ID code: '4NI7' 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' --------------------------------------------------------------------------------- 1139 C1' DG B 1 beta 1135 1140 1138 1161 C1' DG B 2 beta 1157 1162 1160 1181 C1' OMC B 3 beta 1187 1173 1182 1204 C1' DA B 4 beta 1200 1205 1203 1225 C1' DG B 5 beta 1221 1226 1224 1249 C1' OMG B 6 beta 1243 1250 1246 1270 C1' DUZ B 7 beta 1285 1262 1271 1299 C1' DUZ B 8 beta 1314 1291 1300 1328 C1' UPE B 9 beta 1344 1320 1329 1359 C1' DG B 10 beta 1355 1360 1358 1381 C1' DG B 11 beta 1377 1382 1380 1401 C1' 2JU B 12 beta 1402 1403 1400 1436 C1' DA B 13 beta 1432 1437 1435 1456 C1' DUZ B 14 beta 1471 1448 1457 1485 C1' DUZ B 15 beta 1500 1477 1486 1515 C1' A2M B 16 beta 1510 1517 1513 1538 C1' DA B 17 beta 1534 1539 1537 1559 C1' DC B 18 beta 1555 1560 1558 1582 C1' DG B 21 beta 1578 1583 1581 1603 C1' DUZ B 22 beta 1618 1595 1604 1632 C1' DUZ B 23 beta 1647 1624 1633 1662 C1' DA B 24 beta 1658 1663 1661 1683 C1' DA B 25 beta 1679 1684 1682 1704 C1' DG B 26 beta 1700 1705 1703 1725 C1' DUZ B 27 beta 1740 1717 1726 1753 C1' OMC B 28 beta 1759 1745 1754 1776 C1' DG B 29 beta 1772 1777 1775 1797 C1' DUZ B 30 beta 1812 1789 1798 1827 C1' DG B 31 beta 1823 1828 1826 1849 C1' DG B 32 beta 1845 1850 1848 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1138 C2' DG B 1 1139 1136 1160 C2' DG B 2 1161 1158 1182 C2' OMC B 3 OK 1181 1185 1183 1203 C2' DA B 4 1204 1201 1224 C2' DG B 5 1225 1222 1246 C2' OMG B 6 OK 1249 1244 1247 1271 C2' DUZ B 7 1270 1281 1300 C2' DUZ B 8 1299 1310 1329 C2' UPE B 9 1328 1339 1358 C2' DG B 10 1359 1356 1380 C2' DG B 11 1381 1378 1400 C2' 2JU B 12 1401 1399 1435 C2' DA B 13 1436 1433 1457 C2' DUZ B 14 1456 1467 1486 C2' DUZ B 15 1485 1496 1513 C2' A2M B 16 OK 1515 1511 1514 1537 C2' DA B 17 1538 1535 1558 C2' DC B 18 1559 1556 1581 C2' DG B 21 1582 1579 1604 C2' DUZ B 22 1603 1614 1633 C2' DUZ B 23 1632 1643 1661 C2' DA B 24 1662 1659 1682 C2' DA B 25 1683 1680 1703 C2' DG B 26 1704 1701 1726 C2' DUZ B 27 1725 1736 1754 C2' OMC B 28 OK 1753 1757 1755 1775 C2' DG B 29 1776 1773 1798 C2' DUZ B 30 1797 1808 1826 C2' DG B 31 1827 1824 1848 C2' DG B 32 1849 1846 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1136 C3' DG B 1 OK 1134 1137 1138 1158 C3' DG B 2 OK 1156 1159 1160 1185 C3' OMC B 3 OK 1186 1188 1182 1201 C3' DA B 4 OK 1199 1202 1203 1222 C3' DG B 5 OK 1220 1223 1224 1244 C3' OMG B 6 OK 1242 1245 1246 1281 C3' DUZ B 7 OK 1284 1282 1271 1310 C3' DUZ B 8 OK 1313 1311 1300 1339 C3' UPE B 9 OK 1343 1340 1329 1356 C3' DG B 10 OK 1354 1357 1358 1378 C3' DG B 11 OK 1376 1379 1380 1399 C3' 2JU B 12 OK 1398 1425 1400 1433 C3' DA B 13 OK 1431 1434 1435 1467 C3' DUZ B 14 OK 1470 1468 1457 1496 C3' DUZ B 15 OK 1499 1497 1486 1511 C3' A2M B 16 OK 1509 1512 1513 1535 C3' DA B 17 OK 1533 1536 1537 1556 C3' DC B 18 OK 1554 1557 1558 1579 C3' DG B 21 OK 1577 1580 1581 1614 C3' DUZ B 22 OK 1617 1615 1604 1643 C3' DUZ B 23 OK 1646 1644 1633 1659 C3' DA B 24 OK 1657 1660 1661 1680 C3' DA B 25 OK 1678 1681 1682 1701 C3' DG B 26 OK 1699 1702 1703 1736 C3' DUZ B 27 OK 1739 1737 1726 1757 C3' OMC B 28 OK 1758 1760 1754 1773 C3' DG B 29 OK 1771 1774 1775 1808 C3' DUZ B 30 OK 1811 1809 1798 1824 C3' DG B 31 OK 1822 1825 1826 1846 C3' DG B 32 OK 1844 1847 1848 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1134 C4' DG B 1 OK 1136 1133 1135 1156 C4' DG B 2 OK 1158 1155 1157 1186 C4' OMC B 3 OK 1185 1189 1187 1199 C4' DA B 4 OK 1201 1198 