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

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"
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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
1dno B21 Bout B197, B198, B199, B200, B201, B202 DG:B19
1egk C6 Bout C45, C46, C47, C48, C49, C50 G:C113
1egk C14 Bout C93, C94, C95, C96, C97, C98 G:C118
1vs5 A1565 Bout A1708, A1709, A1710, E179, E182, E184 G:A21
1vs5 A1569 Bout A1727, A1728, A1729, A1730, A1731, A1732 G:A941
1vt2 A3034 Bout A3630, A3631, A3632, A3633, 4755, 4760 G:A2742
2avy A1564 Bout A1705, A1706, A1707, A1708, E168, E171 G:A21
2avy A1567 Bout A1721, A1722, A1723, A1724, A1725, A1726 G:A941
2i2p A1561 Bout A1692, A1693, A1694, A1695, A1696 G:A1050
2i2t B2907 Bout B3034, B3035, B3036, B3037, B3038, B3039 G:B1259
2i2u A1589 Bout A1829, A1830, A1831, I238, I240 G:A1370
2qal A2219 Bout A2220, A2221, A2222, A2223, A2224, A2225 G:A917
2qam B3246 Bout B3810, B3811, B3812, B3813, B3814, B3815 U:B434
2qb9 A2129 Bout A2463, A2464, A2465, E2130, E2133, E2135 G:A21
2qba B3194 Bout B3770, B3771, B3772, B3773, B3774, B3775 C:B650
2qbc B3389 Bout B3937, B3938, B3939, B3940, B3941, B3942 U:B652
2qbd A2294 Bout A2295, A2296, A2297, A2298, A2299, A2300 G:A38
2qbe B3194 Bout B3769, B3770, B3771, B3772, B3773, B3774 G:B651
2qbh A1564 Bout A1705, A1706, E167, E168, E169, E170 G:A21
2qbj A1561 Bout A1687, A1688, A1689, A1690, A1691, A1692 G:A1077
2qbj A1571 Bout A1749, A1750, A1751, A1752, A1753, A1754 G:A941
2qbk B2969 Bout B3327, B3328, B3329, B3330, B3331, B3332 U:B580
2qou A1567 Bout A2017, A2018, A2019, A2020, A2021, A2022 G:A377
2qou A1556 Bout A1958, A1959, A1960, A1961, A1962, A1963 G:A1047
2qoy A1564 Bout A2004, A2005, A2006, E167, E1711, E1713 G:A21

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>