MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3007, See in JSmolClick on the image to toggle views Site type: 7Bout Schematic drawing for 7Bout List of all 7 Mg2+ binding sites with the site type 7Bout 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 1 of 1

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2i2v B2905 7Bout B3024, B3025, B3026, B3027, B3028, B3029 U:B2075, A:B2077, G:B2238, G:B2242, U:B2243, A:B2241, U:B2074 2qp1 B2905 7Bout B3522, B3523, B3524, B3525, B3526, B3527 U:B2075, A:B2077, G:B2238, G:B2242, U:B2243, A:B2241, U:B2074 3df2 B3007 7Bout B4008, B4009, B4010, B4011, B4012, B4013 U:B2074, G:B2238, A:B2241, G:B2242, U:B2075, A:B2077, U:B2243 4gau A3063 7Bout A3500, A3501, A3502, A3503, A3504, A3505 G:A2238, A:A2241, G:A2242, U:A2243, U:A2075, U:A2074, A:A2077 4qct A3582 7Bout A4821, A4822, A4823, A4824, A4825, A4826 A:A2077, G:A2238, G:A2242, A:A2241, U:A2074, U:A2243, U:A2075 4tox A3073 7Bout A3528, A3529, A3530, A3531, A3532 C:A2055, U:A2500, U:A2504, G:A2032, G:A2454, C:A2499, A:A2453 4tp7 A3067 7Bout A3495, A3496, A3497, A3498, A3499, A3500 A:A2077, G:A2238, G:A2242, U:A2074, U:A2075, U:A2243, A:A2241

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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