`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

Back to Classification Home Download this subset in: CSV, XML, JSON

List of Mg2+ binding sites in structure 3oar




3OAR (3.25Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the e. coli ribosome bound to telithromycin. this file contains the 30s subunit of the second 70s ribosome.
List of all 40 Mg2+ binding sites in the PDB structure 3oar 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"
Page 1 of 2 | « Previous | | 1 | 2
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3oar A1536 Ob G:A362(O6) A1583, A1584, A1585, A1586, A1587 G:A361
3oar A1564 Nb G:A324(N7) A1723, A1724, A1725, A1726, A1727 U:A323, G:A324
3oar A1558 2Nb G:A858(N7), G:A869(N7) A1697, A1698, A1699, A1700 G:A858, C:A868, G:A869
3oar A1547 Oph C:A934(OP1) A1637, A1638, A1639, A1640, A1641
3oar A1548 Oph A:A937(OP2) A1642, A1643, A1644, A1645, A1646 A:A938, G:A939
3oar A1557 Oph G:A21(OP1) A1692, A1693, A1694, A1695, A1696 G:A568, G:A567 G:A567
3oar A1570 Oph G:A100(OP2) A1750, A1751, A1752, A1753, A1754 G:A64, C:A99, G:A100, A:A101
3oar A1539 Oph·Pout A:A547(OP1) A1598, A1599, A1600, A1601, A1602 G:A548 G:A402
3oar A1562 Oph·Pout A:A1433(OP2) A1715, A1716, A1717, A1718, A1719 A:A1434 G:A1435, A:A1434
3oar A1540 Oph·2Pout A:A560(OP2) A1603, A1604, A1605, A1606, A1607 A:A563, U:A562 G:A566, A:A300
3oar A1546 Oph·2Pout U:A891(OP2) A1632, A1633, A1634, A1635, A1636 A:A892, G:A903 U:A905, A:A906
3oar A1566 Oph·2Pout A:A608(OP2) A1732, A1733, A1734, A1735, A1736 A:A607, A:A609 A:A630, A:A609, U:A610, A:A608
3oar A1567 Oph·2Pout A:A1110(OP2) A1737, A1738, A1739, A1740, A1741 C:A1109, A:A1111 U:A1189, A:A1110, A:A1111
3oar A1542 Oph·3Pout C:A578(OP1) A1611, A1612, A1613, A1614, A1615 C:A576, C:A817, U:A820 G:A821
3oar A1561 Oph·4Pout G:A1198(OP1) A1711, A1712, A1713, A1714 A:A964, U:A965, C:A1054, U:A1199
3oar A1563 Oph·Ob G:A558(OP1) G:A299(O6) A1720, A1721, A1722, E187 G:A297 G:A566
3oar A1565 Oph·Ob A:A533(OP1) U:A516(O4) A1728, A1729, A1730, A1731 G:A515, G:A517
3oar A1571 Oph·Ob A:A195(OP2) U:A180(O4) A1755, A1756, A1757, A1758 C:A194, A:A179 A:A179
3oar A1545 trans-2Oph G:A577(OP2), A:A814(OP2) A1628, A1629, A1630, A1631 A:A815
3oar A1569 cis-2Oph·Or A:A1500(OP2), G:A1505(OP2) G:A1504(O2') A1747, A1748, A1749 A:A1499 U:A1498 C:A1501, A:A1500

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>