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Center for Structural Genomics of Infectious Diseases

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

Mg2+ site A8004 in 1NJI (3Å) -- RIBOSOME : Structure of chloramphenicol bound to the 50s ribosomal subunit

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Binding environment of Mg2+ A8004

Site type*

Oph·Ob

Inner
sphere
Oph A:A459(OP1)
Or
Ob+Nb G:A456(O6)
Water A3773, A7754, A9048, A9772
Other
Outer
sphere
Pout A:A455, A:A460, A:A477
Rout
Bout A:A455
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):
Nucleic Acid Cartoon:
Spin:
Antialiasing:
On Off
On Off
On Off
On Off
On Off
On Off
On Off
On Off

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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