`
Center for Structural Genomics of Infectious Diseases

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

Mg2+ site 08002 in 1VQ8 (2.2Å) -- RIBOSOME : The structure of ccda-phe-cap-bio and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui

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+ 08002

Site type*

cis-2Oph·Ob

Inner
sphere
Oph A:02483(OP1), C:02534(OP1)
Or
Ob+Nb G:0627(O6)
Water 08282, 08283, 09881
Other
Outer
sphere
Pout U:02535
Rout U:0625, G:02482
Bout C:02071
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>