Hello
I have a protein structure I've been working on (seemingly forever),
which includes a bound metal. In fact, I have the same structure with
different metals bound (that's it's job, so it's not a surprise).
My question is this - the metals I'm talking about now are Ni+2, Cd+2,
and either Zn+2 or Mg+2. If I look at the electron density, the
environment around the metal is truly tetrahedral geometry (in all cases
actually). I'm fine with that, it's highly likely based on other
systems that that is correct. However, I just want to make sure the
metal environment is not due to the fact that I did something wrong in
my refinement script - thus making it tetrahedral because it was refined
as tetrahedral. For example, my nickel structure could potentially be
octahedral (with waters filling in for the other 2 ligands, or perhaps a
side chain moving not too far). If my refinement program is doing
something to make it tetrahedral, would it also change the appearance of
the maps?
Is that possible? Should I worry about this, or can I trust the
electron density to tell me what I think it's telling me. I don't use
CCP4 for refinement, I use CNS, but I'm hoping somebody will be able to
guide me here.
Thanks
Dave Roberts
