MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbb:A2049, See in JSmolClick on the image to toggle views Site type: 2Pout·Bout Schematic drawing for 2Pout·Bout List of all 169 Mg2+ binding sites with the site type 2Pout·Bout 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 5 of 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4dv1 A1823 2Pout·Bout A2249, A2250, A2251, A2252, A2253 G:A1224, G:A951 A:A977 4dr7 A1820 2Pout·Bout A2486, A2487, A2488, A2489, A2490, A2491 G:A438, G:A492 G:A494 4dv2 A1818 2Pout·Bout A2205, A2206, A2207, A2208 A:A353, A:A53 A:A353 4duy A1799 2Pout·Bout A2164, A2165, A2166, A2167, A2168 G:A1385, G:A1386 G:A1386 4dr5 A1799 2Pout·Bout A2186, A2187, A2188, A2189, A2190, A2191 G:A594, U:A641 G:A595 3v2e A1768 2Pout·Bout A2214, A2215, A2216, A2217 A:A374, G:A384 A:A453 4ji1 A1766 2Pout·Bout A2284, A2285, A2286, A2287, A2288, A2289 A:A1394, A:A918 A:A919 4ji1 A1758 2Pout·Bout A2237, A2238, A2239, A2240, A2241, A2242 C:A307, C:A308 G:A309 4ji1 A1751 2Pout·Bout A2195, A2196, A2197, A2198, A2199, A2200 G:A361, G:A362 G:A362 4dr2 A1743 2Pout·Bout A2357, A2358, A2359, A2360, A2361 G:A1416, G:A1417 G:A1417 4dr2 A1736 2Pout·Bout A2333, A2334, A2335, A2336 U:A17, U:A13 U:A14 4dr4 A1730 2Pout·Bout A2247, A2248, A2249, A2250 G:A475, G:A476 G:A477 3v28 A1718 2Pout·Bout A1903, A1904, A1905, A1906, A1907, A1908 G:A265, G:A266 G:A258 4dr2 A1657 2Pout·Bout A2108, A2109, A2110, A2111 U:A560, C:A562 G:A566 4dr2 A1642 2Pout·Bout A2068, A2069, A2070, D404 A:A431, G:A407 A:A408 4ji7 A1638 2Pout·Bout A2172, A2173, A2174, A2175 C:A754, U:A646 G:A587 4tp2 A1636 2Pout·Bout A1867, A1868, A1869, A1870 C:A1303, G:A1305 G:A1305 4gas A1632 2Pout·Bout A1849, A1850, A1851, A1852 C:A1054, A:A1197 U:A1199 4dr4 A1631 2Pout·Bout A2032, A2033, A2034, D401, D402 C:A620, A:A621 G:A617 4dr2 A1630 2Pout·Bout A2039, A2040, A2041, A2042, A2043 C:A620, G:A617 G:A617 4gaq A1623 2Pout·Bout A1807, A1808, A1809, A1810, A1811, K201 U:A798, A:A780 G:A799 4dr5 A1612 2Pout·Bout A1933, A1934, A1935, A1936, A1937 C:A620, A:A621 G:A617 4ji7 A1609 2Pout·Bout A2119, A2120, A2121, A2122, A2123 C:A620, A:A621 G:A617 4ji8 A1609 2Pout·Bout A2019, A2020, A2021, A2022, A2023 C:A620, A:A621 G:A617 4dr1 A1608 2Pout·Bout A1913, A1914, A1915, A1916 C:A651, U:A751 G:A752

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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