MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df4:B3602, See in JSmolClick on the image to toggle views Site type: Pout·Rout·2Bout Schematic drawing for Pout·Rout·2Bout List of all 40 Mg2+ binding sites with the site type Pout·Rout·2Bout 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 2 of 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3v29 A3426 Pout·Rout·2Bout A4126, A4127, A4128, A4129 U:A2696 G:A1707 G:A1758, G:A1707 3v2d A3664 Pout·Rout·2Bout A5557, A5558, A5559, A5560, A5561 A:A983 U:A562 A:A572, C:A975 4bpe A5078 Pout·Rout·2Bout A2391, A2392, A2398, A2399, A2400, A2470 U:A1277 G:A1276 G:A1296, A:A1297 4bpe A5056 Pout·Rout·2Bout A2003, A2209, A2210, A2331, A2332, A2333 G:A1113 U:A8 G:A1113, G:A1114 4bpn A5072 Pout·Rout·2Bout A6570, A6571, A6572, A6573, A6574, A6576 U:A1467 C:A1466 A:A1457, U:A1492 4bpo A5056 Pout·Rout·2Bout A2002, A2214, A2215, A2426, A2427, A2428 G:A1113 U:A8 G:A1113, G:A1114 4bpo A5078 Pout·Rout·2Bout A2251, A2254, A2258, A2259, A2260, A2467 U:A1277 G:A1276 G:A1296, A:A1297 4dv1 A1822 Pout·Rout·2Bout A2244, A2245, A2246, A2247, A2248 C:A1303 G:A1331 G:A1305, G:A1304 4dv1 A1745 Pout·Rout·2Bout A2080, A2081, A2082, A2083 A:A642 U:A641 G:A595, G:A593 4gd2 A1630 Pout·Rout·2Bout A1843, A1844, A1845, N201, N202, N203 A:A977 C:A1359 A:A1360, C:A980 4nvy A3221 Pout·Rout·2Bout A4150, A4151, A4152, V201 C:A1496 U:V17 G:A1497, U:A1498 4nw1 A3256 Pout·Rout·2Bout A4074, A4075, A4076, A4077 U:A2696 G:A1707 G:A1707, G:A1758 4qcr A3341 Pout·Rout·2Bout A4165, A4166, A4167, A4168 U:A2708 G:A1754 G:A1789, G:A1754 4qct A3619 Pout·Rout·2Bout A4920, A4921, A4922, A4923, A4924, A4925 G:A396 U:A395 G:A397, G:A398 4tpb A3064 Pout·Rout·2Bout A3488, A3489, A3490, A3491 G:A2502 A:A2060 G:A2446, G:A2445

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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