`
Center for Structural Genomics of Infectious Diseases

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

Mg2+ site A1604 in 1VS7 (3.46Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with the antibiotic kasugamyin at 3.5a resolution. this file contains the 30s subunit of one 70s ribosome. the entire crystal structure contains two 70s ribosomes and is

Viewer options: (Jmol | JSmol) | Close this window to return to the list of Mg2+ binding sites being investigated
JSmol: HTML5 canvas version of the Jmol molecule viewer http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
Binding environment of Mg2+ A1604

Site type*

Oph

Inner
sphere
Oph C:A980(OP1)
Or
Ob+Nb
Water A1896, A1897, A1898, A1899, A1900
Other
Outer
sphere
Pout
Rout
Bout G:A1221, G:A1220, A:A1219
Each outer-sphere moiety is listed only once and only if it does not form inner-sphere interaction
Mouse click action:
Left-Click to rotate
Shift-Left-Click up & down to zoom
Right-Click for Jmol's context menu
Access console here
Additional controls:
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/)
For any help please contact <dust@iwonka.med.virginia.edu>