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

April 26, 2017group hec hem heme prepare Prime protein Residue structure

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

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To prepare the structure, you can use the Protein Preparation Wizard, and select the Treat metals and Fix for Prime options. If you want to prepare it manually, do the following: • Delete the four bonds to Fe. • Assign a -1 formal charge to the two N atoms in the porphyrin ring that have only two single bonds. • Change the PDB residue name of the isolated Fe atom to “FE1”, for example,and change the residue number to “900” or some other number that is unique in the structure. • Add hydrogens.