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

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Representative site 4bpe:A5058, See in JSmolMgRNA representative site for type PO-6BO         Click on the image to toggle views

Site type: Pout·6Bout

Schematic drawing for

MgRNA type PO-6BO
List of all 4 Mg2+ binding sites with the site type Pout·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
4bpe A5058 Pout·6Bout A2211, A2212, A2214, A2219, A2221, A2274 G:A1264 G:A1264, U:A1265, G:A1276, G:A1266, U:A1275, U:A1274
4bpn A5058 Pout·6Bout A6215, A6216, A6217, A6218, A6219, A6220 G:A1264 U:A1265, G:A1266, U:A1275, G:A1264, G:A1276, U:A1274
4bpo A5058 Pout·6Bout A2238, A2239, A2240, A2247, A2249, A2364 G:A1264 G:A1264, U:A1265, G:A1276, G:A1266, U:A1275, U:A1274
4bpp A5058 Pout·6Bout A7939, A7940, A7941, A7942, A7943, A7944 G:A1264 U:A1265, G:A1266, U:A1275, G:A1276, U:A1274, G:A1264

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>