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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 3ofy



3OFY (3.29Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to clindamycin. this file contains the 30s subunit of the second 70s ribosome
List of all 40 Mg2+ binding sites in the PDB structure 3ofy 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
3ofy A1536 Ob G:A362(O6) A1584, A1585, A1586, A1587, A1588 G:A361
3ofy A1553 Ob G:A1417(O6) A1667, A1668, A1669, A1670, A1671 G:A1416 G:A1415
3ofy A1565 Nb G:A324(N7) A1723, A1724, A1725, A1726, A1727 U:A323, G:A324
3ofy A1559 2Nb G:A858(N7), G:A869(N7) A1697, A1698, A1699, A1700 G:A858, G:A869, C:A868
3ofy A1571 Oph G:A100(OP2) A1750, A1751, A1752, A1753, A1754 G:A64, G:A100, A:A101
3ofy A1558 Oph G:A21(OP1) A1692, A1693, A1694, A1695, A1696 G:A568, G:A567 A:A573, G:A567
3ofy A1563 Oph A:A1433(OP2) A1715, A1716, A1717, A1718, A1719 C:A1466, A:A1434
3ofy A1547 Oph C:A934(OP1) A1638, A1639, A1640, A1641, A1642
3ofy A1539 Oph·Pout A:A547(OP1) A1599, A1600, A1601, A1602, A1603 G:A548 G:A402
3ofy A1575 Oph·Pout C:A352(OP2) A1767, A1768, A1769, A1770, A1771 G:A354 C:A352 C:A330, G:A354, A:A59
3ofy A1540 Oph·2Pout A:A560(OP2) A1604, A1605, A1606, A1607, A1608 A:A563, U:A562 A:A559 G:A566, A:A300
3ofy A1542 Oph·2Pout C:A578(OP1) A1612, A1613, A1614, A1615, A1616 C:A576, C:A817 G:A575, G:A821
3ofy A1546 Oph·2Pout U:A891(OP2) A1633, A1634, A1635, A1636, A1637 A:A892, G:A903 U:A905, U:A904
3ofy A1567 Oph·2Pout A:A608(OP2) A1732, A1733, A1734, A1735, A1736 A:A607, A:A609 C:A631, A:A609, U:A610, A:A630, A:A608
3ofy A1568 Oph·2Pout A:A1110(OP2) A1737, A1738, A1739, A1740, A1741 C:A1109, A:A1111 U:A1189, A:A1110, A:A1111
3ofy A1562 Oph·4Pout G:A1198(OP1) A1711, A1712, A1713, A1714 A:A964, U:A965, C:A1054, U:A1199
3ofy A1538 Oph·Or A:A510(OP2) A:A509(O5') A1595, A1596, A1597, A1598 A:A509, G:A506, C:A507 U:A508 A:A510
3ofy A1572 Oph·Ob A:A195(OP2) U:A180(O4) A1755, A1756, A1757, A1758 C:A194, A:A179 A:A179
3ofy A1566 Oph·Ob A:A533(OP1) U:A516(O4) A1728, A1729, A1730, A1731 G:A515, G:A517
3ofy A1564 Oph·Ob G:A558(OP1) G:A299(O6) A1720, A1721, A1722, E187 G:A297 A:A300, A:A298

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>