Center for Structural Genomics of Infectious Diseases

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

Mg2+ site 08027 in 1KQS (3.1Å) -- RIBOSOME : The haloarcula marismortui 50s complexed with a pretranslocational intermediate in protein synthesis

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Binding environment of Mg2+ 08027

Site type*


Oph C:0240(OP1)
Ob+Nb G:0269(O6)
Water 03380, 03520, 03661, L8654
Pout G:0267, U:0268
Each outer-sphere moiety is listed only once and only if it does not form inner-sphere interaction
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Inner-sphere Residue Name:
Outer-sphere Moiety Name:
Metal Distances:
Outer-sphere Distances:
B factor(Occupancy):
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Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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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