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

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Representative site 1vs5:A1545, See in JSmolMgRNA representative site for type PO-BO          Click on the image to toggle views

Site type: Pout·Bout

Schematic drawing for

MgRNA type PO-BO
List of all 223 Mg2+ binding sites with the site type Pout·Bout in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" 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
1dul B804 Pout·Bout B835, B865, B870, B890, B891, B892 A:B156 G:B154
1hq1 B1804 Pout·Bout B9046, B9058, B9285, B9286, B9287 A:B156 G:B154
1hr2 B25 Pout·Bout B386, B387, B388, B389, B390, B391 G:B180 G:B181
1vs5 A1545 Pout·Bout A1609, A1610, A1611, A1612, A1613, A1614 G:A1079 G:A1077
1vs5 A1551 Pout·Bout A1640, A1641, A1642, A1643, A1644, A1645 A:A315 G:A319
1vs7 A1552 Pout·Bout A1644, A1645, A1646, A1647, A1648, A1649 A:A172 G:A148
1vs7 A1569 Pout·Bout A1730, A1731, A1732, A1733, E204 U:A20 G:A21
1vs7 A1603 Pout·Bout A1892, A1893, A1894, A1895, T366, T369 G:A259 G:A259
1vs8 B2997 Pout·Bout B3444, B3445, B3446, B3447, B3448, 2556 U:B686 G:B770
1vt2 A3036 Pout·Bout A3639, A3640, A3641, A3642, A3643, A3644 G:A2004 A:A1650
1vt2 A2977 Pout·Bout A3385, A3386, A3387, A3388, A3389 C:A2310 U:A2302
1y26 X103 Pout·Bout X278, X279, X280, X281, X282, X283 G:X44 G:X32
2avy A1565 Pout·Bout A1709, A1710, A1711, A1712, A1713, A1714 A:A729 G:A727
2avy A1544 Pout·Bout A1607, A1608, A1609, A1610, A1611, A1612 G:A1079 G:A1077
2aw7 A1569 Pout·Bout A1735, A1736, A1737, A1738, A1739, A1740 G:A727 G:A727
2aw7 A1568 Pout·Bout A1731, A1732, A1733, A1734, E195 U:A20 G:A21
2aw7 A1602 Pout·Bout A1894, A1895, A1896, A1897, A1898, T360 G:A259 G:A259
2aw7 A1551 Pout·Bout A1644, A1645, A1646, A1647, A1648, A1649 A:A172 G:A148
2awb B2998 Pout·Bout B3446, B3447, B3448, B3449, 2555, 2556 U:B686 G:B770
2i2p A1556 Pout·Bout A1666, A1667, A1668, A1669, A1670, A1671 A:A1046 G:A1047
2i2p A1565 Pout·Bout A1712, A1713, A1714, A1715, A1716, A1717 G:A727 G:A727
2i2p A1564 Pout·Bout A1707, A1708, A1709, A1710, A1711, E170 U:A561 G:A21
2i2p A1544 Pout·Bout A1608, A1609, A1610, A1611, A1612, A1613 G:A1079 G:A1077
2i2p A1599 Pout·Bout A1879, A1880, A1881, A1882, A1883, A1884 G:A259 G:A259
2i2t B2997 Pout·Bout B3444, B3445, B3446, B3447, B3448, 2650 U:B769 G:B770

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>