MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qam:B3600, See in JSmolClick on the image to toggle views Site type: 3Pout·Rout·2Bout Schematic drawing for 3Pout·Rout·2Bout List of all 58 Mg2+ binding sites with the site type 3Pout·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 3 of 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4tom A3129 3Pout·Rout·2Bout A3773, A3774, A3775, A3776, A3777, L305 G:A570, A:A973, U:A569 A:A972 A:A820, A:A821 4too A3048 3Pout·Rout·2Bout A3407, A3408, A3409, A3410, A3411 G:A1455, A:A1453, G:A1456 C:A1454 U:A1457, G:A1456 4tox A3018 3Pout·Rout·2Bout A3280, A3281, A3282, A3283, A3284, A3285 G:A583, A:A1253, A:A582 C:A1251 G:A583, C:A584 4tox A3130 3Pout·Rout·2Bout A3772, A3773, A3774, A3775, A3776, A3777 G:A570, A:A973, U:A569 A:A972 A:A820, A:A821 4tp3 A3018 3Pout·Rout·2Bout A3281, A3282, A3283, A3284, A3285, A3286 A:A582, A:A1253, G:A583 C:A1251 G:A583, C:A584 4tpb A3018 3Pout·Rout·2Bout A3281, A3282, A3283, A3284, A3285, A3286 G:A583, A:A1253, A:A582 C:A1251 G:A583, A:A582 4tpb A3063 3Pout·Rout·2Bout A3484, A3485, A3486, A3487 G:A2056, G:A2057, G:A2505 A:A2503 G:A2057, A:A2058 4tpf A3064 3Pout·Rout·2Bout A3485, A3486, A3487, A3488 G:A2056, G:A2057, G:A2505 A:A2503 G:A2057, A:A2058

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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