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 7 of 14 | « Previous | Next » | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3ofc A2993 3Bout A3460, A3461, A3462, A3463, A3464, A3465 U:A1411, G:A1410, A:A1590 3ofz A2992 3Bout A3449, A3450, A3451, A3452, A3453, A3454 G:A1410, U:A1411, U:A1409 1vs6 B2984 3Bout B3394, B3395, B3396, B3397, B3398, B3399 G:B2550, G:B2557, C:B2558 2i2t B2984 3Bout B3400, B3401, B3402, B3403, B3404, B3405 G:B2550, G:B2557, G:B2549 2qov B2984 3Bout B3394, B3395, B3396, B3397, B3398, B3399 G:B2549, G:B2550, G:B2557 3i1t A2982 3Bout A3411, A3412, A3413, A3414, A3415, A3416 G:A2549, G:A2550, C:A2551 3r8t A2972 3Bout A3392, A3393, A3394, A3395, A3396 G:A2304, U:A2302, G:A2303 3i1p A2972 3Bout A3359, A3360, A3361, A3362, A3363, A3364 G:A2242, U:A2243, A:A2241 3ofd A2971 3Bout A3358, A3359, A3360, A3361, A3362, A3363 G:A2242, U:A2243, A:A2241 2qbg B2971 3Bout B3344, B3345, B3346, B3347, B3348, B3349 A:B756, A:B739, G:B757 2i2v B2970 3Bout B3343, B3344, B3345, B3346, B3347, B3348 C:B758, A:B739, G:B757 2qox B2970 3Bout B3338, B3339, B3340, B3341, B3342, B3343 A:B756, G:B757, A:B739 2awb B2970 3Bout B3334, B3335, B3336, B3337, B3338, B3339 A:B756, A:B739, G:B757 2qp1 B2969 3Bout B3835, B3836, B3837, B3838, B3839, B3840 U:B1258, G:B1259, U:B580 1vs8 B2969 3Bout B3333, B3334, B3335, B3336, B3337, B3338 A:B756, A:B739, G:B757 2i2v B2968 3Bout B3331, B3332, B3333, B3334, B3335, B3336 A:B1260, U:B580, U:B1258 2qox B2968 3Bout B3326, B3327, B3328, B3329, B3330, B3331 U:B580, U:B1258, G:B1259 1vs8 B2968 3Bout B3327, B3328, B3329, B3330, B3331, B3332 C:B650, G:B651, U:B652 1vs8 B2967 3Bout B3321, B3322, B3323, B3324, B3325, B3326 U:B580, U:B1258, G:B1259 2qbk B2965 3Bout B3306, B3307, B3308, B3309, B3310, B3311 U:B521, G:B17, U:B18 2qp1 B2965 3Bout B3814, B3815, B3816, B3817, B3818, B3819 G:B17, U:B18, U:B521 2qbg B2965 3Bout B3311, B3312, B3313, B3314, B3315, B3316 G:B17, U:B521, U:B18 2awb B2964 3Bout B3303, B3304, B3305, B3306, B3307, B3308 C:B16, G:B17, U:B18 2i2v B2964 3Bout B3310, B3311, B3312, B3313, B3314, B3315 G:B17, U:B521, A:B522 2qox B2964 3Bout B3305, B3306, B3307, B3308, B3309, B3310 G:B17, U:B18, U:B521

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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