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Center for Structural Genomics of Infectious Diseases

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

Mg2+ site B3006 in 2QBK (4Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with gentamicin and ribosome recycling factor (rrf). this file contains the 50s subunit of the second 70s ribosome, with gentamicin and rrf bound. the entire crystal structure

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Binding environment of Mg2+ B3006

Site type*

Oph·Or

Inner
sphere
Oph U:B1379(OP2)
Or A:B1378(O2')
Ob+Nb
Water B3477, B3478, B3479
Other
Outer
sphere
Pout G:B1380
Rout
Bout G:B1380
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].


Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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