C4 zinc finger protein

Hi, I have been trying to make a haddock model of a zinc finger protein and I need to restrain the cysteine residues to the zinc atom. I have created a tbl file with distance restraints but one of the 4 cysteines does not appear to dock correctly and I’m unsure how to fix this. Also, in my models the cysteine-zinc models appear to be covalently linked (ie in pymol the zinc ion is attached to the cysteine), am I doing something wrong?
Sarah

Hi Sarah

Remember that the HADDOCK forum is searchable. You will need to restrain your zinc coordination. See

And the way to define distance restraint to the Zinc is explained in the following thread:

Hi Alexandre, thanks for your reply. I’m aware that the forum is searchable and have already used both of these references when creating my restraints file. I mapped the distances using NMR data as follows:

assign (resid 295 and segid A and name SG) (resid 298 and segid A and name SG) 3.8 3.8 3.8
assign (resid 298 and segid A and name SG) (resid 316 and segid A and name SG) 3.8 3.8 3.8
assign (resid 295 and segid A and name SG) (resid 316 and segid A and name SG) 3.7 3.7 3.7
assign (resid 295 and segid A and name SG) (resid 319 and segid A and name SG) 3.8 3.8 3.8
assign (resid 316 and segid A and name SG) (resid 319 and segid A and name SG) 3.7 3.7 3.7
assign (resid 298 and segid A and name SG) (resid 319 and segid A and name SG) 3.5 3.5 3.5
assign (resid 295 and segid A and name SG) (resid 1 and segid Z and name “ZN+2”) 2.7 2.7 2.7
assign (resid 298 and segid A and name SG) (resid 1 and segid Z and name “ZN+2”) 2.7 2.7 2.7
assign (resid 316 and segid A and name SG) (resid 1 and segid Z and name “ZN+2”) 2.7 2.7 2.7
assign (resid 319 and segid A and name SG) (resid 1 and segid Z and name “ZN+2”) 2.7 2.7 2.7

As I said, 3 of the 4 cysteines do maintain their position in the tetrahedron, but one doesn’t which is why I’m not sure what I’ve done wrong. Would I need to create additional restraints?

Thanks
Sarah

Hi Sarah

Your distance restraints are very loose! Probably you misunderstood the meaning of the three numbers:

  • first is target distance
  • second is the lower limit correction
  • third is the upper limit correction

The distance range is this:

Lower limit: first-second
Upper limit: first+third

So in your restraints, e.g. the first one, the distance range is between 0 and 7.6A