I am an MRes student trying to do some bioinformatics if anyone could help me that would be really appreciated. I have looked to see if my question has been answered and I cannot see the particulars that I am looking for.
I used Phyre2 to model the predicted 3D structure for my protein of interest. Homologues of this protein use Mg2+ which is coordinated to 3 Aspartate residues in the active site. I used both 3DLigandSite and COFACTOR from I-TASSER SUITE to introduce the Mg2+ in my model. However, when looked at it on the site it clearly specified it was the divalent cation but when I opened it on PyMol the formal charge was listed as zero when looking at charge wizard. It also was not co-ordinating as expected with the residues. I tried to manually alter it (PyMOL>alter sele, formal_charge=2) which did not work, I am not sure really why but it never changed.
Another thing was when I was prepping it for docking with autodock vina it noted that the Mg2+ was non-bonded
I also tried to manually edit the PDB file with textedit - writing CONECT bonds to the expected residues based on the homologue and also by specifying the charge (I typed this: HETNAM MG MAGNESIUM ION
FORMUL 2 MG MG 2+) which was present on the PDB file of the homologue but it did nothing! I am really not sure how to fix this.
If anyone has any insight that would be amazing!
Sorry if this has been answered already!
Thank you very much,
My cofactor (mg) is "non bonded" and uncharged
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