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 3v25 A3309 3Bout A3779, A3780, A3781, A3782, A3783, A3784 G:A1309, G:A1311, G:A1310 3v25 A3385 3Bout A4024, A4025, A4026, A4027 G:A259, U:A239, G:A258 3v25 A3415 3Bout A4124, A4125, A4126, A4127, A4128, A4129 G:A1389, U:A1390, G:A1388 3v25 A3395 3Bout A4054, A4055, A4056, A4057 G:A496, G:A494, G:A495 3v23 A3447 3Bout A4443, A4444, A4445, A4446, A4447 G:A496, G:A495, G:A494 3v23 A3576 3Bout A4872, A4873, A4874, A4875, A4876 G:A2625, G:A2624, G:A2777 3v23 A3489 3Bout A4601, A4602, A4603, A4604, A4605, A4606 C:A1305, G:A1623, G:A1624 3v23 A3460 3Bout A4491, A4492, A4493, A4494, A4495, A4496 A:A1412, G:A1413, G:A1414 3v23 A3603 3Bout A5012, A5013, A5014, A5015, A5016, A5017 G:A2009, G:A2010, U:A2011 3v22 A1696 3Bout A1904, A1905, A1906, A1907 G:A46, G:A394, C:A366 3ssf A14 3Bout A44, A45, A46, A57 A:A10, G:A11, G:A12 3r8t A2972 3Bout A3392, A3393, A3394, A3395, A3396 G:A2304, U:A2302, G:A2303 3r8t A2923 3Bout A3167, A3168, A3169, A3170, A3171, A3172 G:A757, A:A756, A:A739 3r8t A2919 3Bout A3144, A3145, A3146, A3147, A3148, A3149 G:A579, G:A1259, U:A580 3r1l C1027 3Bout C1055, C1056, C1057, C1058, C1059, C1060 U:C36, G:C37, G:C78 3p49 A736 3Bout A750, A751, A752, A753, A754 G:A8, G:A9, G:A62 3oxm A112 3Bout A124, A125, A129, A144, A145, A146 U:A46, G:A47, G:A55 3ox0 A110 3Bout A146, A147, A148, A149, A150, A151 G:A25, G:A26, U:A27 3orb A2996 3Bout A3475, A3476, A3477, A3478, A3479, A3480 G:A1465, U:A1466, G:A1464 3or9 A1543 3Bout A1621, A1622, A1623, A1624, A1625, A1626 G:A592, U:A593, G:A645 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 3ofz A2992 3Bout A3449, A3450, A3451, A3452, A3453, A3454 G:A1410, U:A1411, U:A1409 3ofz A2999 3Bout A3485, A3486, A3487, A3488, A3489, A3490 G:A1824, U:A1825, G:A1823 3ofz A2995 3Bout A3465, A3466, A3467, A3468, A3469, A3470 G:A1465, U:A1466, G:A1464

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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