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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 3ora



3ORA (3.3Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to cem-101. this file contains the 30s subunit of the second 70s ribosome.
List of all 40 Mg2+ binding sites in the PDB structure 3ora 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
3ora A1536 Ob G:A362(O6) A1588, A1589, A1590, A1591, A1592 G:A361
3ora A1553 Ob G:A1417(O6) A1671, A1672, A1673, A1674, A1675 G:A1415, G:A1482
3ora A1565 Nb G:A324(N7) A1729, A1730, A1731, A1732, A1733 U:A323, G:A324
3ora A1558 Oph G:A21(OP1) A1697, A1698, A1699, A1700, A1701 G:A568, G:A567 G:A567
3ora A1564 Oph G:A558(OP1) A1726, A1727, A1728, E187 G:A297 G:A299, A:A300
3ora A1571 Oph G:A100(OP2) A1756, A1757, A1758, A1759, A1760 G:A64, A:A101
3ora A1547 Oph C:A934(OP1) A1642, A1643, A1644, A1645, A1646
3ora A1548 Oph A:A937(OP2) A1647, A1648, A1649, A1650, A1651 A:A938, G:A939
3ora A1551 Oph C:A1054(OP2) A1661, A1662, A1663, A1664 G:A1053 U:A1199, G:A1198
3ora A1563 Oph·Pout A:A1433(OP2) A1721, A1722, A1723, A1724, A1725 A:A1434 G:A1435, C:A1466, A:A1434
3ora A1539 Oph·Pout A:A547(OP1) A1603, A1604, A1605, A1606, A1607 G:A548 G:A402
3ora A1567 Oph·2Pout A:A608(OP2) A1738, A1739, A1740, A1741, A1742 A:A607, A:A609 A:A630, A:A609, U:A610, A:A608
3ora A1546 Oph·2Pout U:A891(OP2) A1637, A1638, A1639, A1640, A1641 A:A892, G:A903 U:A905, A:A906, U:A904
3ora A1545 Oph·2Pout A:A814(OP2) A1633, A1634, A1635, A1636 A:A815, G:A577
3ora A1568 Oph·2Pout A:A1110(OP2) A1743, A1744, A1745, A1746, A1747 C:A1109, A:A1111 U:A1189, A:A1110, A:A1111, C:A1112
3ora A1540 Oph·3Pout A:A560(OP2) A1608, A1609, A1610, A1611, A1612 A:A563, U:A562, G:A557 A:A559 G:A566
3ora A1542 Oph·3Pout C:A578(OP1) A1616, A1617, A1618, A1619, A1620 C:A576, C:A817, U:A820
3ora A1562 Oph·4Pout G:A1198(OP1) A1717, A1718, A1719, A1720 A:A964, U:A965, C:A1054, U:A1199
3ora A1566 Oph·Ob A:A533(OP1) U:A516(O4) A1734, A1735, A1736, A1737 G:A515, G:A517
3ora A1572 Oph·Ob A:A195(OP2) U:A180(O4) A1761, A1762, A1763, A1764 C:A194, C:A178, A:A179 A:A179

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>