Hi,
Sulfilimine bond was identified in collagen IV using mass spec and NMR.
https://www.ncbi.nlm.nih.gov/pubmed/19729652
Best,
Abhishek
On 4/18/18, Jonathan Davies <[log in to unmask]> wrote:
> Dear All,
>
>
> Thanks for all of the responses so far..
>
>
> Mark - I don't think it's caused by radiation damage, although this is
> certainly a concern. Using only a small subset of images from the start of
> data collection still gives fairly clear density with no positive or
> negative peaks around the cys and lys.
>
>
> Christian - I haven't used jligand before but that was nice and simple.. I
> think a simple link record may suffice here though.
>
>
> Matthew - Definitely a weird bond, potentially the cys was oxidised first
> and the beam caused more weirdness, I really have no idea! Having said that,
> I don't think this is the cause (see above).
>
>
> David - Thanks for the paper!
>
> Focco - Thanks for the publication!
>
>
> Paul - I tried the "Make link via Acedrg" route but had some issues (my
> model exploded).. I'll send you the details off list later! Cheers!
>
>
> Jonathan
>
>
>
> ________________________________
> From: Jonathan Davies
> Sent: 17 April 2018 18:03
> To: [log in to unmask]
> Subject: Cys Lys bond?
>
>
> Dear CCP4BB,
>
> I've recently solved a structure to 1.15 Angstrom which has extremely clear
> density for what appears to be a lysine covalently bound to a cysteine
> (S-N). The distance between the cys-S and lys-N is 1.8 A. I thought
> initially that there may be a methyl group between the two (based on this
> paper http://doi.org/10.1002/pro.2958) but there definitely isn't enough
> space.
>
> Some more info:
> The protein was purified from recombinant E. coli expression, standard
> buffers (Tris, NaCl).
> Crystallisation condition contains sodium acetate and PEG.
> The residues in question are not part of an active-site.
>
> I have two questions:
>
> Has anyone seen a cys that is involved in a sulfanamide bond with a lys?
>
> How would one go about modeling this bond in a way that doesn't upset coot,
> refmac or PDB validation?
>
> Thanks in advance!
> Jonathan
>
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