MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs8:B2991, See in JSmolClick on the image to toggle views Site type: trans,cis-4Oph Schematic drawing for trans,cis-4Oph List of all 29 Mg2+ binding sites with the site type trans,cis-4Oph 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 4kj5 A3106 trans,cis-4Oph U:A826(OP1), C:A2427(OP1), G:A2428(OP1), G:A2429(OP1) A3693 U:A827 4kx2 A3112 trans,cis-4Oph U:A826(OP1), C:A2427(OP1), G:A2428(OP1), G:A2429(OP1) 4tom A3109 trans,cis-4Oph U:A826(OP1), C:A2427(OP1), G:A2428(OP1), G:A2429(OP1) A3698, A3699 U:A827 4tp5 A3110 trans,cis-4Oph U:A826(OP1), C:A2427(OP1), G:A2428(OP1), G:A2429(OP1) A3703, A3704 U:A827

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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