ID code: '2ZI0' 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' --------------------------------------------------------------------------------- 1007 C1' A C 1 beta 1002 1008 1005 1029 C1' G C 2 beta 1024 1030 1027 1052 C1' A C 3 beta 1047 1053 1050 1074 C1' C C 4 beta 1069 1075 1072 1094 C1' A C 5 beta 1089 1095 1092 1116 C1' G C 6 beta 1111 1117 1114 1139 C1' C C 7 beta 1134 1140 1137 1159 C1' A C 8 beta 1154 1160 1157 1181 C1' U C 9 beta 1176 1182 1179 1201 C1' U C 10 beta 1196 1202 1199 1221 C1' A C 11 beta 1216 1222 1219 1243 C1' U C 12 beta 1238 1244 1241 1263 C1' G C 13 beta 1258 1264 1261 1286 C1' C C 14 beta 1281 1287 1284 1306 C1' U C 15 beta 1301 1307 1304 1326 C1' G C 16 beta 1321 1327 1324 1349 C1' U C 17 beta 1344 1350 1347 1369 C1' C C 18 beta 1364 1370 1367 1389 C1' U C 19 beta 1384 1390 1387 1413 C1' A D 1 beta 1408 1414 1411 1435 C1' G D 2 beta 1430 1436 1433 1458 C1' A D 3 beta 1453 1459 1456 1480 C1' C D 4 beta 1475 1481 1478 1500 C1' A D 5 beta 1495 1501 1498 1522 C1' G D 6 beta 1517 1523 1520 1545 C1' C D 7 beta 1540 1546 1543 1565 C1' A D 8 beta 1560 1566 1563 1587 C1' U D 9 beta 1582 1588 1585 1607 C1' U D 10 beta 1602 1608 1605 1627 C1' A D 11 beta 1622 1628 1625 1649 C1' U D 12 beta 1644 1650 1647 1669 C1' G D 13 beta 1664 1670 1667 1692 C1' C D 14 beta 1687 1693 1690 1712 C1' U D 15 beta 1707 1713 1710 1732 C1' G D 16 beta 1727 1733 1730 1755 C1' U D 17 beta 1750 1756 1753 1775 C1' C D 18 beta 1770 1776 1773 1795 C1' U D 19 beta 1790 1796 1793 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1005 C2' A C 1 OK 1007 1003 1006 1027 C2' G C 2 OK 1029 1025 1028 1050 C2' A C 3 OK 1052 1048 1051 1072 C2' C C 4 OK 1074 1070 1073 1092 C2' A C 5 OK 1094 1090 1093 1114 C2' G C 6 OK 1116 1112 1115 1137 C2' C C 7 OK 1139 1135 1138 1157 C2' A C 8 OK 1159 1155 1158 1179 C2' U C 9 OK 1181 1177 1180 1199 C2' U C 10 OK 1201 1197 1200 1219 C2' A C 11 OK 1221 1217 1220 1241 C2' U C 12 OK 1243 1239 1242 1261 C2' G C 13 OK 1263 1259 1262 1284 C2' C C 14 OK 1286 1282 1285 1304 C2' U C 15 OK 1306 1302 1305 1324 C2' G C 16 OK 1326 1322 1325 1347 C2' U C 17 OK 1349 1345 1348 1367 C2' C C 18 OK 1369 1365 1368 1387 C2' U C 19 OK 1389 1385 1388 1411 C2' A D 1 OK 1413 1409 1412 1433 C2' G D 2 OK 1435 1431 1434 1456 C2' A D 3 OK 1458 1454 1457 1478 C2' C D 4 OK 1480 1476 1479 1498 C2' A D 5 OK 1500 1496 1499 1520 C2' G D 6 OK 1522 1518 1521 1543 C2' C D 7 OK 1545 1541 1544 1563 C2' A D 8 OK 1565 1561 1564 1585 C2' U D 9 OK 1587 1583 1586 1605 C2' U D 10 OK 1607 1603 1606 1625 C2' A D 11 OK 1627 1623 1626 1647 C2' U D 12 OK 1649 1645 1648 1667 C2' G D 13 OK 1669 1665 1668 1690 C2' C D 14 OK 1692 1688 1691 1710 C2' U D 15 OK 1712 1708 1711 1730 C2' G D 16 OK 1732 1728 1731 1753 C2' U D 17 OK 1755 1751 1754 1773 C2' C D 18 OK 1775 1771 1774 1793 C2' U D 19 OK 1795 1791 1794 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1003 C3' A C 1 OK 1001 