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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 3i1z



3I1Z (3.71Å) -- 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 3i1z 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 1 of 2 | « Previous | | 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
3i1z A1554 Ob G:A1417(O6) A1672, A1673, A1674, A1675, A1676 G:A1415 G:A1416, G:A1482
3i1z A1565 Nb G:A324(N7) A1722, A1723, A1724, A1725, A1726 U:A323, G:A324
3i1z A1536 Nb G:A362(N7) A1589, A1590, A1591, A1592, L124 G:A362
3i1z A1559 2Nb G:A858(N7), G:A869(N7) A1697, A1698, A1699, A1700 G:A858, C:A857, C:A868
3i1z A1548 Oph A:A937(OP2) A1648, A1649, A1650, A1651, A1652 A:A937, A:A938, G:A939
3i1z A1558 Oph G:A21(OP1) A1692, A1693, A1694, A1695, A1696 G:A567 G:A567, A:A573
3i1z A1569 Oph·Pout U:A1095(OP2) A1741, A1742, A1743, A1744 C:A1096 G:A1094 C:A1109, G:A1108
3i1z A1539 Oph·Pout A:A547(OP1) A1603, A1604, A1605, A1606, A1607 G:A548 G:A402
3i1z A1547 Oph·Pout C:A934(OP1) A1643, A1644, A1645, A1646, A1647 U:A1345 U:A1345
3i1z A1568 Oph·Pout A:A1110(OP2) A1736, A1737, A1738, A1739, A1740 C:A1109 A:A1110, A:A1111, U:A1189
3i1z A1572 Oph·Pout G:A100(OP2) A1753, A1754, A1755, A1756, A1757 A:A101 G:A64, G:A100, A:A101
3i1z A1576 Oph·Pout C:A352(OP2) A1770, A1771, A1772, A1773, A1774 G:A354 G:A331, C:A352 A:A59
3i1z A1546 Oph·2Pout U:A891(OP2) A1638, A1639, A1640, A1641, A1642 A:A892, G:A903 U:A905, A:A906, U:A904
3i1z A1567 Oph·2Pout A:A608(OP2) A1731, A1732, A1733, A1734, A1735 A:A607, A:A609 C:A631, A:A609, A:A630, A:A608, U:A610
3i1z A1542 Oph·3Pout C:A578(OP1) A1616, A1617, A1618, A1619, A1620 C:A576, C:A817, U:A820 G:A575
3i1z A1545 Oph·3Pout A:A814(OP2) A1633, A1634, A1635, A1636, A1637 U:A904, G:A577, A:A815
3i1z A1564 Oph·Ob G:A558(OP1) G:A299(O6) A1718, A1719, A1720, A1721 A:A560 G:A297 A:A298, G:A566
3i1z A1566 Oph·Ob A:A533(OP1) U:A516(O4) A1727, A1728, A1729, A1730 C:A514, G:A515 G:A515
3i1z A1573 Oph·Ob A:A195(OP2) U:A180(O4) A1758, A1759, A1760, A1761 C:A194, A:A179 A:A181
3i1z A1551 cis-2Oph C:A1054(OP2), A:A1197(OP2) A1659, A1660, A1661, A1662 A:A1196, G:A1053 G:A1198, U:A1199, A:A1197

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>