Article ID: 486 - Last Modified: December 6, 2011
I was trying to add an oxygen atom to the iron (Heme) of the P450 x-ray structure (2f9q), but Maestro did not allow it due to a "valence violation". What's the right way to do so?
The best way of adding an oxygen atom is to use the Draw tool on the Build toolbar, for which valence violations are ignored. It is helpful to align the heme unit first, so that it's easy to draw in the right direction. You can use the following instructions to add the oxygen atom.
- Run through the pre-processing step of the Protein Preparation Wizard.
- In the Review and Modify tab, select the desired heme group in the het table. This should zoom in to the group you want.
- Choose View → Align to open the Align Atoms panel.
- Select Y for aligning two atoms to an axis, and select "Pick atoms" underneath this option.
- Click the CYS sulfur, then the iron atom. They should be aligned vertically in the Workspace, with the sulfur below the iron.
- Rotate the structure around the y axis so you can see the iron atom. (Use Shift with the middle mouse button to ensure rotation about y only, and drag horizontally.)
- On the Build toolbar, choose O from the Draw button menu (pencil icon).
- Click on the iron atom, then click somewhere above it to place the O atom; click again to exit draw mode.
- On the Edit toolbar, choose Distances from the Adjust button menu.
- Click on the iron atom, then the oxygen atom, and adjust the distance to the appropriate value. (To clear the markers, choose Delete Adjustments from the Adjust button menu.)
- Right-click on the iron-oxygen bond and choose Order → Zero. The bond should be displayed as a dotted line. Modeling software usually treats bonds to metal as formally ionic.
To run calculations on this special oxo complex with the OPLS_2005 force field, you should also change the charge on the Fe to +3, and ensure that the charge on the O atom is zero.
Keywords: metalloprotein, Fe
#288: How do I prepare a cytochrome structure that has an oxygen bound to the heme iron?
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