Sandbox Reserved 1063: Difference between revisions

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OCA, Zach LaRoche, Paxton Schowe, Geoffrey C. Hoops, Alexi Zaniker, Shandeep Singh, Isaac C. Gluesenkamp

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 == '''Zn(II) Binding''' ==
-Zinc-Dependent Transcriptional Regulator AdcR has <scene name='69/694230/2_binding_sites/1'>two binding sites</scene> on each of its two protomers and can bind a total of four Zn(II). The <scene name='69/694230/Alpha1-alpha2_loop/1'>α1-α2 loop</scene> combined with the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> and <scene name='69/694230/Alpha_2/1'>α2  helix</scene> make up the <scene name='69/694230/2_binding_sites/1'>metal binding sites</scene>. Each protomer has one high affinity site (Binding site 1; KZn1 = 10<sup>12</sup> M; pH 8) and one low affinity binding site (Binding Site 2; KZn2 = 10<sup>7</sup> M; pH 8) <ref name="Reyes">PMID:20804771</ref>. The metal binding pockets of the AdcR MarR transcriptional regulator are made up of the DNA binding domain with the extended α1-α2 loop. The two different Zn(II) binding sites are connected via <scene name='69/694230/Hydrogen_bonding/4'>hydrogen bonding</scene> of H108 and E41.
+Zinc-Dependent Transcriptional Regulator AdcR has <scene name='69/694230/2_binding_sites/2'>two binding sites</scene> on each of its two protomers and can bind a total of four Zn(II). The <scene name='69/694230/Alpha1-alpha2_loop/1'>α1-α2 loop</scene> combined with the <scene name='69/694230/Alpha_five/1'>α5 helix</scene> and <scene name='69/694230/Alpha_2/1'>α2  helix</scene> make up the <scene name='69/694230/2_binding_sites/1'>metal binding sites</scene>. Each protomer has one high affinity site (Binding site 1; KZn1 = 10<sup>12</sup> M; pH 8) and one low affinity binding site (Binding Site 2; KZn2 = 10<sup>7</sup> M; pH 8) <ref name="Reyes">PMID:20804771</ref>. The metal binding pockets of the AdcR MarR transcriptional regulator are made up of the DNA binding domain with the extended α1-α2 loop. The two different Zn(II) binding sites are connected via <scene name='69/694230/Hydrogen_bonding/4'>hydrogen bonding</scene> of H108 and E41.
 === Binding Site 1 ===
 <scene name='69/694230/Binding_site_1/5'>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<sup>9</sup> - 10<sup>10</sup> M<sup>-1</sup>, but at pH 8 the binding affinity increases to 10<sup>12</sup> M<sup>-1</sup> <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" />.