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 9 of 14 | « Previous | Next » | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3v27 A3646 3Bout A5313, A5314, A5315, A5316, A5317, A5318 G:A1594, U:A1406, G:A1595 3v28 A1765 3Bout A2063, A2064, A2065, A2066, A2067 U:A375, G:A376, G:A377 3v29 A3440 3Bout A4179, A4180, A4181, A4182, A4183, A4184 G:A2719, G:A2717, G:A2718 3v29 A3593 3Bout A4751, A4752, A4753, A4754, A4755, A4756 U:A350, G:A348, G:A349 3v29 A3504 3Bout A4411, A4412, A4413, A4414, A4415 G:A496, G:A495, G:A494 3v29 A3447 3Bout A4207, A4208, A4209, A4210, 7102, 7103 G:A1310, G:A1311, G:A1309 3v2c A1804 3Bout A2313, A2314, A2315, A2316, A2317 G:A126, G:A127, U:A125 3v2d A3578 3Bout A5343, A5344, A5345, A5346 G:A407, G:A406, U:A421 3v2e A1697 3Bout A2036, A2037, A2038, A2039, A2040 G:A126, G:A127, U:A125 3v2e A1733 3Bout A2125, A2126, A2127, A2128 G:A376, G:A377, U:A375 3v2f A3479 3Bout A4788, A4789, A4790, A4791, A4792 G:A494, G:A495, G:A496 3v2f A3421 3Bout A4618, A4619, A4620, A4621, A4622 G:A2524, G:A2525, G:A2523 4a17 066 3Bout 05635, 05636, 05637, 05638, 05639, 05640 G:215, G:216, U:217 4a1a 0117 3Bout 05859, 05860, 05861, 05862, 05863, 05864 G:382, G:383, A:381 4a1a 066 3Bout 05507, 05508, 05509, 05510, 05511, 05512 G:216, U:217, G:215 4a1a 0347 3Bout 07971, 07972, 07973, 07974, 07975, 07976 G:369, G:370, U:368 4a1c 0117 3Bout 05619, 05620, 05621, 05622, 05623, 05624 G:382, G:383, A:381 4a1c 066 3Bout 05331, 05332, 05333, 05334, 05335, 05336 G:215, G:216, U:217 4a1e 066 3Bout 05571, 05572, 05573, 05574, 05575, 05576 G:216, G:215, U:217 4a1e 0347 3Bout 08131, 08132, 08133, 08134, 08135, 08136 G:369, G:370, U:368 4bpe A5044 3Bout A2169, A2170, A2186, A2187, A2308, A2309 G:A958, C:A999, U:A1000 4bpe A5070 3Bout A2412, A2413, A2424, A2455, A2472, A2473 U:A1448, G:A1449, G:A1450 4bpe A5024 3Bout A2213, A2215, A2220, A2275, A2276, A2277 G:A1266, G:A1267, U:A1274 4bpe A5059 3Bout A2228, A2229, A2230, A2336, A2337, A2338 G:A1633, C:A1692, C:A1691 4bpe A5023 3Bout A2018, A2084, A2085, A2086, A2087, A2273 A:A456, G:A457, G:A459

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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