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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 3oaq




3OAQ (3.25Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the e. coli ribosome bound to telithromycin. this file contains the 30s subunit of the first 70s ribosome.
List of all 37 Mg2+ binding sites in the PDB structure 3oaq 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
3oaq A1536 Nb G:A362(N7) A1589, A1590, A1591, A1592, L124
3oaq A1565 Nb G:A324(N7) A1724, A1725, A1726, A1727, A1728 U:A323, G:A324
3oaq A1559 2Nb G:A858(N7), G:A869(N7) A1699, A1700, A1701, A1702 G:A858, G:A869, C:A857, C:A868
3oaq A1548 Oph A:A937(OP2) A1648, A1649, A1650, A1651, A1652 A:A938, G:A939
3oaq A1558 Oph G:A21(OP1) A1694, A1695, A1696, A1697, A1698 G:A568, G:A567 A:A573, A:A574, G:A567
3oaq A1572 Oph·Pout G:A100(OP2) A1755, A1756, A1757, A1758, A1759 A:A101 G:A64, G:A100, A:A101
3oaq A1539 Oph·Pout A:A547(OP1) A1603, A1604, A1605, A1606, A1607 G:A548 G:A402, C:A403
3oaq A1547 Oph·Pout C:A934(OP1) A1643, A1644, A1645, A1646, A1647 U:A1345 U:A1345
3oaq A1568 Oph·Pout A:A1110(OP2) A1738, A1739, A1740, A1741, A1742 C:A1109 A:A1111, U:A1065, U:A1189
3oaq A1576 Oph·Pout C:A352(OP2) A1773, A1774, A1775, A1776, A1777 G:A354 C:A330, G:A331, C:A352 A:A59
3oaq A1545 Oph·2Pout A:A814(OP2) A1633, A1634, A1635, A1636, A1637 G:A577, A:A815 A:A816
3oaq A1546 Oph·2Pout U:A891(OP2) A1638, A1639, A1640, A1641, A1642 G:A903, A:A892 U:A905, A:A906, U:A904
3oaq A1561 Oph·2Pout A:A964(OP1) A1709, A1710, A1711, A1712 G:A1198, U:A1199
3oaq A1567 Oph·2Pout A:A608(OP2) A1733, A1734, A1735, A1736, A1737 A:A607, A:A609 C:A631, A:A609, A:A630, A:A608, U:A610
3oaq A1542 Oph·3Pout C:A578(OP1) A1616, A1617, A1618, A1619, A1620 C:A576, C:A817, U:A820 G:A575
3oaq A1540 Oph·4Pout A:A560(OP2) A1608, A1609, A1610, A1611, A1612 U:A562, A:A563, G:A557, G:A558 A:A559 G:A566
3oaq A1573 Oph·Ob A:A195(OP2) U:A180(O4) A1760, A1761, A1762, A1763 C:A194, A:A179 A:A181, A:A179
3oaq A1566 Oph·Ob A:A533(OP1) U:A516(O4) A1729, A1730, A1731, A1732 G:A515, G:A517
3oaq A1569 Oph·Ob U:A1095(OP2) G:A1108(O6) A1743, A1744, A1745, A1746 C:A1096
3oaq A1538 cis-2Oph A:A509(OP2), A:A510(OP2) A1599, A1600, A1601, A1602 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>