MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qou:A1560, See in JSmolClick on the image to toggle views Site type: Nb Schematic drawing for Nb List of all 284 Mg2+ binding sites with the site type Nb 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 3 of 12 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2otj 08111 Nb G:02609(N7) 03314, 03715, 03739, 05637, 05785 G:02609 U:02610, G:02606 2otj 08112 Nb A:0187(N1) 03745, 03789, 09131, 09336 U:0207, C:0155 G:0206 C:0438, C:0188 2qal A2103 Nb G:A362(N7) A2104, A2105, A2106, A2108, L2107 G:A361, G:A362 2qam B3164 Nb G:B1371(N7) B3744, B3745, B3746, B3747 G:B1358, C:B1357, C:B1370 G:B1358 2qan A2036 Nb G:A362(N7) A2037, A2038, A2039, A2040, A2041 G:A362 G:A361 G:A361 2qan A2250 Nb G:A324(N7) A2251, A2252, A2253, A2254, A2255 G:A324 2qb9 A2103 Nb G:A362(N7) A2443, A2444, A2445, L2107, L2108 G:A362, A:A364 2qb9 A2231 Nb G:A324(N7) A2545, A2546, A2547, A2548, T2236 U:A323, G:A324 2qbb A2250 Nb G:A324(N7) A2575, A2576, A2577, A2578, T2255 G:A324, G:A326 2qbb A2036 Nb G:A362(N7) A2399, A2400, A2401, A2402, A2403 G:A361, G:A362 G:A361 2qbd A2231 Nb G:A324(N7) A2232, A2233, A2234, A2235, T2236 U:A323, G:A324 2qbd A2103 Nb G:A362(N7) A2104, A2105, A2106, A2107, A2108 G:A361 2qbe B3164 Nb G:B1371(N7) B3746, B3747, B3748, B3749 G:B1358, C:B1357, C:B1370 G:B1358 2qbf A1549 Nb G:A362(N7) A1633, A1634, A1635, A1636, A1637 G:A361, G:A362 G:A361 2qbf A1583 Nb G:A324(N7) A1807, A1808, A1809, A1810, A1811 U:A323, G:A324 2qbh A1560 Nb G:A362(N7) A1685, A1686, A1687, L124, L125 G:A362, A:A364 2qbh A1581 Nb G:A324(N7) A1786, A1787, A1788, A1789, T236 U:A323, G:A324 2qbj A1549 Nb G:A362(N7) A1634, A1635, A1636, A1637, L124 G:A361, G:A362 G:A361 2qbj A1583 Nb G:A324(N7) A1805, A1806, A1807, A1808, T255 U:A323, G:A324 2qou A1560 Nb G:A362(N7) A1980, A1981, A1982, A1983, A1984 G:A362, A:A364 G:A361 2qou A1581 Nb G:A324(N7) A2084, A2085, A2086, A2087, A2088 G:A326 2qow A1549 Nb G:A362(N7) A1913, A1914, A1915, L124, L1633 G:A361 G:A361 2qow A1567 Nb G:A324(N7) A2005, A2006, A2007, A2008, A2009 U:A323, G:A326 2qox B3012 Nb G:B1190(N7) B3506, B3507, B3508, L612 A:B1189, G:B1191 2qoy A1581 Nb G:A324(N7) A2086, A2087, A2088, A2089, A2090 U:A323, G:A326

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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