1200 1220 C4' DG B 5 OK 1222 1219 1221 1242 C4' OMG B 6 OK 1244 1241 1243 1284 C4' DUZ B 7 OK 1281 1286 1285 1313 C4' DUZ B 8 OK 1310 1315 1314 1343 C4' UPE B 9 OK 1339 1345 1344 1354 C4' DG B 10 OK 1356 1353 1355 1376 C4' DG B 11 OK 1378 1375 1377 1398 C4' 2JU B 12 OK 1399 1397 1402 1431 C4' DA B 13 OK 1433 1430 1432 1470 C4' DUZ B 14 OK 1467 1472 1471 1499 C4' DUZ B 15 OK 1496 1501 1500 1509 C4' A2M B 16 OK 1511 1508 1510 1533 C4' DA B 17 OK 1535 1532 1534 1554 C4' DC B 18 OK 1556 1553 1555 1577 C4' DG B 21 OK 1579 1576 1578 1617 C4' DUZ B 22 OK 1614 1619 1618 1646 C4' DUZ B 23 OK 1643 1648 1647 1657 C4' DA B 24 OK 1659 1656 1658 1678 C4' DA B 25 OK 1680 1677 1679 1699 C4' DG B 26 OK 1701 1698 1700 1739 C4' DUZ B 27 OK 1736 1741 1740 1758 C4' OMC B 28 OK 1757 1761 1759 1771 C4' DG B 29 OK 1773 1770 1772 1811 C4' DUZ B 30 OK 1808 1813 1812 1822 C4' DG B 31 OK 1824 1821 1823 1844 C4' DG B 32 OK 1846 1843 1845 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1133 C5' DG B 1 1132 1134 1155 C5' DG B 2 1154 1156 1189 C5' OMC B 3 1190 1186 1198 C5' DA B 4 1197 1199 1219 C5' DG B 5 1218 1220 1241 C5' OMG B 6 1240 1242 1286 C5' DUZ B 7 1287 1284 1315 C5' DUZ B 8 1316 1313 1345 C5' UPE B 9 1346 1343 1353 C5' DG B 10 1352 1354 1375 C5' DG B 11 1374 1376 1397 C5' 2JU B 12 1396 1398 1430 C5' DA B 13 1429 1431 1472 C5' DUZ B 14 1473 1470 1501 C5' DUZ B 15 1502 1499 1508 C5' A2M B 16 1507 1509 1532 C5' DA B 17 1531 1533 1553 C5' DC B 18 1552 1554 1576 C5' DG B 21 1575 1577 1619 C5' DUZ B 22 1620 1617 1648 C5' DUZ B 23 1649 1646 1656 C5' DA B 24 1655 1657 1677 C5' DA B 25 1676 1678 1698 C5' DG B 26 1697 1699 1741 C5' DUZ B 27 1742 1739 1761 C5' OMC B 28 1762 1758 1770 C5' DG B 29 1769 1771 1813 C5' DUZ B 30 1814 1811 1821 C5' DG B 31 1820 1822 1843 C5' DG B 32 1842 1844 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1151 P DG B 2 distorted distorted 1137 1152 1153 1154 1191 P OMC B 3 OK OK 1159 1192 1193 1190 1194 P DA B 4 distorted distorted 1188 1195 1196 1197 1215 P DG B 5 distorted distorted 1202 1216 1217 1218 1237 P OMG B 6 OK OK 1223 1238 1239 1240 1261 P DUZ B 7 distorted distorted 1245 1288 1289 1287 1290 P DUZ B 8 OK OK 1282 1317 1318 1316 1319 P UPE B 9 distorted distorted 1311 1347 1348 1346 1349 P DG B 10 distorted distorted 1340 1350 1351 1352 1371 P DG B 11 distorted distorted 1357 1372 1373 1374 1393 P 2JU B 12 distorted distorted 1379 1394 1395 1396 1426 P DA B 13 distorted distorted 1425 1427 1428 1429 1447 P DUZ B 14 distorted distorted 1434 1474 1475 1473 1476 P DUZ B 15 distorted distorted 1468 1503 1504 1502 1505 P A2M B 16 distorted distorted 1497 1506 1527 1507 1528 P DA B 17 distorted distorted 1512 1529 1530 1531 1549 P DC B 18 distorted distorted 1536 1550 1551 1552 1568 P A2M B 19 OK OK 1557 1569 1571 1570 1572 P DG B 21 OK OK 1573 1574 1575 1594 P DUZ B 22 OK OK 1580 1621 1622 1620 1623 P DUZ B 23 OK OK 1615 1650 1651 1649 1652 P DA B 24 distorted distorted 1644 1653 1654 1655 1673 P DA B 25 distorted distorted 1660 1674 1675 1676 1694 P DG B 26 distorted distorted 1681 1695 1696 1697 1716 P DUZ B 27 distorted distorted 1702 1743 1744 1742 1763 P OMC B 28 distorted distorted 1737 1764 1765 1762 1766 P DG B 29 distorted distorted 1760 1767 1768 1769 1788 P DUZ B 30 OK OK 1774 1815 1816 1814 1817 P DG B 31 distorted distorted 1809 1818 1819 1820 1839 P DG B 32 distorted distorted 1825 1840 1841 1842 ---------------------------------------------------------------------------------