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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 3ofo



3OFO (3.1Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to erythromycin. this file contains the 30s subunit of the first 70s ribosome.
List of all 36 Mg2+ binding sites in the PDB structure 3ofo 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
3ofo A1567 Ob G:A1108(O6) A1739, A1740, A1741, A1742 C:A1096
3ofo A1536 Nb G:A362(N7) A1587, A1588, A1589, A1590, L124 G:A361, G:A362 G:A361
3ofo A1563 Nb G:A324(N7) A1720, A1721, A1722, A1723, A1724 U:A323, G:A326, G:A324
3ofo A1557 2Nb G:A858(N7), G:A869(N7) A1695, A1696, A1697, A1698 G:A858, G:A869, C:A868
3ofo A1574 Oph C:A352(OP2) A1768, A1769, A1770, A1771, A1772 G:A331, C:A352 G:A354, A:A59
3ofo A1556 Oph G:A21(OP1) A1690, A1691, A1692, A1693, A1694 G:A568, G:A567 G:A567, A:A573, A:A563
3ofo A1546 Oph·Pout U:A891(OP2) A1636, A1637, A1638, A1639, A1640 A:A892 U:A905, A:A906, U:A904
3ofo A1547 Oph·Pout C:A934(OP1) A1641, A1642, A1643, A1644, A1645 U:A1345
3ofo A1548 Oph·Pout A:A937(OP2) A1646, A1647, A1648, A1649, A1650 A:A938 A:A938, G:A939
3ofo A1566 Oph·Pout A:A1110(OP2) A1734, A1735, A1736, A1737, A1738 C:A1109 A:A1188, A:A1111, U:A1065, U:A1189
3ofo A1570 Oph·Pout G:A100(OP2) A1750, A1751, A1752, A1753, A1754 A:A101 G:A64, G:A100, A:A101, G:A102
3ofo A1539 Oph·Pout A:A547(OP1) A1601, A1602, A1603, A1604, A1605 G:A548 G:A402
3ofo A1565 Oph·2Pout A:A608(OP2) A1729, A1730, A1731, A1732, A1733 A:A607, A:A609 A:A609, A:A630, A:A608, U:A610
3ofo A1545 Oph·2Pout A:A814(OP2) A1631, A1632, A1633, A1634, A1635 G:A577, A:A815 A:A816
3ofo A1540 Oph·3Pout A:A560(OP2) A1606, A1607, A1608, A1609, A1610 G:A557, U:A562, A:A563 A:A559 U:A565, G:A566
3ofo A1564 Oph·Ob A:A533(OP1) U:A516(O4) A1725, A1726, A1727, A1728 A:A532 G:A517
3ofo A1571 Oph·Ob A:A195(OP2) U:A180(O4) A1755, A1756, A1757, A1758 C:A194, A:A179 A:A181
3ofo A1551 cis-2Oph C:A1303(OP1), G:A1304(OP2) A1666, A1667, A1668, A1669 G:A1305
3ofo A1538 cis-2Oph A:A509(OP2), A:A510(OP2) A1597, A1598, A1599, A1600 G:A506, C:A507 U:A508 A:A510
3ofo A1549 cis-2Oph C:A1054(OP2), A:A1197(OP2) A1656, A1657, A1658, A1659 A:A1196, G:A1053 A:A1197, G:A1198, U:A1199

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>