Knowledge Base

Article ID: 1363 - Last Modified: April 19, 2011

My protein structure contains a heme group (residue name HEM or HEC). How should I prepare the structure for Prime refinement?

To prepare the structure, you can use the Protein Preparation Wizard, and select the Create zero-order bonds to metals option. (In earlier releases, select the Treat metals and Fix for Prime options.) If you want to prepare it manually, do the following:

  1. Change the four bonds to Fe to zero-order bonds.
  2. Assign a -1 formal charge to the two N atoms in the porphyrin ring that have only two single bonds.
  3. Add hydrogens.

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