Zinc finger protein

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2

Dear Developers!

I’m trying to dock a C2H2 type zing finger containing peptide to a protein.
The N-terminal of the peptide is the zinc finger (contains B-sheet and L-helix) and the C-terminal of the peptide is disordered.
We already know from mutational analysis and NMR titration experiment, that both of the disordered segment and the zinc-finger containing microdomain are essential for the strong binding to the partner protein.
We have already get nice results according to expectation with HADDOCK docking, except the we cannot maintain the original structure of the zinc-finger (mainly the orientation of histidines), despite of the unambiguous restraint file which contain the restraints of the zinc finger.

I think it would help if we generate parameter file for the C2H2 type zing finger as it exists for HEM group?

Am I correct? Or there is other possible explanation?

Thank you for your kind reply!

Klara Kirsch

Which kind of restraints did you define to maintain the geometry of the zinc finger?

To get proper results make sure to define distance restraints between:

  • all atoms coordinating the zinc (basically define the tetrahedron connecting them
  • each coordinating atom and the zinc atom.

Note that the distance restraints must have the zinc atom name between double quotes because of the + in the name.
The correct nomenclature for HADDOCK for the zinc is:

  • residue name: ZN2
  • atom name: ZN+2 (shifted one character to the left in the PDB file

Also you might use CYF for the cysteines coordinating your zinc (those will not carry the hydrogen on the sulfur)

1 Like

Thanks for your reply!

I have created an unambigous distance restraint file which contain the distances between ZN+2 and the four coordinating atoms. It is a good idea to strengthen the restrain file with distance restraints between the all atom of the tetrahedron.
I will try it, and let you know the progress.

I have already use CYF which helps a lot - the zinc always coordinated by the two cystein - but I cannot do this with histidines. Before that, when I used CYS the zinc may move farther to an other amino acid which have a negatively charged site chain.

Thank you for your advices!


For the Histidines you should specify either HISE or HISD in the run.cns (or on the server if you use the server). Check with of the two nitrogens faces the zine.

1 Like

Thank you, these ideas helped a lot for maintaining the correct ZN geometry. (approximately 80% of the models have the correct geometry)

Now I have an other problem:

I have the final model which I would like to refine in the “refinement” interface, but it seems to be not dealing with metal ion.

Error message:
First pdb file contains an unknown amino acid or nucleic acid base ZN2
Make sure to use three letter code for bases and amino acid

Do you have any suggestion how to refine my model?

Must be defined as HETATM

Prof. A.M.J.J. Bonvin | Faculty of Science
Utrecht University | bonvinlab.orghttp://bonvinlab.org
a.m.j.j.bonvin@uu.nlmailto:a.m.j.j.bonvin@uu.nl | T: +31 30 2533859

1 Like

Thank you, it is worked!

Unfortunately in this refinement stage, the Zn finger started to disintegrate. Is there an option to add distance restraints in this stage?

Hi Klara

Did you define distance restraints between the zinc and its coordinating atoms? And between the coordinating atoms?
Input them as unambiguous.
Also make sure to put the zinc atom name between double quote in the restraints:


assign (resid XX and name “ZN+2 and segid A) (resid YY and name ZZ and segid A) …