[phenixbb] Mn - O distances

Nigel Moriarty nwmoriarty at lbl.gov
Wed Nov 23 08:32:31 PST 2011


I did a survey of the literature some time ago and used Harding, Acta
Cryst. D62 (2006), 678-682 for the data used in
phenix.metal_coordination. I recently added the data from Zheng et al.
Journal of Inorganic Biochemistry 102 (2008) 1765-1776 and plan to
include it soon.

You are quite correct that the coordination number affects the bond
length. This is currently ignored in PHENIX but it may well be useful.
I'll read Shannon and Prewitt with a view to improving the
coordination code.

One thing you can do is add the slack option to the edits giving the
bond potential a flat bottom. This allow complete freedom for the
metal to use the electron density for fitting within the slack
distance of the ideal.

refinement.geometry_restraints.edits {
   bond {
        action = *add
        atom_selection_1 = chain F and resid 1 and name FE1
        atom_selection_2 = chain A and resid 69 and name SG
        distance_ideal = 2.35
        sigma = 0.1
        slack = 0.1

I'm very interested in discussing your situation and making it better.
If you send me your model (off line) we can investigate a better


NB. Any files sent to me will be held in strictest confidence.

On Tue, Nov 22, 2011 at 2:48 PM, Timothy Springer
<springer at idi.harvard.edu> wrote:
> Hi, We are refining structures with Ca binding sites that are replaced by
> Mn. Using the coordination restraints in Phenix (distance only) obtained
> with phenix.metal_coordination, we wind up with the ligands coming somewhat
> too close, so there is positive density on the opposite side of the ligating
> residue from the metal. We may have a series of problems, including
> incomplete replacement of Ca by Mn. However, the bigger issue I want to
> address is coordination number.
> In the work by Shannon and Prewitt, such as Acta Cryst. B25, 925, metal
> oxides are examined, and the point is made that the Mn-O distance with a
> coordination number of 6 is shorter than for 7. Ca commonly has either 6 or
> 7 ligands, and with 7 ligands (most common) the O cannot squeeze as tightly
> together and are farther away from Ca. Mn more commonly has 6 ligands, but
> can have 7.
> What are the distance restraints in Phenix based on? They seem similar to
> those in Harding MM, Acta Cryst D62, 678 (2006). This paper lumps
> measurements for different coordination numbers together for Mn-O and Ca-O
> distances, but not for Co, Cu, and Zn.
> It does seem to help to add metal ion restraints in Phenix. Things don't
> seem to come out as well without them.
> Would it be helpful to treat 6 and 7-coordinate metals differently? Or
> should we just loosen the restraints?
> How does Refmac treat metals? One does not need to add restraints in its
> case.
> With my best regards,
> Tim
> Timothy A. Springer, Ph.D.
> Latham Family Professor of Biological Chemistry and Molecular Pharmacology
> Harvard Medical School                   http://idi.harvard.edu/springer
> Immune Disease Institute                 springer at idi.harvard.edu
> Program in Cellular and Molecular Medicine, Dept. Medicine
> Div. Hematology                                 Children's Hospital Boston
> 3 Blackfan Circle, Rm 3103              phone:  617-713-8200
> Boston MA 02115                               fax:        617-713-8232
> _______________________________________________
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

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