I have to agree with Pat here – it highly unlikely that a heme would have another contaminating metal in the porphyrin ring (speaking as someone who has used HF to remove Fe from a cytochrome, albeit luckily only once!). The iron in a heme cofactor is typically not going to have lower occupancy than one because the metal is tightly bound in the heme.
One other thing to consider is what type of restraints (or constraints) are being used on the porphryin ring during refinement... if the heme is ruffling or doming or undergoing any distortions from planarity, that could impact the position of the iron atom. So another thing to consider. Best, Sarah PS Hope that lead sandwich was yummy, Pat! Sarah EJ Bowman PhD Associate Professor | Department of Biochemistry | Jacobs School of Medicine and Biomedical Sciences | University at Buffalo Director | National Crystallization Center | UB Hauptman Woodward Institute 700 Ellicott Street | Buffalo, NY 14203 From: CCP4 bulletin board <[email protected]> on behalf of Patrick Loll <[email protected]> Reply-To: Patrick Loll <[email protected]> Date: Friday, September 5, 2025 at 11:50 AM To: "[email protected]" <[email protected]> Subject: [ccp4bb] Fwd: [ccp4bb] Green density over Fe in heme You don't often get email from [email protected]. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Far be it from me to quibble with an AI, but…while it is certainly possible that a heme prep is contaminated with other metals, things like lead aren’t going to combine with a porphyrin to form a heme-like structure. Metals much heavier than iron are too large to sit in the plane of the porphyin. So while it is indeed possible to make porphyrin complexes with heavier metals, those metals tend to sit above the plane of the porphyrin (forming an open-face sandwich); or sometimes a second porphyrin is recruited to form a proper sandwich. The map doesn’t look consistent with either of these scenarios. Pat ps It’s lunchtime here, and now I find myself contemplating a lead sandwich… ————————————----------------------------------------------- Patrick J. Loll, Ph. D. (he, him, his) Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102 USA (215) 762-7706 [email protected] [email protected] On Sep 5, 2025, at 11:23 AM, Oganesyan, Vaheh <[email protected]> wrote: 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 Patrick Loll [email protected] ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
