MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3464, See in JSmolClick on the image to toggle views Site type: 3Bout Schematic drawing for 3Bout List of all 341 Mg2+ binding sites with the site type 3Bout 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 14 of 14 | « Previous | Next » | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4bpn A5044 3Bout A6117, A6118, A6119, A6120, A6121, A6122 G:A958, C:A999, U:A1000 4bpe A5044 3Bout A2169, A2170, A2186, A2187, A2308, A2309 G:A958, C:A999, U:A1000 4bpp A5044 3Bout A7715, A7716, A7717, A7718, A7719, A7720 G:A958, C:A999, U:A1000 4bpo A5059 3Bout A2306, A2307, A2308, A2431, A2432, A2433 G:A1633, C:A1692, C:A1691 4bpe A5059 3Bout A2228, A2229, A2230, A2336, A2337, A2338 G:A1633, C:A1692, C:A1691 4bpn A5067 3Bout A6535, A6536, A6537, A6538, A6539, A6540 G:A1478, G:A1479, U:A1480 4bpo A5070 3Bout A2272, A2273, A2284, A2452, A2453, A2454 U:A1448, G:A1449, G:A1450 4bpe A5070 3Bout A2412, A2413, A2424, A2455, A2472, A2473 U:A1448, G:A1449, G:A1450 4bpe A5073 3Bout A2395, A2396, A2397, A2460, A2461, A2462 G:A1281, U:A1282, U:A1287 4bpn A5073 3Bout A6578, A6579, A6580, A6581, A6582, A6583 G:A1281, U:A1282, U:A1287 4bpo A5073 3Bout A2255, A2256, A2257, A2459, A2460, A2461 G:A1281, U:A1282, U:A1287 4bpo A5074 3Bout A2261, A2262, A2263, A2264, A2265, A2462 U:A1385, A:A1388, G:A1389 4bpp A5074 3Bout A8195, A8196, A8197, A8198, A8199, A8200 G:A1389, U:A1385, A:A1388 2q1r A8002 3Bout A9001, A9002, A9009, A9019, A9021, A9032 G:A1004, U:A1007, A:A1005 1n8r A8063 3Bout A4573, A7389, A7814, A8246, A8395, A8445 G:A1364, U:A1362, G:A1363 1yjn 08063 3Bout 04199, 07005, 07430, 07745, 07823, C8673 G:01364, U:01362, G:01363

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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