MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs7:A1593, See in JSmolClick on the image to toggle views Site type: 2Pout Schematic drawing for 2Pout List of all 191 Mg2+ binding sites with the site type 2Pout 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 8 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4dv3 A1687 2Pout A2054, A2055, A2268, A2269 G:A1048, U:A1049 4dv4 J202 2Pout A2216, I201, J301, J302, N202 C:A1189, A:A1188 4dv4 A1782 2Pout A2106, A2107, A2108, A2109 C:A1200, C:A1051 4dv7 A1842 2Pout A2181, A2182, A2183, A2184 G:A576, G:A577 4gar A3054 2Pout A3456, A3457, A3458, C403, C404 G:A1828, G:A1972 4gar A3028 2Pout A3340, A3341, A3342, A3343, A3344, A3345 G:A822, A:A947 4ji1 A1770 2Pout A2312, A2313, A2314, A2315, E305, E306 U:A863, A:A864 4ji1 A1769 2Pout A2306, A2307, A2308, A2309, A2310, A2311 U:A552, A:A553 4ji1 A1771 2Pout A2316, A2317, A2318, A2319, A2320, A2321 U:A1345, C:A934 4ji2 A1608 2Pout A1913, A1914, A1915, A1916 U:A652, U:A751 4ji6 A1850 2Pout A2716, A2717, A2718, A2719, A2720, A2721 U:A552, A:A553 4ji7 A1906 2Pout A2946, A2947, A2948, A2949, A2950, A2951 U:A552, A:A553 4jnx D303 2Pout D405, D406, D407, D408, D409, G504 U:G412, C:G411 4nvu A3205 2Pout A4129, A4130, E202, E203 A:A864, U:A863 4nvv A3612 2Pout A4871, A4872, A4873, A4874 G:A2609, G:A1926 4nvv A3591 2Pout A4815, A4816, A4817, A4818 U:A869, G:A992 4nvv A3602 2Pout A4843, A4844, A4845, A4846 G:A2793, U:A2792 4nvy A3205 2Pout A4129, A4130, A4131, E203 A:A864, U:A863 4nvz A3587 2Pout A4816, A4817, A4818, A4819 U:A869, G:A992 4nvz A3598 2Pout A4844, A4845, A4846, A4847 G:A2793, U:A2792 4peb A3073 2Pout A3543, A3544, A3545, A3546 C:A2611, C:A2579 4qcm A1812 2Pout A4210, A4211, E3101, E3102 A:A864, U:A863 4qcq A3172 2Pout A4162, A4163, A4164, A4165 A:A814, C:A904 4qct A3426 2Pout A4481, A4482, A4483, P305 A:A1246, G:A662 4qcv A3481 2Pout A4555, A4556, A4557, A4558 U:A2894, U:A2842

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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