MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2avy:A1578, See in JSmolClick on the image to toggle views Site type: Pout·Rout Schematic drawing for Pout·Rout List of all 37 Mg2+ binding sites with the site type Pout·Rout 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 2 of 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4bpo A5052 Pout·Rout A2144, A2145, A2146, A2147, A2414, A2415 C:A672 A:A675 4bpp A5007 Pout·Rout A7123, A7124, A7125, A7126, A7127, A7128 A:A600 C:A4 4dha A3579 Pout·Rout A4305, A4306, A4307, A4308, A4309 C:A1990 G:A1667 4dr2 A1731 Pout·Rout A2313, A2314, A2315, A2316 G:A485 G:A481 4dr2 A1749 Pout·Rout A2380, A2381, A2382, A2383, A2384 G:A541 U:A427 4dr4 A1752 Pout·Rout A2298, A2299, A2300, A2301, A2302 G:A428 U:A427 4dr5 A1805 Pout·Rout A2220, A2221, A2222, A2223, A2224, A2225 G:A771 A:A802 4dv1 A1648 Pout·Rout A1995, A1996, A1997, A1998 G:A903 G:A890 4dv1 A1766 Pout·Rout A2101, A2102, A2103, A2104, A2105 A:A777 G:A713 4nxn A1808 Pout·Rout A2133, A2134, A2135, A2136, A2137 A:A777 G:A713 4tp3 A3016 Pout·Rout A3271, A3272, A3273, A3274, A3275, E302 G:A1256 U:A1255 4tpb A3016 Pout·Rout A3271, A3272, A3273, A3274, A3275, E302 G:A1256 U:A1255

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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