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 10 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 4bpe A5073 3Bout A2395, A2396, A2397, A2460, A2461, A2462 G:A1281, U:A1282, U:A1287 4bpe A5000 3Bout A2029, A2030, A2068, A2242, A2243, A2244 U:A94, G:A375, G:A374 4bpe A5031 3Bout A2151, A2152, A2153, A2158, A2160, A2286 G:A863, G:A903, A:A904 4bpe A5011 3Bout A2235, A2236, A2237, A2238, A2255, A2256 G:A1730, G:A1731, U:A1732 4bpe A5040 3Bout A2019, A2026, A2027, A2028, A2304, A2305 U:A57, U:A84, G:A85 4bpn A5011 3Bout A6275, A6283, A6289, A6296, A6303, A6310 G:A1730, U:A1732, G:A1731 4bpn A5023 3Bout A6421, A6422, A6423, A6424, A6425, A6426 A:A456, G:A459, G:A457 4bpn A5067 3Bout A6535, A6536, A6537, A6538, A6539, A6540 G:A1478, G:A1479, U:A1480 4bpn A5073 3Bout A6578, A6579, A6580, A6581, A6582, A6583 G:A1281, U:A1282, U:A1287 4bpn A5044 3Bout A6117, A6118, A6119, A6120, A6121, A6122 G:A958, C:A999, U:A1000 4bpn A5031 3Bout A6469, A6470, A6471, A6472, A6473, A6474 G:A863, G:A903, A:A904 4bpn A5024 3Bout A6427, A6428, A6429, A6430, A6431, A6432 G:A1267, G:A1266, U:A1274 4bpn A5000 3Bout A6000, A6001, A6002, A6003, A6004, A6005 G:A374, U:A94, G:A375 4bpn A5040 3Bout A6089, A6090, A6091, A6092, A6093, A6094 U:A57, U:A84, G:A85 4bpo A5023 3Bout A2018, A2082, A2083, A2084, A2085, A2361 A:A456, G:A457, G:A459 4bpo A5073 3Bout A2255, A2256, A2257, A2459, A2460, A2461 G:A1281, U:A1282, U:A1287 4bpo A5070 3Bout A2272, A2273, A2284, A2452, A2453, A2454 U:A1448, G:A1449, G:A1450 4bpo A5059 3Bout A2306, A2307, A2308, A2431, A2432, A2433 G:A1633, C:A1692, C:A1691 4bpo A5000 3Bout A2030, A2031, A2066, A2320, A2321, A2322 U:A94, G:A375, G:A374 4bpo A5011 3Bout A2313, A2314, A2315, A2316, A2339, A2340 G:A1730, G:A1731, U:A1732 4bpo A5074 3Bout A2261, A2262, A2263, A2264, A2265, A2462 U:A1385, A:A1388, G:A1389 4bpo A5040 3Bout A2019, A2026, A2027, A2028, A2029, A2400 U:A57, U:A84, G:A85 4bpo A5024 3Bout A2241, A2242, A2243, A2248, A2362, A2363 G:A1266, G:A1267, A:A1268 4bpo A5031 3Bout A2157, A2158, A2163, A2165, A2380, A2381 G:A863, G:A903, A:A904 4bpo A5044 3Bout A2173, A2174, A2190, A2191, A2404, A2405 G:A958, C:A999, U:A1000

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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