Hi Lumbini,

There are couple of queries I have before commenting on this issue.

1) how many Cysteine residues are there in your protein

2) have you calculated their solvent accessible surface area ?

3) What is the final concentration of Sodium dithionite ?

Cysteine is highly prone to get thiol covalently modified if it is quite
accessible to the solvent in its free form. As you know, sodium dithionite
is having almost same chemical structure like BME. And you will find N
numbers of papers about how BME covalently modifies the accessible cysteine
in the protein. It seems to me that it modified by sodium dithionite by air
oxidation.

Please check the facts and try to fit with manually built derivative of the
sodium dithionite with this cysteine residue.

Good luck

P.P

On Tue, 9 Jul 2019, 04:32 Lumbini Yadav, <lumbin...@gmail.com> wrote:

> Dear all,
>
>
>
> We have found a huge Fo-Fc density close to cysteine residue (see attached
> image) in the structure with resolution of 1.2A. In the crystallization
> condition, we have PEG 3350, Potassium phosphate monobasic, glycerol and
> protein was in Tris and NaCl. Before freezing the crystals were soaked in
> mother liquor containing sodium dithionite.
>
>
>
> I have tried different modified cysteine (CSX, CSO, OCS, CME, CSS, SNC, CSD,
> CXM, SCH, CSU) from the library and also SO3, SO2 and peroxide. But in
> all the screenings we do see some part of Fo-Fc density unaddressed at 3
> sigma.
>
>
>
> Does anyone have an idea about what this density could be? Covalent
> modification?
>
>
>
> Thanks.
>
>
>
> Kind regards,
>
> Lumbini
>
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