MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 3i1q 3I1Q (3.81Å) -- RIBOSOME : Crystal structure of the e. coli 70s ribosome in an intermediate state of ratcheting List of all 40 Mg2+ binding sites in the PDB structure 3i1q in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID" Page 2 of 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3i1q A1538 cis-2Oph A:A509(OP2), A:A510(OP2) A1596, A1597, A1598, A1599 G:A506 A:A510 3i1q A1553 cis-2Oph C:A1303(OP1), G:A1304(OP2) A1666, A1667, A1668, A1669 3i1q A1551 cis-2Oph C:A1054(OP2), A:A1197(OP2) A1657, A1658, A1659, A1660 A:A1196, G:A1053 G:A1198, A:A1197 3i1q A1555 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1675, A1676, A1677 C:A1501 G:A1504 3i1q A1575 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1764, A1765, A1766 A:A288 U:A118 3i1q A1570 2Bout A1743, A1744, A1745, A1746, U222, U225 G:A1525, G:A1526 3i1q A1 Pout·Bout A1577, A1578, A1579, A1580, T87, T88 G:A259 G:A260 3i1q A1556 Pout·2Bout A1678, A1679, A1680, A1681, A1682, A1683 G:A266 G:A257, G:A258 3i1q A1549 Pout·2Bout A1650, A1651, A1652, N121, N124, N125 A:A1360 G:A1361, C:A980 3i1q A1560 Pout·2Bout A1699, A1700, A1701, A1702, A1703, A1704 G:A1385 G:A1386, G:A1385 3i1q A1557 Pout·3Bout A1684, A1685, A1686, A1687, A1688, A1689 A:A781 G:A800, U:A798, G:A799 3i1q A1543 Pout·4Bout A1618, A1619, A1620, A1621, A1622, A1623 G:A645 G:A646, G:A592, U:A593, G:A645 3i1q A1563 2Pout·Bout A1711, A1712, A1713, A1714, A1715 A:A1433, A:A1434 G:A1435 3i1q A1552 2Pout·Bout A1661, A1662, A1663, A1664, A1665, E167 G:A1077, U:A1076 G:A1077 3i1q A1544 2Pout·2Bout A1624, A1625, A1626, A1627, A1628, A1629 G:A803, U:A804 G:A771, U:A772 3i1q A1537 2Pout·2Bout A1590, A1591, A1592, A1593, A1594, A1595 A:A415, G:A416 G:A417, G:A425 3i1q A1535 2Pout·3Bout A1581, A1582, A1583, A1584, A1585, A1586 A:A329, A:A315 A:A320, G:A318, G:A319 3i1q A1550 3Pout A1653, A1654, A1655, A1656, N128, N132 C:A1203, A:A1204, G:A1048 3i1q A1574 3Pout·Rout A1759, A1760, A1761, A1762, A1763, L240 C:A504, C:A536, C:A503 C:A522 3i1q A1540 4Pout·Rout·Bout A1605, A1606, A1607, A1608, A1609 G:A557, A:A560, U:A562, G:A558 A:A559 A:A300

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations used for Mg2+ "Site type"	Mg2+ inner-sphere ligands	Geometry for inner-sphere OP	Mg2+ outer-sphere moieties
	Oph phosphate oxygen (OP1/OP2) Or ribose oxygen (O2'/O4')      or oxygen bridging phosphate and ribose (O3'/O5') Ob nucleobase oxygen      Nb nucleobase nitrogen	cis- two OP ligands adopt cis- isoform trans- two OP ligands adopt trans- isoform fac- three OP ligands adopt fac- isoform mer- three OP ligands adopt mer- isoform	Pout phosphate moiety Rout ribose moiety Bout nucleobase moiety
Reference:	Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

---

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>