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 4gau 4GAU (3.3Å) -- RIBOSOME/ANTIBIOTIC : Allosteric control of the ribosome by small-molecule antibiotics List of all 120 Mg2+ binding sites in the PDB structure 4gau 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 2 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 4gau A3025 Oph·Pout A:A802(OP1) A3328, A3329, A3330, A3331, A3332 G:A674 U:A803, A:A804, G:A674 4gau A3020 Oph·Pout A:A751(OP1) A3306, A3307, A3308, A3309 A:A1614 G:A1613 A:A789, C:A1617 4gau A3077 Oph·Pout A:A572(OP1) A3567, A3568, A3569, A3570, A3571 A:A983 A:A572 4gau A3056 Oph·Pout A:A1970(OP2) A3467, A3468, A3469, A3470, A3471 A:A1900 G:A1835 4gau A3100 Oph·Pout A:A2705(OP2) A3682, A3683, A3684, A3685, A3686 C:A2704 A:A2706, A:A2705 4gau A3036 Oph·2Pout C:A2006(OP1) A3376, A3377, A3378, A3379 A:A1268, G:A2048 U:A1267 4gau A3034 Oph·2Pout G:A1187(OP2) A3365, A3366, A3367, A3368, A3369 C:A816, C:A817 G:A1185 G:A1187, C:A817, G:A818 4gau A3026 Oph·2Pout U:A810(OP1) A3333, A3334, A3335, A3336 U:A566, U:A811 A:A1253 4gau A3014 Oph·2Pout A:A574(OP2) A3263, A3264, A3265, A3266, A3267 U:A576, U:A573 G:A577, G:A578 4gau A3039 Oph·2Pout U:A1313(OP1) A3386, A3387, A3388, A3389, T201 G:A1333, G:A1334 4gau A3012 Oph·2Pout U:A567(OP1) A3255, A3256, A3257, A3258, A3259 G:A808, G:A809 G:A809, G:A808 4gau A3008 Oph·2Pout G:A450(OP2) A3238, A3239, A3240, A3241, A3242 A:A449, G:A452 G:A450 4gau A3006 Oph·2Pout G:A297(OP2) A3228, A3229, A3230, A3231, A3232 G:A338, G:A298 G:A298, G:A297 4gau A3086 Oph·2Pout A:A1327(OP2) A3611, A3612, A3613, A3614, A3615 U:A1326, A:A1328 A:A1328, G:A1324 4gau A3079 Oph·2Pout C:A817(OP2) A3578, A3579, A3580, A3581 G:A818, G:A1186 G:A818, G:A1187, G:A1186 4gau A3066 Oph·2Pout A:A2270(OP2) A3514, A3515, A3516, A3517, A3518 G:A2269, A:A2267 G:A2271, U:A2272 4gau A3055 Oph·2Pout G:A2592(OP1) A3463, A3464, A3465, A3466 G:A1973, G:A1968 4gau A3052 Oph·2Pout G:A1776(OP2) A3447, A3448, A3449, A3450, A3451 U:A1775, A:A1981 G:A1980 G:A1776 4gau A3051 Oph·2Pout C:A1774(OP1) A3442, A3443, A3444, A3445, A3446 U:A1775, A:A1786 A:A1772 A:A1772, G:A1980, G:A1776 4gau A3049 Oph·2Pout U:A1671(OP2) A3433, A3434, A3435, A3436 C:A1670, G:A2550

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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