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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 3i21



3I21 (3.71Å) -- RIBOSOME : Crystal structure of the e. coli 70s ribosome in an intermediate state of ratcheting
List of all 39 Mg2+ binding sites in the PDB structure 3i21 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
3i21 A1550 Ob G:A1417(O6) A1667, A1668, A1669, A1670, A1671 G:A1415
3i21 A3 Nb G:A362(N7) A1583, A1584, A1585, A1586, A1587 G:A361
3i21 A1556 2Nb G:A858(N7), G:A869(N7) A1698, A1699, A1700, A1701 G:A858, C:A868, G:A869, C:A857
3i21 A1545 Oph A:A937(OP2) A1642, A1643, A1644, A1645, A1646 A:A938, G:A939
3i21 A1555 Oph G:A21(OP1) A1693, A1694, A1695, A1696, A1697 G:A568, G:A567 A:A563, G:A567
3i21 A1560 Oph A:A1433(OP2) A1717, A1718, A1719, A1720, A1721 G:A1435, C:A1466, A:A1434
3i21 A1561 Oph G:A558(OP1) A1722, A1723, A1724, A1725 G:A297 G:A299, G:A566
3i21 A1568 Oph G:A100(OP2) A1754, A1755, A1756, A1757, A1758 G:A64, G:A100, A:A101, G:A102
3i21 A1544 Oph C:A934(OP1) A1637, A1638, A1639, A1640, A1641
3i21 A1537 Oph·Pout A:A560(OP2) A1603, A1604, A1605, A1606, A1607 U:A562 A:A559 U:A565, G:A566, A:A300
3i21 A1572 Oph·Pout C:A352(OP2) A1771, A1772, A1773, A1774, A1775 G:A354 C:A330, C:A352 C:A330, G:A354, A:A59
3i21 A1536 Oph·Pout A:A547(OP1) A1598, A1599, A1600, A1601, A1602 G:A548 G:A402, C:A403
3i21 A1543 Oph·2Pout U:A891(OP2) A1632, A1633, A1634, A1635, A1636 A:A892, G:A903 A:A906, U:A904
3i21 A1565 Oph·2Pout A:A1110(OP2) A1740, A1741, A1742, A1743, A1744 C:A1109, A:A1111 U:A1189, A:A1110, A:A1111
3i21 A1564 Oph·2Pout A:A608(OP2) A1735, A1736, A1737, A1738, A1739 A:A607, A:A609 A:A630, C:A631, A:A609, A:A608, U:A610
3i21 A1539 Oph·3Pout C:A578(OP1) A1611, A1612, A1613, A1614, A1615 C:A576, C:A817, U:A820 G:A575, G:A821
3i21 A1559 Oph·4Pout G:A1198(OP1) A1713, A1714, A1715, A1716 A:A964, U:A965, C:A1054, U:A1199
3i21 A1569 Oph·Ob A:A195(OP2) U:A180(O4) A1759, A1760, A1761, A1762 C:A194, C:A178, A:A179 A:A179
3i21 A1563 Oph·Ob A:A533(OP1) U:A516(O4) A1731, A1732, A1733, A1734 G:A517, G:A515
3i21 A1542 cis-2Oph G:A577(OP1), A:A814(OP2) A1628, A1629, A1630, A1631 A:A815

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/)
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