Hi All,
I am looking for some input regarding an unusual feature in one of our
structures. Maybe someone has come across something similar or has some
thoughts about it...
We have a 1.9 A crystal structure with well-defined density in the
N-terminal region. The side chain of His3 is oriented towards the
N-terminal amino group of Met1 and there is a nice difference density
'ball' right in between the His and the amino group suggesting that
there is an additional atom that is covalently linked. There are two
molecules in the asu and both show the same feature (no ncs refinement).
My problem is that I cannot come up with a reaction that would result in
such a linkage and there is not much to be found in the literature.
If I place a hypothetical atom in the difference density peak, I can
measure distances and angles. Here are some numbers: Distance from atom
X to the N-terminal nitrogen 1.72 (1.64 in chain B). Distance from atom
X to His NE2 1.58 (1.45 in chain B; the temperature factors of the His
side chain are slightly more consistent with this ring orientation
compared to the 180 degree flip that would bring CE1 towards atom X).
Atom X is coplanar with the His ring. The angle between NE2 - X - N1 is
95 deg (106 in chain B). The angle between X - N1 - Calpha1 is 111
degrees in both chains. As the N-terminal methionine is still present,
it is possible that the methionine formyl-group was present before the
hypothetical reaction. However, there is only one 'atom' in the
difference density.
Any comments or suggestions would be highly welcome.
Gerwald
