MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs5:A1545, See in JSmolClick on the image to toggle views Site type: Pout·Bout Schematic drawing for Pout·Bout List of all 223 Mg2+ binding sites with the site type Pout·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 7 of 9 | « 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 4bpp A5071 Pout·Bout A8147, A8148, A8149, A8150, A8151, A8152 C:A1418 C:A1185 4bpp A5006 Pout·Bout A7107, A7108, A7109, A7110, A7111, A7112 G:A1271 G:A1269 4dh9 A1931 Pout·Bout A2279, A2280, A2281, A2282, A2283 U:A641 G:A595 4dha A3863 Pout·Bout A5308, A5309, A5310, A5311 A:A2377 G:A2375 4dha A3600 Pout·Bout A4363, A4364, A4365, A4366, A4367 G:A465 G:A463 4dha A3847 Pout·Bout A5257, A5258, A5259, A5260 G:A1488 U:A1489 4dhc A3417 Pout·Bout A3913, A3914, A3915, A3916 C:A574 G:A577 4dr2 A1786 Pout·Bout A2505, A2506, A2507, A2508 C:A1431 G:A1432 4dr2 A1738 Pout·Bout A2341, A2342, A2343, A2344 A:A918 A:A919 4dr2 A1648 Pout·Bout A2083, A2084, A2085, A2086 U:A20 G:A21 4dr3 A1628 Pout·Bout A1957, A1958, A1959, A1960 G:A21 G:A21 4dr4 A1756 Pout·Bout A2311, A2312, A2313, A2314 U:A1450 G:A700 4dr4 A1754 Pout·Bout A2306, A2307, A2308, A2309 A:A1360 C:A980 4dr4 A1746 Pout·Bout A2281, A2282, A2283, A2284 G:A1417 G:A1417 4dr5 A1682 Pout·Bout A2099, A2100, A2101, A2102 G:A476 G:A477 4dr5 A1621 Pout·Bout A1953, A1954, A1955, D401 A:A431 A:A408 4dr6 A1876 Pout·Bout A2718, A2719, A2720, A2721, A2722, A2723 A:A382 G:A380 4dr7 A1698 Pout·Bout A2240, A2241, A2242, A2243 U:A1450 G:A700 4dv2 A1837 Pout·Bout A2269, A2270, A2271, A2272 G:A21 G:A21 4dv3 A1607 Pout·Bout A1912, A1913, A1914, A1915 U:A751 G:A752 4dv5 A1681 Pout·Bout A2035, A2036, A2037, A2038 A:A415 G:A425 4dv6 A1858 Pout·Bout A2362, A2363, A2364, A2365, A2366, A2367 G:A21 G:A21 4gaq A1601 Pout·Bout A1840, A1841, A1842, A1843, N301, N302 A:A1360 C:A980 4gaq A1639 Pout·Bout A1883, A1884, A1885, A1886, A1887, A1888 G:A1523 G:A1525 4gar A3059 Pout·Bout A3479, A3480, A3481, A3482 A:A2033 G:A2027

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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