MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df3:A2121, See in JSmolClick on the image to toggle views Site type: 2Pout·Rout·2Bout Schematic drawing for 2Pout·Rout·2Bout List of all 33 Mg2+ binding sites with the site type 2Pout·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 4qcv A3458 2Pout·Rout·2Bout A4504, A4505, A4506, A4507 G:A593, A:A1018 G:A1017 A:A867, A:A868 4qcx A3377 2Pout·Rout·2Bout A4281, A4282, A4283, A4284, A4285 C:A1617, G:A1619 C:A1617 G:A1613, G:A1619 4qcy A3182 2Pout·Rout·2Bout A4127, A4128, A4129, V3101 C:A1496, G:A1497 U:V17 G:A1497, U:A1498 4qcz A3461 2Pout·Rout·2Bout A4509, A4510, A4511, A4512 C:A1663, G:A1665 A:A1664 G:A1665, G:A1666 4too A3130 2Pout·Rout·2Bout A3767, A3768, A3769, A3770, A3771, A3772 G:A570, A:A973 U:A569 A:A820, A:A821 4tox A3049 2Pout·Rout·2Bout A3410, A3411, A3412, A3413, A3414 G:A1455, A:A1453 C:A1454 U:A1457, G:A1456 4tpb A3082 2Pout·Rout·2Bout A3566, A3567, A3568, A3569, A3570, A3571 A:A574, C:A2055 A:A2054 A:A574, G:A2035 4tpf A3083 2Pout·Rout·2Bout A3570, A3571, A3572, A3573, A3574, 0101 A:A574, C:A2055 A:A2054 A:A574, G:A2035

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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