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 2 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 2i2u A1577 Pout·Bout A1760, A1761, A1762, A1763, A1764, A1765 G:A1079 G:A1077 2i2u A1575 Pout·Bout A1751, A1752, A1753, A1754, T159, T161 G:A259 G:A259 2i2v B2998 Pout·Bout B3453, B3454, B3455, B3456, B3457, 2957 U:B686 G:B770 2qal A2007 Pout·Bout A2008, A2009, A2010, A2011, A2012, A2013 G:A1079 G:A1077 2qan N2091 Pout·Bout A2093, A2094, A2096, N2092, N2095 A:A1360 C:A980 2qan A2049 Pout·Bout A2050, A2051, A2052, A2053, A2054, A2055 A:A172 G:A148 2qb9 A2136 Pout·Bout A2466, A2467, A2468, A2469, A2470, A2471 G:A727 G:A727 2qb9 A2335 Pout·Bout A2630, A2631, A2632, A2633, A2634, A2635 C:A1400 G:A926 2qbb A2107 Pout·Bout A2455, A2456, A2457, A2458, A2459, A2460 G:A1079 G:A1077 2qbb A2155 Pout·Bout A2496, A2497, A2498, A2499, A2500 U:A20 G:A21 2qbf A1551 Pout·Bout A1644, A1645, A1646, A1647, A1648, A1649 A:A172 G:A148 2qbf A1568 Pout·Bout A1733, A1734, A1735, A1736, A1737, A1738 G:A727 G:A727 2qbh A1544 Pout·Bout A1609, A1610, A1611, A1612, A1613, A1614 G:A1079 G:A1077 2qbj A1568 Pout·Bout A1731, A1732, A1733, A1734, A1735, A1736 G:A727 G:A727 2qbj E167 Pout·Bout A1728, A1729, A1730, E168, E169 U:A20 G:A21 2qex 08100 Pout·Bout 03595, 04098, 05360, 06008, 06448 C:02077 G:02079 2qou A1544 Pout·Bout A1902, A1903, A1904, A1905, A1906, A1907 G:A1079 G:A1077 2qou A1564 Pout·Bout A2002, A2003, A2004, E167, E168, E169 U:A20 G:A21 2qow A1582 Pout·Bout A2077, A2078, A2079, A2080, A2081, A2082 G:A1079 G:A1077 2qow A1558 Pout·Bout A1960, A1961, A1962, A1963, A1964, A1965 U:A854 G:A727 2qoy A1579 Pout·Bout A2076, A2077, A2078, A2079, A2080, A2081 U:A916 U:A916 2qoy A1556 Pout·Bout A1961, A1962, A1963, A1964, A1965, A1966 A:A1046 G:A1047 2qoy A1544 Pout·Bout A1904, A1905, A1906, A1907, A1908, A1909 G:A1079 G:A1077 2qp0 A1551 Pout·Bout A1925, A1926, A1927, A1928, A1929, A1930 A:A172 G:A148 2qp0 A1582 Pout·Bout A2076, A2077, A2078, A2079, A2080, E242 G:A1079 G:A1077

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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