MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qba:B3573, See in JSmolClick on the image to toggle views Site type: Oph·2Or Schematic drawing for Oph·2Or List of all 8 Mg2+ binding sites with the site type Oph·2Or 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 2i2t B3006 Oph·2Or G:B1380(OP2) A:B1378(O2'), U:B1379(O5') B3485, B3486, B3487 U:B1379 2i2v B3005 Oph·2Or G:B1380(OP2) A:B1378(O2'), U:B1379(O5') B3482, B3483, B3484 U:B1379 G:B1380 2qba B3573 Oph·2Or G:B1380(OP2) A:B1378(O2'), U:B1379(O5') B4073, B4074, B4075 U:B1379 G:B1380 3oat A3024 Oph·2Or G:A1380(OP2) A:A1378(O3') A3581, A3582, A3583 G:A1380 3r8s A3027 Oph·2Or G:A1380(OP2) A:A1378(O2'), U:A1379(O5') A3659, A3660, A3661 A:A1347 G:A1380 3r8t A3026 Oph·2Or G:A1380(OP2) A:A1378(O2') A3628, A3629, A3630 A:A1347 U:A1379 G:A1380 3u2e D6 Oph·2Or G:D601(OP1) G:D602(O3') B65, D64 3u2e C5 Oph·2Or G:C601(OP1) G:C602(O3') A149, A150, A151

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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