[ccp4bb]: Ions in the internal protein cavities

[Petr Leiman <leiman@purdue.edu>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

Hello,

I have a fairly spherical piece of density on a crystallographic 3-fold
axis to which 3 symmetry related Asps are pointed. The piece is pretty
big. Its volume is slightly larger than that corresponding to S in the
nearby Mets if contoured at the same contour level. The height of the
density peak in that piece is aging slightly (about 1 sigma) greater
than any protein density around it. Apart from 3 Asps, the piece is
surrounded by hydrophobic residues.  The distance from the center of the
piece to the nearby Asp is about 4.0 A. The distance between the O's of
the corresponding Asps is 6.9 A.  I have several data sets and this
piece of density present in all of them. The piece is there when I
calculate the maps using the heavy atom phases as well when I use the
model phases. Because the piece is surrounded by the hydrophobics I
think that the material of the piece is there from the moment when the
protein get folded and this material did not come from the purification
or crystallization solutions.

The distances are to long for any metal I can think of. And the density
is not high enough. I had a suggestion that the the piece is just
water(s) artificially enhanced by the crystallographic 3-fold but I do
not buy it. Too long distances for 1 water molecule. If I put 3 they
_have_ to be covalently bound then, because they would be something like
1.9 A apart.

I have only 1 candidate now - a phosphate. Has anyone ever seen the
phosphate buried inside the protein molecule and coordinated by 3 Asps?
Any other suggestions? If anyone knows a positively charged molecule
with a triangular or tetrahedral geometry that is present in the cell it
would be of great help.

Petr

P.S. Sorry for such a long letter.
P.S. # 2: The resolution of my maps is 3 A.