Member Site Forums Rosetta 3 Rosetta 3 – General Modeling phosphate ion binding site in protein. Reply To: Modeling phosphate ion binding site in protein.


    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