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 3ivk C124 3Bout C150, C151, C152, C153, C154, C155 G:C72, A:C73, G:C105 3ivk C129 3Bout C171, C172, C173, C174, C175, C176 G:C17, G:C18, U:C16 3ivk M124 3Bout M150, M151, M152, M153, M154, M155 G:M72, A:M73, G:M105 3oaq A1570 3Bout A1747, A1748, A1749, A1750, A1751, U219 G:A1525, G:A1526, C:A1510 3oar A1560 3Bout A1707, A1708, A1709, A1710, I169 G:A1371, U:A1372, G:A1370 3oas A2904 3Bout A3037, A3038, A3039, A3040, A3041, A3042 U:A18, U:A521, G:A17 3oat A2995 3Bout A3463, A3464, A3465, A3466, A3467, A3468 G:A1465, U:A1466, G:A1464 3ofc A2922 3Bout A3134, A3135, A3136, A3137, A3138, A3139 G:A757, A:A756, A:A739 3ofc A2996 3Bout A3476, A3477, A3478, A3479, A3480, A3481 G:A1465, U:A1466, G:A1464 3ofc A2993 3Bout A3460, A3461, A3462, A3463, A3464, A3465 U:A1411, G:A1410, A:A1590 3ofd A2905 3Bout A3038, A3039, A3040, A3041, A3042, A3043 U:A18, U:A521, G:A17 3ofd A2971 3Bout A3358, A3359, A3360, A3361, A3362, A3363 G:A2242, U:A2243, A:A2241 3ofo A1568 3Bout A1743, A1744, A1745, A1746, U216, U219 C:A1509, G:A1525, G:A1526 3ofq A2920 3Bout A3114, A3115, A3116, A3117, A3118, A3119 C:A581, G:A1259, U:A1258 3ofr A2997 3Bout A3473, A3474, A3475, A3476, A3477, A3478 G:A1465, U:A1466, G:A1464 3ofr A3035 3Bout A3624, A3625, C759, C760, C762 G:A2592, U:A2593, G:A2599 3ofz A2999 3Bout A3485, A3486, A3487, A3488, A3489, A3490 G:A1824, U:A1825, G:A1823 3ofz A2992 3Bout A3449, A3450, A3451, A3452, A3453, A3454 G:A1410, U:A1411, U:A1409 3ofz A2995 3Bout A3465, A3466, A3467, A3468, A3469, A3470 G:A1465, U:A1466, G:A1464 3og0 A2904 3Bout A3036, A3037, A3038, A3039, A3040, A3041 U:A18, U:A521, G:A17 3og0 A2918 3Bout A3112, A3113, A3114, A3115, A3116, A3117 U:A580, C:A581, U:A1258 3or9 A1543 3Bout A1621, A1622, A1623, A1624, A1625, A1626 G:A592, U:A593, G:A645 3orb A2996 3Bout A3475, A3476, A3477, A3478, A3479, A3480 G:A1465, U:A1466, G:A1464 3ox0 A110 3Bout A146, A147, A148, A149, A150, A151 G:A25, G:A26, U:A27 3oxm A112 3Bout A124, A125, A129, A144, A145, A146 U:A46, G:A47, G:A55

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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