Molecular Origami is a great way to study the molecular environment
of a single atom or a group of atoms. It is a powerful tool for making comparisons
of bond distances and angles of similar molecules. In this sample study, iron and zinc atoms in
proteins were chosen. The views of the molecules were made using
Molecular Origami and x-ray
crystal data presented in the Brookhaven Protein
Data Bank. The four digit database code for each molecule is listed in
parentheses. All molecules in the view are part of the named protein. It
is possible to view 3D models of all of the iron and zinc centers shown here by
clicking on the 3D Chime link. Viewing these 3D models requires a Netscape plugin which
is not on all computers.
Iron is a very interesting atom because it occurs naturally in two common oxidation states: Fe(II) and Fe(III). Because of this, iron can have many possible geometries. The average adult human has about 4 grams of iron in their body, 75% of which is in hemoglobin. Click below to view one of the four possible environments for iron shown in this study:
Iron in a Heme Group
Isolated Non-Heme Iron
Iron-Sulfur Systems
Two Other Interesting Proteins
Zinc is also an interesting atom. It is common in several important proteins. The average adult human has about 2 grams of zinc in their body, most of which is in protein. Zinc is a divalent metal which has several geometric possibilities. Click below to view one of the four possible environments for zinc shown in this study:
Tetrahedral Zinc Center
Trigonal Pyramidal Zinc Center
Trigonal Bipyramidal Zinc Center
Two Other Interesting Proteins
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