| Proteins are BIG, metal sites are small! Its impossible to overemphasize how important the SHAPES and SURFACES of proteins are. We are more concerned with the inorganic chemistry, but we must understand how the protein can control and influence this chemistry. For example, myoglobin has a very accessible heme pocket, which allows ready binding of dioxygen (and other ligands) to the Fe center. We can see this in the space-filling model shown to the left, in which the heme is colored red. |  |
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Much more detail is evident using a stick model, but it gets very complicated for larger proteins like the cytochrome P450 shown. It is quite difficult to identify different protein strands and sidegroups at this scale image. |
| A common method of displaying proteins is a ribbon structure; here only the protein backbone itself displayed, the -(C-C-N)- polymeric structure which clearly shows the secondary structure, typically alpha-helical, as in the apomyoglobin shown, or beta-sheets. |  |
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All the interesting chemistry involves specific
sidegroups and cofactors which are not a part of the protein backbone.
So often you see mixed displays which give a ribbon structure with important
functionalities, like the heme cofactor, shown in the proper positions
as defined by crystallographic studies.
Metmyoglobin ribbon structure w/ cofactor and a few significant residues shown. |
| In this course, we are more concerned with the local environment around the metal sites. Therefore, in class I will only draw cartoons of the active site structures, these webpages are intended to give you access to the real structures, as seen for myoglobin at left. In this view you can see the protein environment above and below the heme. The cofactor is bound to the protein by an axial histidine from below, in what is called the proximal pocket. Above the heme is the distal pocket, where ligands and substrates can bind to the Fe. Distal ligands, such as histidines and arginines, which can H-bind to Fe-bound ligands, are often important players in the chemistry of these proteins. |  |
