Hi all, I am trying to coordinate zinc to the NMR structure PDB ID: 1sp1 (a C2H2 zinc-finger) using HADDOCK. To make it clear, the PDB structure is zinc coordinated, and I am using it as a system to learn and troubleshoot some issues I am having in HADDOCK.
Briefly, (1) zinc is removed from the NMR structure (1sp1) to generate the protein input file (Chain A), (2) protein is removed from 1sp1 to generate the zinc ion input file (Chain number was changed to D (Chain D)).
Inputting both files to HADDOCK has no error.
Everything on the HADDOCK server was set to default except inputting the unambiguous restrain file (file name: test.tbl; please see the file contents below).
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assign (segid A and resid 5 and name SG) (segid D and resid 30 and name “ZN+2”) 3.0 0.5 0.5
assign (segid A and resid 8 and name SG) (segid D and resid 30 and name “ZN+2”) 3.0 0.5 0.5
assign (segid A and resid 21 and name NE2) (segid D and resid 30 and name “ZN+2”) 3.0 0.5 0.5
assign (segid A and resid 25 and name NE2) (segid D and resid 30 and name “ZN+2”) 3.0 0.5 0.5
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HADDOCK generated clusters within ~12 hours, but the zinc ion is >10 nm away from the protein coordination site. Please see the link below with all the input data I used to generate a complex.
I would appreciate it if someone guides me in troubleshooting what is wrong I am doing here or if I am missing something that I need to input.
https://drive.google.com/drive/folders/1684hG6_MbJpqGppBxFi68WAq2EkXg_45?usp=sharing
HADDOCK results are accessible (see the link below)for your reference
https://wenmr.science.uu.nl/haddock2.4/result/2701304514/250966-1sp1
Thanks!
HADDOCK is not for docking any metal ions to proteins. Neither any other docking tools supports that.
You can model the Zinc ion coordination complex to a protein (say using modeller) and run MD simulation for a minimum of 100ns to validate and restrain/refine the model. Also, Sometimes you might have to model the surrounding residues/loops so that it can form a proper coordination complex.
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