The Protein Preparation Wizard should do most of this metal center treatment for you, but there are a few extra steps you need to take. First, when you preprocess the structure, if you've chosen to delete waters, don't make the cutoff smaller than 2 Å, or the water deletion code might remove the iron-bound oxygen, too. Second, the preprocessing step that adds hydrogens to the structure might add hydrogens to the iron-bound oxygen. If this occurs, you can delete these extra hydrogens manually, using the "Delete" toolbar button (the large "X"). Deleting atoms invalidates the tables in the Protein Preparation Wizard panel, so you'll have to click "Analyze Workspace" to refresh the tables. Finally, the iron might be assigned a +2 formal charge by default. If so, you'll have to change the formal charge; this can be done manually, with the "Increment formal charge" Build toolbar button; or after you click "Generate Het States" you'll be able to choose the +2 or +3 iron state.
wizard bound by metal download
The flexibility of YtgA Asp299 has similarity to Asp280 of Streptococcus pneumoniae PsaA (31). In PsaA, this equivalent carboxylate residue influences metal ion selection and reversibility of the metal-PsaA complex, resulting in impacts upon metal ion transport (23, 31, 36, 43). Consistent with these insights, YtgA was also shown to be highly promiscuous for interaction with a range of metal ions, despite their preference for distinct coordination geometries. Nevertheless, our analyses also revealed differences in the stabilities of the resultant YtgA-metal complexes. The metal ligands Co(II), Zn(II), and Cd(II) all form highly stable complexes with YtgA, as shown by the large Tm shifts and the inability of EDTA to extract the bound metal ion. Notably, we also observed that YtgA bound Fe(III) irreversibly, rendering Fe(III) an unlikely physiological ligand. This is consistent with the previous finding that YtgA bound Fe(III) could not be replaced by 59Fe(III) (19). Interestingly, the metal ion did not significantly shift the protein Tm at concentrations similar to those of the other metal ligands. We speculate that this may be due to a slow on rate; alternatively, it may reflect a solubility issue associated with the FeCl3 salt in the DSF assay. Irrespective of the precise technical basis for this issue, our data indicate that YtgA stabilization with Fe(III), Co(II), Zn(II), and Cd(II) is highly thermodynamically favorable. 2ff7e9595c
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