Hi Try putting water molecule into this green density. It is often reported for redox protein where water molecule is bonded to heme through u oxo bridge.
OR there it is a binuclear catalytic center with additional metal ion such as Fe or Zn linked with heme center through water molecule..kindly see pdb id: 8bgw for more information. Best wishes Firdous On Fri, 5 Sept 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 > > > > > ------------------------------ > > 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/
