Hello Catherine
There are different oxidation states possible (resting state, compounds
I-III) and you will most likely have a mix of those. See for example
here 10.3390/ijms21218057 <https://doi.org/10.3390/ijms21218057>
and structures of Myeloperoxidase in the PDB or in the aggregated PDB
pdbe-kb (knowledge base).
As you isolate the protein, you anyhow have an oxidated state being an
oxygen on the Fe, perpendicular to the HEM ring, eg. compound I:
Por−Fe^4+ =O
Julie
On 06/09/25 01:02, CCP4BB automatic digest system wrote:
There are 21 messages totaling 30393 lines in this issue.
Topics of the day:
1. Green density over Fe in heme (19)
2. Fwd: [ccp4bb] Green density over Fe in heme (2)
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Date: Fri, 5 Sep 2025 09:39:45 +0000
From: Catherine Back <[email protected]>
Subject: Green density over Fe in heme
Good morning,
I am currently solving a structure containing four heme b molecules (res 1.7
Å), each coordinated by two histidines. The refinement is looking good, but the
output from refinement has marked the Fe ions of each heme with positive
density (green) in the FoFc difference map - see image. Any ideas why? I used
the Monomer Library in Coot to add hemes ('HEM') in. Is it something to do with
the oxidation state of the Fe? And if so, is there anything I can do about it?
Best wishes,
Catherine
Dr Catherine R. Back (she/her)
Senior Post-doctoral Research Associate
School of Biochemistry
University of Bristol
UK
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------------------------------
Date: Fri, 5 Sep 2025 12:07:56 +0200
From: Wim Burmeister <[email protected]>
Subject: Re: Green density over Fe in heme
Hello,
ou should try refinement of anisotropic temperature factors.
Wim
Le 05/09/2025 à 11:39, Catherine Back a écrit :
Good morning,
I am currently solving a structure containing four heme b molecules
(res 1.7 Å), each coordinated by two histidines. The refinement is
looking good, but the output from refinement has marked the Fe ions of
each heme with positive density (green) in the FoFc difference map -
see image. Any ideas why? I used the Monomer Library in Coot to add
hemes ('HEM') in. Is it something to do with the oxidation state of
the Fe? And if so, is there anything I can do about it?
Best wishes,
Catherine
Dr Catherine R. Back (she/her)
Senior Post-doctoral Research Associate
School of Biochemistry
University of Bristol
UK
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