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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 3ofx



3OFX (3.29Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to clindamycin. this file contains the 30s subunit of the first 70s ribosome.
List of all 36 Mg2+ binding sites in the PDB structure 3ofx 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
3ofx A1564 Nb G:A324(N7) A1723, A1724, A1725, A1726, A1727 U:A323, G:A326, G:A324
3ofx A1536 Nb G:A362(N7) A1588, A1589, A1590, A1591, L124 A:A364, G:A361
3ofx A1558 2Nb G:A858(N7), G:A869(N7) A1698, A1699, A1700, A1701 G:A858, G:A869, C:A857, C:A868
3ofx A1557 Oph G:A21(OP1) A1693, A1694, A1695, A1696, A1697 G:A568, G:A567 G:A567, A:A573, A:A574
3ofx A1548 Oph A:A937(OP2) A1647, A1648, A1649, A1650, A1651 A:A937, A:A938, G:A939
3ofx A1547 Oph·Pout C:A934(OP1) A1642, A1643, A1644, A1645, A1646 U:A1345
3ofx A1567 Oph·Pout A:A1110(OP2) A1737, A1738, A1739, A1740, A1741 C:A1109 A:A1110, A:A1111, U:A1065, U:A1189
3ofx A1571 Oph·Pout G:A100(OP2) A1754, A1755, A1756, A1757, A1758 A:A101 G:A64, G:A100, A:A101
3ofx A1575 Oph·Pout C:A352(OP2) A1772, A1773, A1774, A1775, A1776 G:A354 C:A330, G:A331, C:A352 A:A59
3ofx A1539 Oph·Pout A:A547(OP1) A1602, A1603, A1604, A1605, A1606 G:A548 G:A402, C:A403
3ofx A1566 Oph·2Pout A:A608(OP2) A1732, A1733, A1734, A1735, A1736 A:A607, A:A609 C:A631, A:A609, A:A630, A:A608, U:A610
3ofx A1545 Oph·2Pout A:A814(OP2) A1632, A1633, A1634, A1635, A1636 G:A577, A:A815 A:A816
3ofx A1546 Oph·2Pout U:A891(OP2) A1637, A1638, A1639, A1640, A1641 G:A903, A:A892 U:A905, A:A906, U:A904
3ofx A1542 Oph·3Pout C:A578(OP1) A1615, A1616, A1617, A1618, A1619 C:A576, C:A817, U:A820 G:A575
3ofx A1540 Oph·4Pout A:A560(OP2) A1607, A1608, A1609, A1610, A1611 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
3ofx A1565 Oph·Ob A:A533(OP1) U:A516(O4) A1728, A1729, A1730, A1731 G:A517
3ofx A1568 Oph·Ob U:A1095(OP2) G:A1108(O6) A1742, A1743, A1744, A1745 C:A1096 G:A1094
3ofx A1572 Oph·Ob A:A195(OP2) U:A180(O4) A1759, A1760, A1761, A1762 C:A194, A:A179 A:A181
3ofx A1560 cis-2Oph A:A964(OP1), U:A1199(OP1) A1708, A1709, A1710, A1711 G:A1198
3ofx A1538 cis-2Oph A:A509(OP2), A:A510(OP2) A1598, A1599, A1600, A1601 G:A506, C:A507 U:A508 A:A510

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>