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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3i1q A1555 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1675, A1676, A1677 C:A1501 G:A1504
3i1q A1556 Pout·2Bout A1678, A1679, A1680, A1681, A1682, A1683 G:A266 G:A257, G:A258
3i1q A1557 Pout·3Bout A1684, A1685, A1686, A1687, A1688, A1689 A:A781 G:A800, U:A798, G:A799
3i1q A1558 Oph·Pout G:A21(OP1) A1690, A1691, A1692, A1693, A1694 U:A561 G:A568 G:A567, A:A573, A:A563
3i1q A1559 2Nb G:A858(N7), G:A869(N7) A1695, A1696, A1697, A1698 G:A858, C:A857, C:A868
3i1q A1560 Pout·2Bout A1699, A1700, A1701, A1702, A1703, A1704 G:A1385 G:A1386, G:A1385
3i1q A1561 cis-2Oph A:A964(OP1), U:A1199(OP1) A1705, A1706, A1707, A1708 G:A1198
3i1q A1563 2Pout·Bout A1711, A1712, A1713, A1714, A1715 A:A1433, A:A1434 G:A1435
3i1q A1564 Ob G:A299(O6) A1716, A1717, A1718, A1719 G:A558, A:A560 G:A297 A:A298, G:A566
3i1q A1565 Nb G:A324(N7) A1720, A1721, A1722, A1723, A1724 U:A323, G:A326, G:A324
3i1q A1566 Oph·Ob A:A533(OP1) U:A516(O4) A1725, A1726, A1727, A1728 A:A532
3i1q A1567 Oph·2Pout A:A608(OP2) A1729, A1730, A1731, A1732, A1733 A:A607, A:A609 C:A631, A:A609, A:A630, A:A608, U:A610
3i1q A1568 Oph·Pout A:A1110(OP2) A1734, A1735, A1736, A1737, A1738 C:A1109 A:A1110, A:A1111, U:A1189
3i1q A1569 Oph·Ob U:A1095(OP2) G:A1108(O6) A1739, A1740, A1741, A1742 C:A1096 G:A1094
3i1q A1570 2Bout A1743, A1744, A1745, A1746, U222, U225 G:A1525, G:A1526
3i1q A1572 Oph·Pout G:A100(OP2) A1750, A1751, A1752, A1753, A1754 A:A101 G:A64, G:A100, A:A101
3i1q A1573 Oph·Ob A:A195(OP2) U:A180(O4) A1755, A1756, A1757, A1758 C:A194, A:A179 A:A181
3i1q A1574 3Pout·Rout A1759, A1760, A1761, A1762, A1763, L240 C:A504, C:A536, C:A503 C:A522
3i1q A1575 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1764, A1765, A1766 A:A288 U:A118
3i1q A1576 Oph·Pout C:A352(OP2) A1767, A1768, A1769, A1770, A1771 G:A354 G:A331, C:A352 C:A330, A:A59

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>