A little bit of history here about PDB format atom names. At the start
of the PDB, the format was 140 columns wide based on the output of the
Diamond real-space refinement program. This was used for the first 100
entries but we realized that we needed to go to a more compact format.
That yielded what is called the PDB format and the first 100 entires
were converted to PDB format. The atom name field is 4 columns wide.
The first 2 are the chemical element, right-justified and the second 2
are a position indicator. This is why it is important to correctly
position the element name if it is 2 characters long, e.g. FE; namely it
must be in the first 2 columns of the 4.
This was over 50 years ago and thanks to modern medicine all of us that
were involved in this are still alive. I am the only one, however, that
follows this list so I decided to explain this aspect of the PDB format
that we designed back then.
Frances Bernstein
On 2025-09-05 11:31, Colbert, Christopher wrote:
Hi all,
One thing I haven't seen mentioned is to be sure that the F for the Fe
atom is in the correct column of the pdb file. Metals are left set from
C, N, O, S, CA, CB, etc.
Cheers,
Chris
--
Christopher L. Colbert, Ph.D.
_Pronouns: he/him/his _
Professor
Department of Chemistry and Biochemistry
NORTH DAKOTA STATE UNIVERSITY
QBB 346
Dept 2710, P.O. Box 6050
Fargo, ND 58108-6050
phone: 701.231.7946
fax: 701.231.8324
[email protected]
From: CCP4 bulletin board <[email protected]> on behalf of
Oganesyan, Vaheh <[email protected]>
Date: Friday, September 5, 2025 at 8:24 AM
To: [email protected] <[email protected]>
Subject: Re: [ccp4bb] Green density over Fe in heme
One more less probable cause: could the haem be contaminated with
metals heavier than Fe?
I've asked that question to Gemini. Below is the response:
Yes, a haem preparation can be contaminated with metals heavier than
iron, including toxic heavy metals like lead (Pb), mercury (Hg),
cadmium (Cd), and arsenic (As). This is a serious concern because these
metals can interfere with normal heme synthesis and cause a range of
health issues.
Mechanisms of contamination
Several pathways can lead to haem preparation contamination with heavy
metals:
* Environmental pollution and bioaccumulation: Heavy metals from
industrial activity, mining, and waste disposal are persistent in the
environment. These metals bioaccumulate in the food chain and can end
up in the biological tissues from which haem is extracted.
* Competition with iron in the body: The heavy metals that contaminate
biological samples can interfere with the final step of heme
biosynthesis, where iron is normally inserted into the protoporphyrin
ring. Lead, for example, is known to inhibit the enzyme ferrochelatase,
disrupting the process.
* Experimental reagents: Contaminated reagents or laboratory equipment
used during the haem preparation and purification process can introduce
heavy metals. Even analytical methods, such as those that involve acid
digestion, must be carefully controlled to prevent external
contamination during analysis.
Vaheh
From: CCP4 bulletin board <[email protected]> On Behalf Of
Catherine Back
Sent: Friday, September 5, 2025 8:51 AM
To: [email protected]
Subject: Re: [ccp4bb] Green density over Fe in heme
Hi All,
Many thanks for all your suggestions. I've had some direct replies as
well as all the ones from the BB.
* The occupancies were definitely 1.0
* I'll refine anisotropically from now on.
* The Bfactors for two of the Fe-atoms were abnormally high, which
contributed to the density. I've altered them and they've gone back
down to similar levels to the surrounding atoms.
* The collection wavelength was 0.976 Å.
* I was using Phenix Refine, though I tried Refmac first.
There is still a little positive density in the area of the Fe, but the
structure is well refined, so possibly this is just amplifying any tiny
errors?
Cheers,
Catherine
Dr Catherine R. Back (she/her)
Senior Post-doctoral Research Associate
School of Biochemistry
University of Bristol
UK
-------------------------
From: CCP4 bulletin board <[email protected]> on behalf of Jon
Cooper <[email protected]>
Sent: 05 September 2025 13:17
To: [email protected] <[email protected]>
Subject: Re: [ccp4bb] Green density over Fe in heme
Treating the iron (Fe) as fluorine (F) is roughly equivalent having the
iron occupancy at (9/26) or 0.34 approx ;-0
Best wishes, Jon Cooper.
[email protected]
Sent from Proton Mail Android
-------- Original Message --------
On 05/09/2025 13:03, Garib Murshudov
<[email protected]> wrote:
In my experience there could be several reasons for green densities
around metal atoms:
1) occupancy. In this case it is unlikely to be a problem
2) effect of f' if it is strong. It is visible at higher resolution
more than at low resolutions.
3) B vallues, isotropic or anisotropic. B value of the metal should be
very similar to that of the well defined surrounding atoms
4) Multiple positions due to mixtures of charges and coordination
geometries
Regards
Garib
On 5 Sep 2025, at 12:47, Ezra Peisach
<[email protected]> wrote:
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--
I know you mentioned that this was not an anomalous map, but what at
wavelength were your data collected at? Fe has a significant f" at
CuKalpha (1.54..) wavelength.
On 9/5/25 7:37 AM, Jon Cooper wrote:
I would check the iron occupancy in case it is less than 1.0 and that
your Fe has the left-shift in the PDB file otherwise it might be
treated as a fluorine? Good old pdb format.
Best wishes, Jon Cooper.
[email protected]
Sent from Proton Mail Android
-------- Original Message --------
On 05/09/2025 10:40, Catherine Back
<[email protected]> wrote:
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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