Reply To: Modeling phosphate ion binding site in protein.

[Anonymous]

Alright.. So I have completed collecting information about the catalytic mechanism and active site residues. So, I will be starting with the enzyme designing part. I am considering the phosphate binding region which I got after docking with autodock as the residues that I have found goes well with the phosphate binding motif..

I am working on low molecular weight phosphotyrosine phosphatase . Here two amino acids are important :-
cys 12- nucleophile attacking the phosphorus atom
asp129 – activates a water molecule which hydrolyses the phosphorylated cysteine.

I think I am having constraints for cys and asp129 but how to put a constraint for that water molecule which is very important for catalysis..

I have attached a file depicting mechanism .

Looking for forward for further suggestions from your side..

Thanks a lot