Hello Jisha,
Did you check for crystal structures of similar proteins with Mg ions?
You could then do homology model.
From my experience Mg ions (especially two of them that are close each
other) are not tightly bound to protein and require anionic ligand to
compensate positive charge. I worked a little bit with nucleotides,
whose triphospate group was bound to protein via two Mg cations. Also
all kinases that I studied contained Mg ions only if ATP was bound.
But you can always use your intuition and hope that MD will equilibriate
to something meaningful.
Juraj
On 17. 10. 20 12:22, Jisha B wrote:
> Could someone please help with this. Has anyone worked on anything similar.
> Any guidance would be helpful
>
> On Fri, 16 Oct 2020 at 03:40, Jisha B <jisha.b.k0511.gmail.com> wrote:
>
>> Dear all,
>> I have a protein which has a two metal activation where in it requires two
>> catalytically active magnesium ions. Since there are no crystal structures
>> with the magnesium ions, I would have to place them based on the
>> information from literature where in they have said which amino acids
>> interact with the metal ions. What would be the right strategy to include
>> the metal ions into the system before proceeding to the simulation? Also is
>> there any method to ensure that the ion stays within the system and not
>> move out during the course of the simulation. Any suggestions would be
>> helpful
>>
>> Thank you.
>> Jisha
>>
>>
>>
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Received on Mon Oct 19 2020 - 00:30:02 PDT
