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

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Representative site 2z4k:A1600, See in JSmolMgRNA representative site for type RO-2BO         Click on the image to toggle views

Site type: Rout·2Bout

Schematic drawing for

MgRNA type RO-2BO
List of all 12 Mg2+ binding sites with the site type Rout·2Bout 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
1k8a A8076 Rout·2Bout A6413, A7444, A7445, 37875 U:A1418 G:A1444, G:A1443
1k9m A8076 Rout·2Bout A6857, A7853, A7905, A7906, 37875 U:A1418 G:A1444, G:A1443
2fqn A202 Rout·2Bout A359, A360, A363, B358, B361, B362 A:B39 U:A10, A:B39
2z4k A1600 Rout·2Bout A1875, A1876, A1877, A1878, A1879, A1880 C:A1399 C:A1399, G:A926
3muv R670 Rout·2Bout R710, R711, R712, R713, R714, R715 G:R19 G:R19, A:R20
3oar A1551 Rout·2Bout A1656, A1657, A1658, A1659 G:A1053 G:A1198, U:A1199
3ofb A1551 Rout·2Bout A1656, A1657, A1658, A1659 G:A1053 G:A1198, U:A1199
3v26 A1715 Rout·2Bout A1962, A1963, A1964, A1965, A1966 U:A870 G:A829, G:A830
3v27 A3345 Rout·2Bout A4003, A4004, A4005, A4006, A4007 G:A1707 G:A1707, G:A1758
4bpp A5077 Rout·2Bout A8243, A8244, A8245, A8246, A8247, A8248 U:A1277 U:A1277, U:A1286
4dv4 A1687 Rout·2Bout A2046, A2047, A2048, N201 C:A1359 C:A980, G:A1361
4qcn A3322 Rout·2Bout A4152, A4153, A4154, A4155 G:A1754 G:A1754, G:A1789

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>