MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3302, See in JSmolClick on the image to toggle views Site type: 2Pout·Rout·4Bout Schematic drawing for 2Pout·Rout·4Bout List of all 9 Mg2+ binding sites with the site type 2Pout·Rout·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 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 2qbg B2959 2Pout·Rout·4Bout B3280, B3281, B3282, B3283, B3284, B3285 A:B582, A:B1253 C:B1251 G:B583, C:B584, A:B582, G:B585 2z4l B2957 2Pout·Rout·4Bout B3258, B3259, B3260, B3261, B3262, B3263 A:B1253, G:B583 C:B1251 C:B584, G:B585, A:B582, G:B583 3df2 B3302 2Pout·Rout·4Bout B4303, B4304, B4305, B4306, B4307, B4308 A:B1253, G:B583 C:B1251 G:B583, C:B584, G:B585, A:B582 3i1r A2905 2Pout·Rout·4Bout A3046, A3047, A3048, A3049, A3050, A3051 U:A29, A:A447 A:A447 G:A473, G:A474, U:A29, C:A31 3og0 A2905 2Pout·Rout·4Bout A3042, A3043, A3044, A3045, A3046, A3047 A:A28, A:A447 A:A447 G:A474, U:A29, G:A30, C:A31 4bpn A5042 2Pout·Rout·4Bout A6103, A6104, A6105, A6106, A6107, A6108 G:A555, A:A574 A:A574 G:A555, G:A556, U:A557, U:A554 4bpo A5042 2Pout·Rout·4Bout A2106, A2107, A2108, A2109, A2110, A2114 G:A555, A:A574 A:A574 U:A554, G:A555, G:A556, U:A557 4bpp A5042 2Pout·Rout·4Bout A7683, A7684, A7685, A7686, A7687, A7688 G:A555, A:A574 A:A574 G:A555, G:A556, U:A557, U:A554 4qcv A3381 2Pout·Rout·4Bout A4323, A4324, A4325, A4326, A4327 A:A473, A:A28 A:A473 G:A500, G:A499, U:A29, G:A30

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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