MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2t:B2935, See in JSmolClick on the image to toggle views Site type: 3Pout·Bout Schematic drawing for 3Pout·Bout List of all 155 Mg2+ binding sites with the site type 3Pout·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 1 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 3ud3 R1 3Pout·Bout R671, R672, R673, R674, R675, R676 G:R40, G:R41, A:R23 G:R42 2z4m E167 3Pout·Bout A1727, A1728, A1729, A1730, E171 U:A20, G:A21, U:A561 G:A21 3v27 B218 3Pout·Bout B330, B331, B332, B333, B334 U:B74, A:B100, G:B75 G:B76 4dha B221 3Pout·Bout B314, B315, B316, B317 A:B102, G:B103, A:B73 G:B103 2qow E291 3Pout·Bout A2117, A2118, A2119, E295, E297, E1832 U:A561, U:A20, G:A21 G:A21 2z4k A1551 3Pout·Bout A1640, A1641, A1642, A1643, A1644, A1645 A:A315, U:A317, C:A316 G:A318 3i1z A1552 3Pout·Bout A1663, A1664, A1665, A1666, A1667, E167 G:A1077, G:A1079, U:A1076 G:A1077 2qou A1559 3Pout·Bout A1974, A1975, A1976, A1977, A1978, A1979 A:A16, U:A13, U:A14 U:A14 2qou A1569 3Pout·Bout A2029, A2030, A2031, A2032, A2033 A:A767, A:A768, U:A804 G:A769 2i2p A1569 3Pout·Bout A1736, A1737, A1738, A1739, A1740 A:A768, A:A767, U:A804 G:A769 2qbh A1569 3Pout·Bout A1731, A1732, A1733, A1734, A1735 A:A768, U:A804, A:A767 G:A769 2aw7 A1573 3Pout·Bout A1759, A1760, A1761, A1762, A1763, A1764 A:A768, C:A805, A:A767 G:A769 1vs7 A1574 3Pout·Bout A1757, A1758, A1759, A1760, A1761, A1762 A:A768, C:A805, A:A767 G:A769 2avy A1597 3Pout·Bout A1862, A1863, A1864, A1865, A1866, A1867 A:A919, A:A1394, A:A918 A:A919 2qoy A1598 3Pout·Bout A2164, A2165, A2166, A2167, A2168, A2169 A:A1394, G:A917, A:A918 A:A919 1vs5 A1598 3Pout·Bout A1866, A1867, A1868, A1869, A1870, A1871 A:A919, A:A1394, A:A918 A:A919 2z4k A1599 3Pout·Bout A1869, A1870, A1871, A1872, A1873, A1874 A:A1394, G:A917, A:A918 A:A919 4ji1 A1606 3Pout·Bout A1912, A1913, A1914, A1915, A1916 C:A620, A:A621, G:A617 G:A617 4gaq A1609 3Pout·Bout A1733, A1734, A1735, A1736, A1737, A1738 A:A315, G:A319, A:A329 G:A319 4dv7 A1611 3Pout·Bout A1923, A1924, A1925, A1926, A1927 G:A617, C:A620, A:A621 G:A617 4duy A1611 3Pout·Bout A1927, A1928, A1929, A1930, A1931 C:A620, A:A621, G:A617 G:A617 4dv5 A1611 3Pout·Bout A1923, A1924, A1925, A1926, A1927 C:A620, A:A621, G:A617 G:A617 4duz A1611 3Pout·Bout A1923, A1924, A1925, A1926, A1927 G:A617, C:A620, A:A621 G:A617 4dv6 A1611 3Pout·Bout A1927, A1928, A1929, A1930, D401 C:A620, A:A621, G:A617 G:A617 4dv4 A1612 3Pout·Bout A1926, A1927, A1928, A1929, A1930 C:A620, A:A621, G:A617 G:A617

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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