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/
