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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 4ji1:A1763, See in JSmolMgRNA representative site for type 2PO-6BO Click on the image to toggle views


Site type: 2Pout·6Bout

Schematic drawing for
2Pout·6Bout
MgRNA type 2PO-6BO
List of all 3 Mg2+ binding sites with the site type 2Pout·6Bout 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
4gaq A1613 2Pout·6Bout A1754, A1755, A1756, A1757, A1758, A1759 A:A414, A:A415 G:A416, G:A417, U:A426, U:A427, A:A415, G:A425
4ji1 A1763 2Pout·6Bout A2266, A2267, A2268, A2269, A2270, A2271 A:A415, A:A414 G:A416, C:A417, G:A426, U:A427, A:A415, G:A428
3v29 A3428 2Pout·6Bout A4135, A4136, A4137, A4138, A4139 A:A2227, C:A2226 G:A2090, U:A2091, A:A2227, U:A2092, C:A2229, G:A2228

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>