C5' C D 4 1640 1642 1661 C5' A D 5 1660 1662 1683 C5' G D 6 1682 1684 1706 C5' C D 7 1705 1707 1726 C5' A D 8 1725 1727 1748 C5' U D 9 1747 1749 1768 C5' U D 10 1767 1769 1788 C5' A D 11 1787 1789 1810 C5' U D 12 1809 1811 1830 C5' G D 13 1829 1831 1853 C5' C D 14 1852 1854 1873 C5' U D 15 1872 1874 1893 C5' G D 16 1892 1894 1916 C5' U D 17 1915 1917 1936 C5' C D 18 1935 1937 1956 C5' U D 19 1955 1957 1976 C5' U D 20 1975 1977 1996 C5' U D 21 1995 1997 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1127 P A C 1 OK OK 1128 1129 1130 1149 P G C 2 distorted distorted 1135 1150 1151 1152 1172 P A C 3 distorted distorted 1157 1173 1174 1175 1194 P C C 4 distorted distorted 1180 1195 1196 1197 1214 P A C 5 distorted distorted 1202 1215 1216 1217 1236 P G C 6 distorted distorted 1222 1237 1238 1239 1259 P C C 7 distorted distorted 1244 1260 1261 1262 1279 P A C 8 distorted distorted 1267 1280 1281 1282 1301 P U C 9 distorted distorted 1287 1302 1303 1304 1321 P U C 10 distorted distorted 1309 1322 1323 1324 1341 P A C 11 distorted distorted 1329 1342 1343 1344 1363 P U C 12 distorted distorted 1349 1364 1365 1366 1383 P G C 13 distorted distorted 1371 1384 1385 1386 1406 P C C 14 distorted distorted 1391 1407 1408 1409 1426 P U C 15 distorted distorted 1414 1427 1428 1429 1446 P G C 16 distorted distorted 1434 1447 1448 1449 1469 P U C 17 distorted distorted 1454 1470 1471 1472 1489 P C C 18 distorted distorted 1477 1490 1491 1492 1509 P U C 19 distorted distorted 1497 1510 1511 1512 1529 P U C 20 distorted distorted 1517 1530 1531 1532 1549 P U C 21 distorted distorted 1537 1550 1551 1552 1570 P A D 1 distorted distorted 1571 1572 1573 1592 P G D 2 distorted distorted 1578 1593 1594 1595 1615 P A D 3 distorted distorted 1600 1616 1617 1618 1637 P C D 4 distorted distorted 1623 1638 1639 1640 1657 P A D 5 distorted distorted 1645 1658 1659 1660 1679 P G D 6 distorted distorted 1665 1680 1681 1682 1702 P C D 7 distorted distorted 1687 1703 1704 1705 1722 P A D 8 distorted distorted 1710 1723 1724 1725 1744 P U D 9 distorted distorted 1730 1745 1746 1747 1764 P U D 10 distorted distorted 1752 1765 1766 1767 1784 P A D 11 distorted distorted 1772 1785 1786 1787 1806 P U D 12 distorted distorted 1792 1807 1808 1809 1826 P G D 13 distorted distorted 1814 1827 1828 1829 1849 P C D 14 distorted distorted 1834 1850 1851 1852 1869 P U D 15 distorted distorted 1857 1870 1871 1872 1889 P G D 16 distorted distorted 1877 1890 1891 1892 1912 P U D 17 distorted distorted 1897 1913 1914 1915 1932 P C D 18 distorted distorted 1920 1933 1934 1935 1952 P U D 19 distorted distorted 1940 1953 1954 1955 1972 P U D 20 distorted distorted 1960 1973 1974 1975 1992 P U D 21 distorted distorted 1980 1993 1994 1995 ---------------------------------------------------------------------------------