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 <[email protected]> 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: [email protected] > 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 >
