HADDOCK Zinc finger protein

1

Hi,
I am trying to coordinate zinc to my C2H2 zinc-finger. I am using the following distance restraint file (input.tbl), but the cluster HADDOCK generating shows the zinc is far far away from the C-C-H-H. There is something wrong happening and I am unable to figure it out.

assign (segid A and resid 38 and name SG)
(segid A and resid 1 and name “ZN+2”) 2.7 0.3 0.3

assign (segid A and resid 42 and name SG)
(segid A and resid 1 and name “ZN+2”) 2.7 0.3 0.3

assign (segid A and resid 53 and name NE2)
(segid A and resid 1 and name “ZN+2”) 2.7 0.3 0.3

assign (segid A and resid 61 and name NE2)
(segid A and resid 1 and name “ZN+2”) 2.7 0.3 0.3

The zinc ion I am using for docking is as follows.
HETATM 3833 ZN+2 ZN2 A 1 21.391 -8.794 33.944 1.00 24.37 ZN

I would appreciate your help in fixing this issue.

Best regards,
Sanjay

2

Is the zinc atom in its binding site at the start?

I see that it has the same chainID as the protein.
If it is not in its binding site then giving the same chainID won’t allow for the zinc to move during the initial rigid body docking stage

1 Like
3

Thanks for your reply. Very much appreciated.
No, I prepared a separate zinc ion. I have now changed the chainID from A to C and trying again to see if that works.

Thanks!

4

I tried again to dock zinc by changing the ID. But, I do not see any improvement. The zinc is >10 nm away from the C-C-H-H binding site. I am checking if I am doing anything wrong. I have modified my systems and trying again. The details are as follows:

Step-1: Inputing the PDB structure, Chain A

(NO ERROR)

Step-2: Inputing the zinc structure obtained from the NMR structure (PDB: 1SP1). Chain D

(NO ERROR) Kind of molecule selected : LIGAND

REMARK BIOVIA PDB file
REMARK Created: 2023-06-14T09:23:10Z
***CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ***
HETATM 1 ZN+2 ZN2 D 30 -0.998 4.266 2.578 1.00 0.81 ZN2+
***TER 2 ZN2 D 30 ***
END

Step-3: Active/Passive residue section (Default, I didn’t define the active residues for both Molecule 1, protein, and Molecule 2, Zinc).

Step-4: You can supply a HADDOCK restraints TBL file with restraints that will always be enforced (unambiguous restraints). FILE NAME: restraints.tbl as follows

assign (segid A and resid 38 and name SG)
(segid D and resid 1 and name “ZN+2”) 3.0 0.5 0.5

assign (segid A and resid 42 and name SG)
(segid D and resid 1 and name “ZN+2”) 3.0 0.5 0.5

assign (segid A and resid 53 and name NE2)
(segid D and resid 1 and name “ZN+2”) 3.0 0.5 0.5

assign (segid A and resid 61 and name NE2)
(segid D and resid 1 and name “ZN+2”) 3.0 0.5 0.5

All other options were default.

Using these steps, the cluster I am generating has no zinc on the active site (>10 nm far).

I am trying to run the docking again by modifying step-3. This time, I am defining the active residues for molecule 1 (38, 42, 53, and 61) and molecule 2 (30).

I would appreciate it if you let me know if I am doing anything wrong and why the zinc is not parsing to the active site at all.

-Sj

5

Your zinc atom has residue number 30 while your restraints use resid 1 …

1 Like
6

Thanks. I have modified it to 30.
Do you recommend using active residues in Step II or leaving it blank as I am parsing the restraints list in step-4?

Please suggest if anything else I should consider for this docking. My protein PDB structure has C-C-H-H that are not oriented perfectly. For instance, the distance between cysteines and one of the histidine is ~ 0.6 - 0.8 nm. I assume HADDOCK will take care of it during docking to energy minimize and refine the structure after zinc is coordinated with the defined distances in the restraint file. Please comment if the distance between C-H in the PDB structure could be an issue and that’s the reason why zinc is not accessing the active site.

~Sj

7

Hi,
I tried modifying the residue number 30 and re-ran it. But the complex is not formed.
I am checking what is wrong going on. Do you have any comments or suggestions to fix this?

~Sj