If you're 100% sure that this is only one atom then amination comes to mind. I have no clue what conditions would favor such reactivity but it is possible that the formyl group on the Met was aminated with the cyclic N of the histidine, resulting in either a substituted bis-amine (requires reduction, may not be stable) or in a cyclic amidine (the latter requires four atoms - N1-C=N-Ca - to be in the same plane). This amidine should have some pretty interesting properties (probably more like a Schiff base than an amidine).
Could you tell us a bit more about the system you're working with? Artem P.S. The bond lengths you describe are not typical for C-N, however at 1.9A resolution it is not very likely that the values you measured actually correspond to the bond lengths (hopefully, because otherwise you have -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of gerwald jogl Sent: Thursday, October 09, 2008 4:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Potential N-terminal cyclization 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
