MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df1:A2096, See in JSmolClick on the image to toggle views Site type: 4Pout Schematic drawing for 4Pout List of all 174 Mg2+ binding sites with the site type 4Pout 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 4bpo A5008 4Pout A2102, A2104, A2115, A2118, A2335, A2336 G:A542, A:A543, C:A577, C:A578 4bpo A5021 4Pout A2012, A2014, A2015, A2122, A2123, A2358 G:A20, U:A21, A:A593, U:A594 4bpo A5051 4Pout A2140, A2141, A2142, A2143, A2148, A2149 A:A629, A:A790, A:A630, A:A789 4bpp A5008 4Pout A7139, A7140, A7141, A7142, A7143, A7144 A:A543, C:A577, C:A578, G:A542 4bpp A5051 4Pout A7827, A7828, A7829, A7830, A7831, A7832 A:A629, A:A630, A:A789, A:A790 4bpp A5021 4Pout A7347, A7348, A7349, A7350, A7351, A7352 A:A593, G:A20, U:A594, U:A21 4dr2 A1756 4Pout A2408, A2409, A2410, A2411 C:A1203, A:A1204, U:A1049, G:A1048 4dr3 A1703 4Pout A2080, A2081, A2082, N201 A:A1204, G:A1048, U:A1049, C:A1203 4dr4 A1683 4Pout A2143, A2144, A2145, A2146 G:A15, A:A16, U:A13, U:A14 4dr5 A1607 4Pout A1919, A1920, A1921, A1922 U:A751, U:A652, G:A752, C:A651 4dr5 A1648 4Pout A2020, A2021, A2022, A2023 G:A15, A:A16, U:A13, U:A14 4duy A1635 4Pout A1976, A1977, A1978, A1979 U:A820, C:A578, C:A817, G:A576 4dv1 A1607 4Pout A1912, A1913, A1914, A1915 U:A751, U:A652, G:A752, C:A651 4dv2 A1836 4Pout A2264, A2265, A2266, A2267, A2268 G:A576, G:A575, G:A577, A:A815 4gar A3084 4Pout A3594, A3595, A3596, A3597, A3598 G:A561, G:A978, A:A981, C:A982 4gar A3073 4Pout A3546, A3547, A3548, A3549, C405 G:A2588, A:A2589, A:A2587, A:A2600 4gar A3169 4Pout A3238, A3239, A3240, A3241, A3242 A:A449, G:A450, G:A452, A:A453 4gau A3093 4Pout A3648, A3649, A3650, A3651, A3652 U:A1636, A:A1637, G:A1300, G:A1299 4gau A3133 4Pout A3814, A3815, A3816, A3817, A3818, N201 G:A2819, C:A2874, G:A2838, A:A2820 4ji0 A1653 4Pout A1999, A2000, A2001, A2002 G:A15, A:A16, U:A13, U:A14 4ji1 A1629 4Pout A1949, A1950, A1951, A1952 A:A16, G:A15, U:A13, U:A14 4ji2 A1653 4Pout A1998, A1999, A2000, A2001 G:A15, A:A16, U:A13, U:A14 4ji3 A1608 4Pout A1913, A1914, A1915, A1916 U:A751, C:A651, U:A652, G:A752 4ji3 A1653 4Pout A1999, A2000, A2001, A2002 G:A15, A:A16, U:A13, U:A14 4ji4 A1652 4Pout A1994, A1995, A1996, A1997 G:A15, A:A16, U:A13, U:A14

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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