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 2qov B2947 3Bout B3214, B3215, B3216, B3217, B3218, B3219 G:B43, U:B434, A:B42 2qbi B2947 3Bout B3212, B3213, B3214, B3215, B3216, B3217 G:B43, U:B434, A:B42 1vs6 B2947 3Bout B3216, B3217, B3218, B3219, B3220, B3221 G:B43, U:B434, A:B42 2qoz B2947 3Bout B3706, B3707, B3708, B3709, B3710, B3711 U:B434, A:B42, G:B43 1vs8 B2951 3Bout B3239, B3240, B3241, B3242, B3243, B3244 G:B2550, G:B2557, G:B2549 2qox B2952 3Bout B3243, B3244, B3245, B3246, B3247, B3248 G:B2549, G:B2550, G:B2557 2awb B2952 3Bout B3243, B3244, B3245, B3246, B3247, B3248 G:B2550, G:B2557, G:B2549 2z4n B2953 3Bout B3245, B3246, B3247, B3248, B3249, B3250 G:B2549, G:B2550, G:B2557 2qbg B2956 3Bout B3264, B3265, B3266, B3267, B3268, B3269 A:B42, G:B43, U:B434 2qox B2956 3Bout B3261, B3262, B3263, B3264, B3265, B3266 A:B42, G:B43, U:B434 2i2v B2956 3Bout B3270, B3271, B3272, B3273, B3274, B3275 A:B42, G:B43, U:B434 2qbk B2956 3Bout B3260, B3261, B3262, B3263, B3264, B3265 G:B43, U:B434, A:B42 2qp1 B2956 3Bout B3767, B3768, B3769, B3770, B3771, B3772 U:B434, A:B42, G:B43 2z4n B2957 3Bout B3263, B3264, B3265, B3266, B3267, B3268 A:B42, G:B43, U:B434 2qoz B2961 3Bout B3774, B3775, B3776, B3777, B3778, B3779 G:B798, G:B799, G:B797 2awb B2964 3Bout B3303, B3304, B3305, B3306, B3307, B3308 C:B16, G:B17, U:B18 2qox B2964 3Bout B3305, B3306, B3307, B3308, B3309, B3310 G:B17, U:B18, U:B521 2i2v B2964 3Bout B3310, B3311, B3312, B3313, B3314, B3315 G:B17, U:B521, A:B522 2qbk B2964 3Bout B3301, B3302, B3303, B3304, B3305 G:B2304, U:B2302, G:B2303 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 1vs8 B2967 3Bout B3321, B3322, B3323, B3324, B3325, B3326 U:B580, U:B1258, G:B1259 2i2v B2968 3Bout B3331, B3332, B3333, B3334, B3335, B3336 A:B1260, U:B580, U:B1258 1vs8 B2968 3Bout B3327, B3328, B3329, B3330, B3331, B3332 C:B650, G:B651, U:B652

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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