What's the cation?
dnicker at ermine.ox.ac.uk
Sun Mar 16 08:12:48 EST 1997
In article <332B5F9A.19F9 at biochem.usyd.edu.au>,
Dr Mitchell Guss <M.Guss at biochem.usyd.edu.au> wrote:
>Identifying a cation using "only" the electron density even
>at relatively high resolution is not a sure thing. However,
>you can try the following:
>1. Place each of the different choices at the site and refine,
> positions and an isotropic B-factor for the cation. See
> which falls in a reasonable range for the B-factor
> when compared with the coordinating groups.
Ah yes, interesting. Coordinating groups are already ANIS - but until
the identity of the cation is pretty clear ANIS refinement seems
>2. Look at the coordination geometry and charge distrbibution of
> the coordinating residues. Calcium ions are often 7 coordinate
> with three carboxyl ligands. Sodium ions are more often six
> coordinate as are manganese and magnesium.
My bets are on potassium at this point actually. . . I note you don't
mention it above - is there no clear trend?
>3. Look what cations you used in the protein purification and
> crystallisation steps to see if what you find makes some sense.
I have of course done this . . . the presence of KCl makes K+ a likely
>4. Don't make certain claims and hope you get an understanding
Of course not. "Convincing the referees" was my way of saying -
doing it in a sound, and convincing way.
>5. Try chemical methods of identification such as AAS or Mass Spec
> if you have enough material.
I'm afraid it's gone - and we'll never have more. Must do the best I
can with the (limited) tools I have.
Thanks so much for your time.
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