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
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