Ok I'm a bit ashamed to even ask this, but I can't seem to get my head around this binding scheme
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058422/figure/F3/
How is it possible that a chloride anion form hydrophobic bonds with valine and two Serine residues. From all I know both serines and chloride anions (especially near an aromatic ring) are both polar.
I have the same problem with binding of the oxygen atom and histidine and valine
Thanks,
Tomek
Hi Tomek, not a stupid question.
What you need to wrap your head around is that the environment that residues face when bound tightly to a protein (or an enzyme) is not the same as they face in aqueous solution. For the most part, protein interiors are not hydrated and any aqueous properties of reactants might not apply.
Tomek,
The chlorine atom is not ionized in that structure (i.e. not a chloride anion) and so is far less hydrophilic and can therefore be accommodated in hydrophobic pockets. In general don't take that interaction map too 'literally', it's not the whole story, shape complimentarily is very important. Also, consider the proteins amide backbone interactions with the molecule that may also be taking place not only with the amino acid side chains.
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