MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3464, See in JSmolClick on the image to toggle views Site type: 3Bout Schematic drawing for 3Bout List of all 341 Mg2+ binding sites with the site type 3Bout 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 3 of 14 | « 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 2i2v B2968 3Bout B3331, B3332, B3333, B3334, B3335, B3336 A:B1260, U:B580, U:B1258 2nug C515 3Bout C535, C538, C559, C563 G:C4, G:C5, U:C6 2nug C519 3Bout C526, C530, C540, C546, C562, F551 G:C12, C:C11, A:F17 2nug D514 3Bout D529, D533, D550, D551, D552 G:D4, G:D5, U:D6 2nug D516 3Bout E513, E526, D522, D531, D535, D562 G:D12, C:D11, A:E17 2q1r A8002 3Bout A9001, A9002, A9009, A9019, A9021, A9032 G:A1004, U:A1007, A:A1005 2qal A2150 3Bout A2151, A2152, A2153, A2154, A2155, A2156 G:A378, G:A376, G:A377 2qal A2270 3Bout A2271, A2272, A2273, A2274, A2275, A2276 G:A1526, G:A1525, C:A1509 2qam B3117 3Bout B3706, B3707, B3708, B3709, B3710, B3711 A:B756, A:B739, G:B757 2qam B3240 3Bout B3805, B3806, B3807, B3808, B3809 G:B2304, U:B2302, G:B2303 2qam B3078 3Bout B3673, B3674, B3675, B3676, B3677, B3678 U:B18, U:B521, G:B17 2qan A2148 3Bout A2149, A2150, A2151, A2152, A2153, A2154 G:A800, U:A798, G:A799 2qao B3301 3Bout B3865, B3866, B3867, B3868, B3869, B3870 A:B42, G:B43, U:B434 2qao B3396 3Bout B3945, B3946, B3947, B3948, B3949, B3950 A:B739, G:B757, A:B756 2qao B3279 3Bout B3847, B3848, B3849, B3850, B3851, B3852 G:B2549, G:B2550, G:B2557 2qb9 A2349 3Bout A2642, A2643, A2644, A2645, A2646 C:A1359, U:A1358, A:A1357 2qba B3117 3Bout B3706, B3707, B3708, B3709, B3710, B3711 A:B756, A:B739, G:B757 2qba B3014 3Bout B3625, B3626, B3627, B3628, B3629, B3630 U:B580, U:B1258, G:B1259 2qba B3078 3Bout B3673, B3674, B3675, B3676, B3677, B3678 U:B521, G:B17, U:B18 2qbc B3301 3Bout B3865, B3866, B3867, B3868, B3869, B3870 G:B43, U:B434, A:B42 2qbc B3382 3Bout B3931, B3932, B3933, B3934, B3935, B3936 G:B1259, A:B1260, U:B580 2qbd A2349 3Bout A2350, A2351, A2352, A2353, A2354 C:A1359, G:A976, U:A1358 2qbe B3078 3Bout B3674, B3675, B3676, B3677, B3678, B3679 U:B521, G:B17, U:B18 2qbe B3464 3Bout B3988, B3989, B3990, B3991, B3992, B3993 G:B2549, G:B2550, G:B2557 2qbf A1590 3Bout A1838, A1839, A1840, A1841, A1842, A1843 C:A1509, G:A1525, G:A1526

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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