MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbd:A2328, See in JSmolClick on the image to toggle views Site type: 3Pout·2Bout Schematic drawing for 3Pout·2Bout List of all 131 Mg2+ binding sites with the site type 3Pout·2Bout 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 1 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3i21 A2 3Pout·2Bout A1577, A1578, A1579, A1580, A1581, A1582 A:A315, A:A329, G:A319 A:A320, G:A319 1l2x A38 3Pout·2Bout A39, A40, A41, A42, A43, A44 C:A26, G:A27, G:A28 G:A27, G:A28 3owz A115 3Pout·2Bout A141, A142, A143, A144, A145, A146 U:A23, C:A24, G:A25 G:A25, G:A26 3v23 B211 3Pout·2Bout B313, B314, B315, B316, B317 U:B74, A:B100, G:B75 G:B75, G:B76 4gaq D301 3Pout·2Bout A1774, A1775, A1776, D401, D402 ARG:D70(NH1) C:A401, A:A547, G:A548 G:A402, C:A401 1dfu N504 3Pout·2Bout M536, N507, N527, N528, N530, N568 A:M99, G:N75, U:N74 G:N76, G:N75 2qoy A1550 3Pout·2Bout A1935, A1936, A1937, A1938, A1939, A1940 A:A315, A:A329, C:A316 G:A318, G:A319 2qp0 A1560 3Pout·2Bout A1975, A1976, A1977, A1978, A1979, A1980 A:A768, C:A805, A:A767 A:A768, G:A769 2qbj A1572 3Pout·2Bout A1755, A1756, A1757, A1758, A1759, A1760 A:A768, C:A805, A:A767 A:A768, G:A769 2i2u A1574 3Pout·2Bout A1745, A1746, A1747, A1748, A1749, A1750 A:A1394, G:A917, A:A918 A:A918, A:A919 2i2u A1596 3Pout·2Bout A1856, A1857, A1858, A1859, X267, X270 G:A1401, U:X2, G:X3 C:A1399, G:A1401 2qbf A1600 3Pout·2Bout A1886, A1887, A1888, A1889, A1890, A1891 A:A1394, G:A917, A:A918 A:A918, A:A919 2qbj A1600 3Pout·2Bout A1883, A1884, A1885, A1886, A1887, A1888 A:A1394, G:A917, A:A918 A:A918, A:A919 2aw7 A1601 3Pout·2Bout A1888, A1889, A1890, A1891, A1892, A1893 A:A1394, G:A917, A:A918 A:A918, A:A919 1vs7 A1602 3Pout·2Bout A1886, A1887, A1888, A1889, A1890, A1891 A:A1394, G:A917, A:A918 A:A918, A:A919 4ji6 A1607 3Pout·2Bout A2020, A2021, A2022, A2023, A2024 G:A617, A:A621, C:A620 G:A616, G:A617 4ji2 A1613 3Pout·2Bout A1927, A1928, A1929, A1930, A1931 C:A620, A:A621, G:A617 G:A617, G:A616 3v2c A1673 3Pout·2Bout A2018, A2019, A2020, A2021, A2022 A:A780, G:A799, C:A779 G:A800, A:A780 4ji5 A1718 3Pout·2Bout A2033, A2034, A2035, A2036, A2037, A2038 G:A869, G:A858, C:A868 G:A858, G:A869 3v26 A1722 3Pout·2Bout A2000, A2001, A2002, A2003 A:A780, G:A799, G:A800 G:A800, A:A780 4dv0 A1788 3Pout·2Bout A2139, A2140, A2141, A2142 C:A307, C:A308, G:A306 G:A309, G:A310 4dv0 A1799 3Pout·2Bout A2174, A2175, A2176, A2177, A2178, A2179 C:A857, C:A868, G:A869 G:A858, G:A869 4dv4 A1800 3Pout·2Bout A2163, A2164, A2165, A2166, A2167, A2168 C:A868, G:A869, C:A857 G:A858, G:A869 4dv1 A1820 3Pout·2Bout A2232, A2233, A2234, A2235, A2236, A2237 U:A757, U:A580, G:A758 G:A581, G:A758 4dv1 A1821 3Pout·2Bout A2238, A2239, A2240, A2241, A2242, A2243 C:A868, G:A869, C:A857 G:A858, G:A869

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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