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

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Representative site 1egk:C14, See in JSmolMgRNA representative site for type BO             Click on the image to toggle views


Site type: Bout

Schematic drawing for
Bout

MgRNA type BO
List of all 132 Mg2+ binding sites with the site type 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"
Page 1 of 6 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1egk C6 Bout C45, C46, C47, C48, C49, C50 G:C113
1egk C14 Bout C93, C94, C95, C96, C97, C98 G:C118
1dno B21 Bout B197, B198, B199, B200, B201, B202 DG:B19
4a17 071 Bout 05715, 05716, 05717, 05718, 05719, 05720 U:210
3v23 0102 Bout A4019, A4020, 0203, 0204, 0205, 0206 G:A2280
4a1e 0117 Bout 05987, 05988, 05989, 05990, 05991, 05992 G:382
4a1e 0334 Bout 08003, 08004, 08005, 08006, 08007, 08008 G:2141
4a17 0334 Bout 08499, 08500, 08501, 08502, 08503, 08504 G:2141
3r1l F1031 Bout F1052, F1053, F1054, F1055, F1056, F1057 G:F105
3ofp A1536 Bout A1584, A1585, A1586, A1587, A1588 G:A362
2qou A1556 Bout A1958, A1959, A1960, A1961, A1962, A1963 G:A1047
2qbj A1561 Bout A1687, A1688, A1689, A1690, A1691, A1692 G:A1077
2i2p A1561 Bout A1692, A1693, A1694, A1695, A1696 G:A1050
2qbh A1564 Bout A1705, A1706, E167, E168, E169, E170 G:A21
2avy A1564 Bout A1705, A1706, A1707, A1708, E168, E171 G:A21
2qoy A1564 Bout A2004, A2005, A2006, E167, E1711, E1713 G:A21
1vs5 A1565 Bout A1708, A1709, A1710, E179, E182, E184 G:A21
2avy A1567 Bout A1721, A1722, A1723, A1724, A1725, A1726 G:A941
2qou A1567 Bout A2017, A2018, A2019, A2020, A2021, A2022 G:A377
1vs5 A1569 Bout A1727, A1728, A1729, A1730, A1731, A1732 G:A941
3ofx A1569 Bout A1746, A1747, A1748, A1749, A1750, U219 G:A1525
2qbj A1571 Bout A1749, A1750, A1751, A1752, A1753, A1754 G:A941
2i2u A1589 Bout A1829, A1830, A1831, I238, I240 G:A1370
2qp0 A1593 Bout A2128, A2129, A2130, A2131, A2132, A2133 G:A941
4dv0 A1610 Bout A1922, A1923, A1924, A1925 G:A1526

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>