Center for Structural Genomics of Infectious Diseases

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

Mg2+ site B2932 in 2QOV (3.93Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with spectinomycin. this file contains the 50s subunit of the first 70s ribosome. the entire crystal structure contains two 70s ribosomes.

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Binding environment of Mg2+ B2932

Site type*


Ob+Nb G:B1371(N7)
Water B3148, B3149, B3150, B3151
Pout G:B1358, C:B1357, G:B1371
Bout G:B1358
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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