MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 4bpe:A5058, See in JSmolClick on the image to toggle views Site type: Pout·6Bout Schematic drawing for Pout·6Bout 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" Page 1 of 1

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
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].

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