Dear Boaz,
You're quite right, in my haste to reply last night I only related part of the
discussion relating to peroxide. In a bid to identify the diatomic ligand,
which appears on oxygen exposure, I quoted the peroxide bond length as being
too long, then went on to say it is much more like dioxygen in
oxyhaemoglobin/myoglobin and referenced structures from yourself and Simon
Phillips.
Best wishes,
Steve
Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717
________________________________
From: Boaz Shaanan <bshaa...@bgu.ac.il>
Sent: 28 November 2022 23:33
To: Carr, Stephen (MRC,RAL,RCAH) <stephen.c...@rc-harwell.ac.uk>
Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries
Hi stephen,
I obviously don't have the full context of your case, but I am not sure why you
invoked peroxide as a reference for the O-O bond length in the context of
oxygen-metal complex. In my good old oxy haemoglobin structure (1HHO) the O-O
bond length in Fe-O-O is 1.22 A. It's also worth checking MbO2 with Fe and
various metals which are most likely higher resolution structures.
I could of course be completely wrong line of thought.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of
stephen.c...@rc-harwell.ac.uk <00008f3604def7f0-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, November 28, 2022 10:03 PM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries
Dear BB,
Thank you for all the helpful responses. To give a bit more context to my
question, I have a 1.2 A structure with a diatomic ligand bound to a metal at
the active site, which we believe is an oxygen species. The bond length is
1.22 A and I made a comment in the discussion that this was unlikely to be a
peroxide species as the bond length was shorter than the 1.48 A typically
observed. The referee has questioned the validity of the 1.48 A, which led to
my original question.
Best wishes,
Steve
PS I have tried Raman spectroscopy with no definitive result.
Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717
________________________________
From: Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
Sent: 28 November 2022 19:20
To: Carr, Stephen (MRC,RAL,RCAH) <stephen.c...@rc-harwell.ac.uk>
Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries
On 28/11/2022 17:29,
stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk> wrote:
Dear CCPBB,
I have a question regarding the origin of the monomer libraries in CCP4. I ask
because I have quoted the bond length listed in the monomer library describing
peroxide in a manuscript and a referee has asked for a reference since they
seem to disagree with the quoted value of ~1.48 A. My understanding is that
parameters describing bond length, angles etc are derived from structures in
the CSD is this the case? Is there an appropriate reference out there
somewhere?
When you say "peroxide," I presume that you mean H2O2. The entry for
that in the monomer library is PEO. The bond length between the oxygen
atoms in PEO is 1.461A. Perhaps your referee is thinking of the
peroxide ion, which indeed would have a different bond length (1.15).
Both PEO and PER would, to my mind, be susceptible to radiation damage,
so one wonders what is actually in the crystal. To address question, one
would make an "Fearly-Flate" map.
One can (in principle) dig into the Acedrg table of bond lengths to examine how
many
examples, of this sort of chemistry exist (I did it a few years ago), but I
don't recall
now how to do it for this example.
Regards,
Paul.
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