1004 1005 1025 C3' G C 2 OK 1023 1026 1027 1048 C3' A C 3 OK 1046 1049 1050 1070 C3' C C 4 OK 1068 1071 1072 1090 C3' A C 5 OK 1088 1091 1092 1112 C3' G C 6 OK 1110 1113 1114 1135 C3' C C 7 OK 1133 1136 1137 1155 C3' A C 8 OK 1153 1156 1157 1177 C3' U C 9 OK 1175 1178 1179 1197 C3' U C 10 OK 1195 1198 1199 1217 C3' A C 11 OK 1215 1218 1219 1239 C3' U C 12 OK 1237 1240 1241 1259 C3' G C 13 OK 1257 1260 1261 1282 C3' C C 14 OK 1280 1283 1284 1302 C3' U C 15 OK 1300 1303 1304 1322 C3' G C 16 OK 1320 1323 1324 1345 C3' U C 17 OK 1343 1346 1347 1365 C3' C C 18 OK 1363 1366 1367 1385 C3' U C 19 OK 1383 1386 1387 1409 C3' A D 1 OK 1407 1410 1411 1431 C3' G D 2 OK 1429 1432 1433 1454 C3' A D 3 OK 1452 1455 1456 1476 C3' C D 4 OK 1474 1477 1478 1496 C3' A D 5 OK 1494 1497 1498 1518 C3' G D 6 OK 1516 1519 1520 1541 C3' C D 7 OK 1539 1542 1543 1561 C3' A D 8 OK 1559 1562 1563 1583 C3' U D 9 OK 1581 1584 1585 1603 C3' U D 10 OK 1601 1604 1605 1623 C3' A D 11 OK 1621 1624 1625 1645 C3' U D 12 OK 1643 1646 1647 1665 C3' G D 13 OK 1663 1666 1667 1688 C3' C D 14 OK 1686 1689 1690 1708 C3' U D 15 OK 1706 1709 1710 1728 C3' G D 16 OK 1726 1729 1730 1751 C3' U D 17 OK 1749 1752 1753 1771 C3' C D 18 OK 1769 1772 1773 1791 C3' U D 19 OK 1789 1792 1793 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1001 C4' A C 1 OK 1003 1000 1002 1023 C4' G C 2 OK 1025 1022 1024 1046 C4' A C 3 OK 1048 1045 1047 1068 C4' C C 4 OK 1070 1067 1069 1088 C4' A C 5 OK 1090 1087 1089 1110 C4' G C 6 OK 1112 1109 1111 1133 C4' C C 7 OK 1135 1132 1134 1153 C4' A C 8 OK 1155 1152 1154 1175 C4' U C 9 OK 1177 1174 1176 1195 C4' U C 10 OK 1197 1194 1196 1215 C4' A C 11 OK 1217 1214 1216 1237 C4' U C 12 OK 1239 1236 1238 1257 C4' G C 13 OK 1259 1256 1258 1280 C4' C C 14 OK 1282 1279 1281 1300 C4' U C 15 OK 1302 1299 1301 1320 C4' G C 16 OK 1322 1319 1321 1343 C4' U C 17 OK 1345 1342 1344 1363 C4' C C 18 OK 1365 1362 1364 1383 C4' U C 19 OK 1385 1382 1384 1407 C4' A D 1 OK 1409 1406 1408 1429 C4' G D 2 OK 1431 1428 1430 1452 C4' A D 3 OK 1454 1451 1453 1474 C4' C D 4 OK 1476 1473 1475 1494 C4' A D 5 OK 1496 1493 1495 1516 C4' G D 6 OK 1518 1515 1517 1539 C4' C D 7 OK 1541 1538 1540 1559 C4' A D 8 OK 1561 1558 1560 1581 C4' U D 9 OK 1583 1580 1582 1601 C4' U D 10 OK 1603 1600 1602 1621 C4' A D 11 OK 1623 1620 1622 1643 C4' U D 12 OK 1645 1642 1644 1663 C4' G D 13 OK 1665 1662 1664 1686 C4' C D 14 OK 1688 1685 1687 1706 C4' U D 15 OK 1708 1705 1707 1726 C4' G D 16 OK 1728 1725 1727 1749 C4' U D 17 OK 1751 1748 1750 1769 C4' C D 18 OK 1771 1768 1770 1789 C4' U D 19 OK 1791 1788 1790 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1000 C5' A C 1 999 1001 1022 C5' G C 2 1021 1023 1045 C5' A C 3 1044 1046 1067 C5' C C 4 1066 1068 1087 C5' A C 5 1086 1088 1109 C5' G C 6 1108 1110 1132 C5' C C 7 1131 1133 1152 C5' A C 8 1151 1153 1174 C5' U C 9 1173 1175 1194 C5' U C 10 1193 1195 1214 C5' A C 11 1213 1215 