Sandbox Reserved 1063: Difference between revisions

=== Binding Site 1 ===

<scene name='69/694230/Binding_site_1/4'>Binding site 1</scene> consists of a distorted tetrahedral geometry around Zn(II). The four amino acids involved in zinc binding are E24, H42, H108, and H112. Binding site 1 is the only binding site that plays a significant role in the protein's regulatory function.  The ability of binding site 1 to coordinate to the Zn(II) ion is pH dependent. At pH 6 the binding affinity for the Zn(II) ion is 10^9 - 10^10 M^-1, but at pH 8 the binding affinity increases to 10^12 M^-1 <ref name="Reyes" />. This is due to the charges on the histidines of the binding site. At pH 6, the histidines are positively charged and are not able to interact with the positively charged Zn(II) ion. However, at pH 8 the histidines are neutrally charged and are able to coordinate with Zn(II), which increases the overall binding affinity. The AdcR MarR transcriptional regulator is able to bind Co(II) in binding site 1 in a way that induces similar conformational changes to Zn(II) binding. Co(II) coordination in binding site 1 is able to allosterically activate DNA binding similarly to Zn(II) binding <ref name="guerra" />.

=== Binding Site 2 ===

<scene name='69/694230/Binding_site_2/3'>Binding site 2</scene> consists of a highly distorted tetrahedral geometry around the zinc ion. There are three amino acids involved in the binding of the zinc ion (C30, E41, and E107) as well as a water molecule. If Cys30 is mutated to an Alanine in binding site 2, it will have no effect on the ability of the protein to bind DNA <ref name="guerra" />. Therefore, binding site 2 has no significant role in the ability of AdcR to bind to DNA and AdcR is still able to function with no zinc bound present in binding site 2.  

== References ==

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