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How do I prepare a cytochrome structure that has an oxygen bound to the heme iron?

The OPLS_2005 force field includes parameters for this iron-oxo species, which are based on QM calculations. To get the correct assignment of these OPLS_2005 parameters, the iron should be represented as Fe3+, and it should be connected via zero-order bonds to 6 neighboring atoms: the four heme nitrogens (two with no formal charge, two with -1 formal charges), the Cysteine sulfur (-1 formal charge), and the oxygen (no formal charge).

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.

If your heme group has non-standard residue or atom names, its bond orders and formal charges might not get set automatically when the PDB structure is imported, which might require manual adjustment.

Keywords: P450, Fe, oxo

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