MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 4bpp:A5039, See in JSmolClick on the image to toggle views Site type: 2Rout·5Bout Schematic drawing for 2Rout·5Bout List of all 3 Mg2+ binding sites with the site type 2Rout·5Bout 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 4bpp A5039 2Rout·5Bout A7635, A7636, A7637, A7638, A7639, A7640 G:A532, A:A531 A:A531, G:A532, G:A533, A:A469, A:A535 4bpo A5039 2Rout·5Bout A2088, A2089, A2090, A2099, A2100, A2101 G:A532, A:A531 G:A532, G:A533, A:A469, A:A531, A:A535 4bpe A5039 2Rout·5Bout A2091, A2092, A2093, A2101, A2102, A2103 G:A532, A:A531 A:A469, A:A531, G:A533, A:A535, G:A532

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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