16 May 2018

MetalPDB website

Web Resources and Apps

Submitted by Anthony L. Fernandez, Merrimack College
Categories
Description: 

When teaching my advanced bioinorganic chemistry course, I extensively incorporate structures from Protein Data Bank in both my assignments and classroom discussions and mini-lectures. I also have students access structures both in and out of class as they complete assignments.

In the past, I have used Metal MACiE to help find metal-containing biological macromolecules and to access information about the metal function and coordination environment. Unfortunately, this site, while still available, has not been updated in several years. I have recently found the MetalPDB website which was created at CERM (University of Florence). This site "collects and allows easy access to the knowledge on metal sites in biological macromolecules" and can be used to explore structures deposited in the PDB.

I also expect my students to use this site to obtain information for their assignments and presentations.

Learning Goals: 

When using this website, students are able to:

  • obtain statistics pertaining to the number of metal-containing structures in the PDB,
  • determine the most common geometry observed for a particular metal in a biological structure,
  • identify the most common ligands attached to the metal when bound in a biological macromolecule, and
  • find information such as the function of, the coordination geometry of, and the coordinated ligands bound to a metal ion in a specific structure from the PDB.

These learning goals are incorporated in the associated in-class activity, which is posted separately.

Implementation Notes: 

I used this site for the first time in my Bioinorganic Chemistry course during the Spring 2018 semester. I routinely use the PDB to access structures of metal-containing biological macromolecules, but it can be very hard to find structures wth specific metals. I used this site to find structures that I could use as examples in class.

To learn how to use the site, I assigned an associated activity (posted separately) that I have the students complete before coming to class. This experience allows the students to use the site to get background information about metal geometry and common ligands for their assignments and presentations.

This site utilizes JavaScript and JSmol so students must ensure that Java functions properly in their preferred web browser. I have found no issues accessing this site with any of the browsers used by myself or my students.

 

Evaluation
Evaluation Methods: 

I kept track of how much my students used information obtained from this site during their literature presentations.

Evaluation Results: 

The students had little difficulty accessing or using the site. Most of my students used information obtained from the site in their presentations and during in-class dicsussions.

Creative Commons License: 
Creative Commons Licence

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