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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 3i1o



3I1O (3.19Å) -- 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 3i1o 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
3i1o A1550 Ob G:A1417(O6) A1667, A1668, A1669, A1670, A1671 G:A1415, G:A1416, G:A1482
3i1o A3 Ob G:A362(O6) A1583, A1584, A1585, A1586, A1587 G:A361 G:A361
3i1o A1562 Nb G:A324(N7) A1725, A1726, A1727, A1728, A1729 U:A323, G:A324
3i1o A1556 2Nb G:A858(N7), G:A869(N7) A1698, A1699, A1700, A1701 G:A858, C:A868, G:A869
3i1o A1545 Oph A:A937(OP2) A1642, A1643, A1644, A1645, A1646 A:A938, G:A939
3i1o A1548 Oph C:A1054(OP2) A1657, A1658, A1659, A1660 G:A1053 G:A1198, U:A1199
3i1o A1555 Oph G:A21(OP1) A1693, A1694, A1695, A1696, A1697 G:A568, G:A567 A:A563, G:A567
3i1o A1568 Oph G:A100(OP2) A1752, A1753, A1754, A1755, A1756 G:A64, G:A100, A:A101
3i1o A1544 Oph C:A934(OP1) A1637, A1638, A1639, A1640, A1641
3i1o A1560 Oph·Pout A:A1433(OP2) A1717, A1718, A1719, A1720, A1721 A:A1434 G:A1435, C:A1466, A:A1434
3i1o A1572 Oph·Pout C:A352(OP2) A1769, A1770, A1771, A1772, A1773 G:A354 C:A352 C:A330, G:A354, A:A59
3i1o A1536 Oph·Pout A:A547(OP1) A1598, A1599, A1600, A1601, A1602 G:A548 G:A402
3i1o A1543 Oph·2Pout U:A891(OP2) A1632, A1633, A1634, A1635, A1636 A:A892, G:A903 U:A905, A:A906, U:A904
3i1o A1564 Oph·2Pout A:A608(OP2) A1734, A1735, A1736, A1737, A1738 A:A607, A:A609 A:A609, U:A610, A:A630, A:A608
3i1o A1565 Oph·2Pout A:A1110(OP2) A1739, A1740, A1741, A1742, A1743 C:A1109, A:A1111 U:A1189, A:A1110, A:A1111, C:A1112
3i1o A1537 Oph·2Pout A:A560(OP2) A1603, A1604, A1605, A1606, A1607 A:A563, U:A562 A:A559 G:A566, A:A300
3i1o A1539 Oph·3Pout C:A578(OP1) A1611, A1612, A1613, A1614, A1615 C:A576, C:A817, U:A820 G:A575, G:A821
3i1o A1559 Oph·4Pout G:A1198(OP1) A1713, A1714, A1715, A1716 A:A964, U:A965, C:A1054, U:A1199
3i1o A1561 Oph·Ob G:A558(OP1) G:A299(O6) A1722, A1723, A1724, E198 A:A300
3i1o A1563 Oph·Ob A:A533(OP1) U:A516(O4) A1730, A1731, A1732, A1733 G:A515, G:A517

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>