What's the cation?

Darren Nickerson 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 
meaningless ;-)

>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
candidate indeed.

>4.  Don't make certain claims and hope you get an understanding
>    referee.

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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