1236 C5' U C 12 1235 1237 1256 C5' G C 13 1255 1257 1279 C5' C C 14 1278 1280 1299 C5' U C 15 1298 1300 1319 C5' G C 16 1318 1320 1342 C5' U C 17 1341 1343 1362 C5' C C 18 1361 1363 1382 C5' U C 19 1381 1383 1406 C5' A D 1 1405 1407 1428 C5' G D 2 1427 1429 1451 C5' A D 3 1450 1452 1473 C5' C D 4 1472 1474 1493 C5' A D 5 1492 1494 1515 C5' G D 6 1514 1516 1538 C5' C D 7 1537 1539 1558 C5' A D 8 1557 1559 1580 C5' U D 9 1579 1581 1600 C5' U D 10 1599 1601 1620 C5' A D 11 1619 1621 1642 C5' U D 12 1641 1643 1662 C5' G D 13 1661 1663 1685 C5' C D 14 1684 1686 1705 C5' U D 15 1704 1706 1725 C5' G D 16 1724 1726 1748 C5' U D 17 1747 1749 1768 C5' C D 18 1767 1769 1788 C5' U D 19 1787 1789 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 996 P A C 1 OK OK 997 998 999 1018 P G C 2 distorted distorted 1004 1019 1020 1021 1041 P A C 3 distorted distorted 1026 1042 1043 1044 1063 P C C 4 distorted distorted 1049 1064 1065 1066 1083 P A C 5 distorted distorted 1071 1084 1085 1086 1105 P G C 6 distorted distorted 1091 1106 1107 1108 1128 P C C 7 distorted distorted 1113 1129 1130 1131 1148 P A C 8 distorted distorted 1136 1149 1150 1151 1170 P U C 9 distorted distorted 1156 1171 1172 1173 1190 P U C 10 distorted distorted 1178 1191 1192 1193 1210 P A C 11 distorted distorted 1198 1211 1212 1213 1232 P U C 12 distorted distorted 1218 1233 1234 1235 1252 P G C 13 distorted distorted 1240 1253 1254 1255 1275 P C C 14 distorted distorted 1260 1276 1277 1278 1295 P U C 15 distorted distorted 1283 1296 1297 1298 1315 P G C 16 distorted distorted 1303 1316 1317 1318 1338 P U C 17 distorted distorted 1323 1339 1340 1341 1358 P C C 18 distorted distorted 1346 1359 1360 1361 1378 P U C 19 distorted distorted 1366 1379 1380 1381 1398 P U C 20 OK OK 1386 1399 1400 1402 P A D 1 distorted distorted 1403 1404 1405 1424 P G D 2 distorted distorted 1410 1425 1426 1427 1447 P A D 3 distorted distorted 1432 1448 1449 1450 1469 P C D 4 distorted distorted 1455 1470 1471 1472 1489 P A D 5 distorted distorted 1477 1490 1491 1492 1511 P G D 6 distorted distorted 1497 1512 1513 1514 1534 P C D 7 distorted distorted 1519 1535 1536 1537 1554 P A D 8 distorted distorted 1542 1555 1556 1557 1576 P U D 9 distorted distorted 1562 1577 1578 1579 1596 P U D 10 distorted distorted 1584 1597 1598 1599 1616 P A D 11 distorted distorted 1604 1617 1618 1619 1638 P U D 12 distorted distorted 1624 1639 1640 1641 1658 P G D 13 distorted distorted 1646 1659 1660 1661 1681 P C D 14 distorted distorted 1666 1682 1683 1684 1701 P U D 15 distorted distorted 1689 1702 1703 1704 1721 P G D 16 distorted distorted 1709 1722 1723 1724 1744 P U D 17 distorted distorted 1729 1745 1746 1747 1764 P C D 18 distorted distorted 1752 1765 1766 1767 1784 P U D 19 distorted distorted 1772 1785 1786 1787 1804 P U D 20 OK OK 1792 1805 1806 ---------------------------------------------------------------------------------