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). One of the two functional domains of AdcR is <scene name='69/694230/Dimerization_domain/1'>the dimerization domain</scene>. This domain is made up of the <scene name='69/694230/Labeled_helix_adcr/2'>α1  helix</scene>, the C-terminus of the <scene name='69/694230/Labeled_helix_adcr/3'>α5 helix</scene> , and the <scene name='69/694230/Labeled_helix_adcr/4'>α6 helix</scene>. This domain is connected to the wHTH domain by the long α5 helix. The <scene name='69/694230/Alpha1-alpha2_loop/1'>α1-α2 loop</scene> along with the α5 and <scene name='69/694230/Labeled_helix_adcr/2'>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 (KZn1 = 10^12 M; pH 8) and one low affinity binding site (KZn2 = 10^7 M; pH 8) <ref>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/1'>two binding sites</scene> on each of its two protomers and can bind a total of four Zn(II). One of the two functional domains of AdcR is <scene name='69/694230/Dimerization_domain/1'>the dimerization domain</scene>. This domain is made up of the <scene name='69/694230/Labeled_helix_adcr/2'>α1  helix</scene>, the C-terminus of the <scene name='69/694230/Labeled_helix_adcr/3'>α5 helix</scene> , and the <scene name='69/694230/Labeled_helix_adcr/4'>α6 helix</scene>. This domain is connected to the wHTH domain by the long α5 helix. The <scene name='69/694230/Alpha1-alpha2_loop/1'>α1-α2 loop</scene> along with the α5 and <scene name='69/694230/Labeled_helix_adcr/2'>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 (KZn1 = 10^12 M; pH 8) and one low affinity binding site (KZn2 = 10^7 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_1/1'>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>PMID:20804771</ref>. This is due to the charges on the histidines of the binding site. At pH 8, the histidines are positively charged and can interact with the negatively charged Zn(II) ion. However, at pH 6 the histidines are neutrally charged and will not coordinate as well with Zn(II).
+<scene name='69/694230/Binding_site_1/1'>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 8, the histidines are positively charged and can interact with the negatively charged Zn(II) ion. However, at pH 6 the histidines are neutrally charged and will not coordinate as well with Zn(II).
 === Binding Site 2 ===
 <scene name='69/694230/Binding_site_2/1'>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 a C30A AdcR missense is present 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 DNA binding.