It is possible that some Fe was turned to Ni isotope, which are very toxic to those small animals. I learnt this story from a beamline scientist at BNL. Not very sure, please validate it with your beamline scientist.
On Mon, Sep 8, 2025 at 9:07 AM Kevin Jin <[email protected]> wrote: > Morning Catherine, > > Here was my explanation to my colleagues before, just a suggestion for > your consideration. > > This could be a common case for the structures of a heme coordinating with > Fe ion. Xtal structure is a thym-dynamic on average. In heme-Fe structures, > it could be a mixture of Fe(II)/Fe(III). In some higher resolution > structures(>1.23Ang), you can even tell the heme-plan bending like a > pyramid with the Fe on the top of the bent heme plane, other than a > symmetric octahedral geometry. A green cloud could always be observed in > the Fe center. It depends on the ratio of Fe(III). > > Based on a normal resolution of protein structures (1.5 - 2.5Ang), indeed > a model, it is difficult to define an exact bond length with its deviation > at atomic level, like classic chemical crystallography. Therefore, what the > heme structure showed is an up-down jumping between Fe(II) and Fe(III) > with the Jahn–Teller effect (or the pseudo Jahn–Teller effect) . > > Because the respective positions of Fe(III) and Fe(II) can not be exactly > defined, there may be a little portion Fe(III) in the heme structure. You > may try to model the structure starting with (98% Fe(II) + 2% Fe(III)) and > refine the occp. Of course, the library needs to be redefined for > heme-Fe(III), but I won't suggest you do it. It is very time consuming. > > Good luck with your project. > > Kevin > > PS. you may put a bran new Iron nail in the protein solution. You may get > a chance to reduce or eliminate the size of the green bubble. > > > > > > > > > > > On Fri, Sep 5, 2025 at 2:40 AM 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 >> >> >> >> >> ------------------------------ >> >> 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/
