would have reacted,
this should occur in non-malonate conditions as well.
Best,
Herman
Von: CCP4 bulletin board Im Auftrag von Ana Ebrecht
Gesendet: Mittwoch, 18. August 2021 13:14
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] malonate and histidine interaction
Hello Jon,
Thanks
Hello Ana,
it looks very much like a covalent bond with the His. You may get
some hints from the chemistry of the reaction, which is normally
catalysed. Are there possible side products involving malonate,
alternative substrates present in the buffer etc ?
No problem, it would be interesting to refine it as a tricarboxy methane amide
of the His imidazole. More info on 2-carboxyl malonic acid here:
https://pubchem.ncbi.nlm.nih.gov/compound/Methanetricarboxylic-acid
Cheers, Jon.C.
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Original Message
On
Hello Jon,
Thanks for the comments. Yes, the His is part of the active site, and the
distances are very close, like a covalent bond. That's why I was wondering
if the malonate can be bound to the His.
We tried to model the malonate in the different conformation, but that
didn't work. But I'll
Hello, only other thought was that malonate might be binding in two
conformations, i.e. dual occupancy, and did you use a protease inhibitor
cocktail, since the constituents can react? The density looks a bit like
citrate, but too close to the His. I couldn't read the distances to the His in
Hi Jon,
Thanks for the reply. I don't think this is acetylation, because I only see
this density in the crystals that grew with malonate. In other conditions
doesn't show anything like that. So I thought it'd be the malonate. But
I'll check on that.
Thanks for the suggestion.
Kind regards
Ana
On
Hello, could the His be partially acetylated?
Best wishes Jon.C.
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Original Message
On 16 Aug 2021, 14:52, Ana Ebrecht wrote:
> Dear all,
>
> I am building the structure of a protein that was crystallized in 0.2 M
> sodium malonate pH 5.0, 20% w/v
Dear all,
I am building the structure of a protein that was crystallized in 0.2 M
sodium malonate pH 5.0, 20% w/v polyethylene glycol 3,350.
During the refinement, we found what we think is a malonate molecule in the
active site, but it seems like is bound somehow to the histidine (this His
is
