MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qan:A2288, See in JSmolClick on the image to toggle views Site type: 4Bout Schematic drawing for 4Bout List of all 105 Mg2+ binding sites with the site type 4Bout 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 5 of 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4tp8 A1610 4Bout A1743, A1744, A1745, A1746, A1747, A1748 G:A646, U:A593, U:A594, G:A645 4tpb A3017 4Bout A3276, A3277, A3278, A3279, A3280, E303 U:A580, A:A1260, U:A1258, G:A1259 4tpb A3021 4Bout A3299, A3300, A3301, A3302, A3303, A3304 U:A755, A:A756, A:A739, G:A757 4tpd A3084 4Bout A3586, A3587, A3588, A3589, A3590, A3591 G:A841, U:A842, G:A843, A:A936 4tpf A3022 4Bout A3297, A3298, A3299, A3300, A3301, A3302 A:A756, G:A757, A:A739, U:A755

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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