MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 3ofq 3OFQ (3.1Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to erythromycin. this file contains the 50s subunit of the second 70s ribosome. List of all 109 Mg2+ binding sites in the PDB structure 3ofq in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID" Page 4 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3ofq A2928 trans-2Oph A:A751(OP1), A:A1614(OP1) A3155, A3156, A3157, A3158 G:A1613 A:A751, C:A1615, A:A789 3ofq A3024 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3580, A3581, A3582 G:A194 3ofq A2938 fac-3Oph C:A948(OP1), G:A962(OP1), U:A963(OP2) A3203, A3204, A3205 A:A947 3ofq A2952 fac-3Oph A:A1395(OP1), A:A1603(OP1), C:A1604(OP2) A3263, A3264, A3265 3ofq A2935 mer-3Oph U:A827(OP1), G:A2429(OP2), A:A2430(OP2) A3191, A3192, A3193 3ofq A2924 Bout A3134, A3135, A3136, A3137, A3138, A3139 G:A651 3ofq A3034 2Bout A3622, A3623, A3624, A3625, 4755, 4760 G:A2742, C:A2755 3ofq A2905 2Bout A3038, A3039, A3040, A3041, A3042, A3043 U:A521, G:A17 3ofq A2930 2Bout A3166, A3167, A3168, A3169, A3170, E202 G:A797, G:A798 3ofq A2982 2Bout A3410, A3411, A3412, A3413, A3414, A3415 G:A2549, G:A2550 3ofq A2920 3Bout A3114, A3115, A3116, A3117, A3118, A3119 C:A581, G:A1259, U:A1258 3ofq A2972 4Bout A3361, A3362, A3363, A3364, A3365, A3366 G:A2238, G:A2242, A:A2241, U:A2243 3ofq A2926 4Bout A3144, A3145, A3146, A3147, A3148, A3149 U:A755, G:A757, A:A739, A:A756 3ofq A2907 Pout A3050, A3051, A3052, A3053, A3054, A3055 C:A41 3ofq A2934 Pout A3185, A3186, A3187, A3188, A3189, A3190 C:A965 3ofq A2995 Pout A3468, A3469, A3470, A3471, A3472 A:A1028 3ofq A2991 Pout·2Bout A3448, A3449, A3450, A3451, A3452, A3453 A:A933 U:A842, G:A841 3ofq A3015 Pout·Rout·2Bout A3543, A3544, A3545, A3546, A3547, 2647 U:A686 A:A685 G:A770, G:A771 3ofq A2977 Pout·3Bout A3383, A3384, A3385, A3386, A3387 C:A2310 G:A2304, U:A2302, G:A2303 3ofq A2980 Pout·3Bout A3399, A3400, A3401, A3402, A3403, A3404 A:A2453 G:A2454, A:A2497, G:A2455

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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