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

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Representative site 1vs5:A1579, See in JSmolMgRNA representative site for type RO-BO          Click on the image to toggle views

Site type: Rout·Bout

Schematic drawing for

MgRNA type RO-BO
List of all 12 Mg2+ binding sites with the site type Rout·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
1hr2 A27 Rout·Bout A389, A390, A391, A392, A393, A394 C:A124 G:A194
1vs5 A1579 Rout·Bout A1776, A1777, A1778, A1779, A1780, A1781 U:A13 G:A917
3v29 A3590 Rout·Bout A4734, A4735, A4736, A4737, A4738, A4739 C:A1908 G:A1907
3v2d A3558 Rout·Bout A5290, A5291, A5292, A5293 A:A282 A:A282
4a1e 080 Rout·Bout 05731, 05732, 05733, 05734, 05735, 05736 U:29 U:29
4bpe A5077 Rout·Bout A2390, A2393, A2394, A2467, A2468, A2469 U:A1277 U:A1277
4bpo A5077 Rout·Bout A2250, A2252, A2253, A2299, A2300, A2466 U:A1277 U:A1277
4dr2 A1752 Rout·Bout A2392, A2393, A2394, A2395 C:A1543 G:A1497
4dr4 A1953 Rout·Bout A2457, A2458, A2459, A2460, A2461 G:A1003 G:A1024
4gar A3018 Rout·Bout A3296, A3297, A3298, L302 G:A620 U:A606
4ji5 A1705 Rout·Bout A1959, A1960, A1961, A1962, A1963, P101 G:A227 C:A137
4p9r A613 Rout·Bout A702, A707, A710, A738 C:A272 U:A547

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>