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 4 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 2qbf A1566 3Bout A1716, A1717, A1718, A1719, A1720, A1721 G:A257, G:A258, G:A259 2qbf A1590 3Bout A1838, A1839, A1840, A1841, A1842, A1843 C:A1509, G:A1525, G:A1526 2qbg B2965 3Bout B3311, B3312, B3313, B3314, B3315, B3316 G:B17, U:B521, U:B18 2qbg B2956 3Bout B3264, B3265, B3266, B3267, B3268, B3269 A:B42, G:B43, U:B434 2qbg B2971 3Bout B3344, B3345, B3346, B3347, B3348, B3349 A:B756, A:B739, G:B757 2qbh A1561 3Bout A1688, A1689, A1690, A1691, A1692 G:A1048, G:A1050, G:A1207 2qbi B2924 3Bout B3108, B3109, B3110, B3111, B3112, B3113 A:B756, A:B739, G:B757 2qbi B2947 3Bout B3212, B3213, B3214, B3215, B3216, B3217 G:B43, U:B434, A:B42 2qbi B2918 3Bout B3075, B3076, B3077, B3078, B3079, B3080 U:B521, G:B17, U:B18 2qbj A1566 3Bout A1716, A1717, A1718, A1719, A1720, A1721 G:A257, G:A258, G:A259 2qbk B2956 3Bout B3260, B3261, B3262, B3263, B3264, B3265 G:B43, U:B434, A:B42 2qbk B2965 3Bout B3306, B3307, B3308, B3309, B3310, B3311 U:B521, G:B17, U:B18 2qbk B2964 3Bout B3301, B3302, B3303, B3304, B3305 G:B2304, U:B2302, G:B2303 2qov B2947 3Bout B3214, B3215, B3216, B3217, B3218, B3219 G:B43, U:B434, A:B42 2qov B2984 3Bout B3394, B3395, B3396, B3397, B3398, B3399 G:B2549, G:B2550, G:B2557 2qox B2956 3Bout B3261, B3262, B3263, B3264, B3265, B3266 A:B42, G:B43, U:B434 2qox B2968 3Bout B3326, B3327, B3328, B3329, B3330, B3331 U:B580, U:B1258, G:B1259 2qox B2970 3Bout B3338, B3339, B3340, B3341, B3342, B3343 A:B756, G:B757, A:B739 2qox B2952 3Bout B3243, B3244, B3245, B3246, B3247, B3248 G:B2549, G:B2550, G:B2557 2qox B2964 3Bout B3305, B3306, B3307, B3308, B3309, B3310 G:B17, U:B18, U:B521 2qoy A1599 3Bout A2170, A2171, A2172, A2173, A2174, A2175 G:A1505, C:A1399, G:A1401 2qoz B2947 3Bout B3706, B3707, B3708, B3709, B3710, B3711 U:B434, A:B42, G:B43 2qoz B2924 3Bout B3603, B3604, B3605, B3606, B3607, B3608 A:B756, A:B739, G:B757 2qoz B2907 3Bout B3522, B3523, B3524, B3525, B3526, B3527 U:B580, U:B1258, G:B1259 2qoz B2961 3Bout B3774, B3775, B3776, B3777, B3778, B3779 G:B798, G:B799, G:B797

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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