[Chimera-users] How to place a metal ion in protein model

Elaine Meng meng at cgl.ucsf.edu
Wed Jan 4 10:21:59 PST 2012

Hi Suneel,
Chimera doesn't have a tool to predict metal binding sites from a structure.  There is a tool called "Add Ions" which will roughly place ions around a structure, but it is meant for adding counterions for simulation purposes and is ineffective for binding site prediction.

First, I would consider the following:

(a) what protein was used as the template for the homology model?  Does it bind metal? If so, the site is probably in the same place.  You could just superimpose the template (with metal ion included) and model structures to see the binding site.

(b) do you have any other data about which residues bind the metal?  You may be able to create a metal ion with Build Structure (under Tools... Structure Editing) and place the metal near the protein yourself, interactively, with the mouse.

(c) I believe there are several web servers that will try to identify metal-binding sites and other active sites from your uploaded protein structure.  I would recommend doing some literature or web searching to find these.  I have used some in the past, but it was a few years ago.  Here are some web server names to search for and try: PAR-3D, PDBSiteScan, PINTS, ProFunc, Protemot, SuMo

Chimera has a Metal Geometry tool (under Tools... Structure Analysis), but it is meant to analyze the binding geometry of structures that already contain the metal ion, or to analyze the possibilities after you have manually placed the metal ion.

Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 2, 2012, at 1:36 AM, Suneel N.A. wrote:

> Hi
> Its my pleasure to introduce myself, I am  Suneel, graduate student from India. I am not a bioinformatician by profession but a eager aspirant of learning bioinformatics. I am new to Chimera, but as I started using it,  the desire for leraning Bioinformatics increased more and more. Chimera is such an awesome tool packed with so many options. I love it . I have small question for you.
> I have a predicted the structure of protein using in silico tools (based on homology modeling). Literature sates that this protein binds to Magnesium. Now I would like to know if I can use chimera to place the metal in the modeled structure and prove/validate it based on metal geometry.
> Please do the needful.
> Thanking you in anticipation
> yours sincerely
> suneel

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