Sandbox Reserved 1063: Difference between revisions
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<StructureSection load='3TGN' size='350' side='right' caption='3TGN' scene=''> | <StructureSection load='3TGN' size='350' side='right' caption='3TGN' scene=''> | ||
== '''Zn(II) Binding''' == | == '''Zn(II) Binding''' == | ||
Zinc-Dependent Transcriptional Regulator AdcR has <scene name='69/694230/Two_binding_sites/1'>two binding sites</scene> on each of its two protomers and can bind a total of four Zn(II) per dimer. <scene name='69/694230/Dimerization_domain/1'>The dimerization domain</scene> is made up of the <font color='blue'>alpha helix 1</font>, <font color='gold'>alpha helix 5</font>, and the <font color='orange'>alpha helix 6</font>. This domain is connected to the HTH winged domain with the long <font color='gold'>alpha helix 5</font>. This dimerization domain connects to the DNA binding domain and together with the <font color='blue'>alpha 1</font> <font color='turquoise'>alpha 2</font> loop make up the <scene name='69/694230/Alpha_1_alpha_2/1'>metal binding sites</scene><ref>PMID:22085181</ref>. 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). The metal binding pockets of the AdcR MarR transcriptional regulator are made up of the DNA binding domain with the extended alpha 1 and alpha 2 loop. The two different Zn(II) binding sites are connected via hydrogen bonding of the Nd1 atom of H108 and then liganding Oe1 atom of E41. | Zinc-Dependent Transcriptional Regulator AdcR has <scene name='69/694230/Two_binding_sites/1'>two binding sites</scene> on each of its two protomers and can bind a total of four Zn(II) per dimer. <scene name='69/694230/Dimerization_domain/1'>The dimerization domain</scene> is made up of the <font color='blue'>alpha helix 1</font>, <font color='gold'>alpha helix 5</font>, and the <font color='orange'>alpha helix 6</font>. This domain is connected to the HTH winged domain with the long <font color='gold'>alpha helix 5</font>. This dimerization domain connects to the DNA binding domain and together with the <font color='blue'>alpha 1</font> <font color='turquoise'>alpha 2</font> loop make up the <scene name='69/694230/Alpha_1_alpha_2/1'>metal binding sites</scene><ref>PMID:22085181</ref>. 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). The metal binding pockets of the AdcR MarR transcriptional regulator are made up of the DNA binding domain with the extended alpha 1 and alpha 2 loop. The two different Zn(II) binding sites are connected via <scene name='69/694230/Hydrogen_bonding/3'>hydrogen bonding</scene> of the Nd1 atom of H108 and then liganding Oe1 atom of E41. | ||
=== Binding Site 1 === | === 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 Oe1, H42 Nd1, H108 Ne2, and H112 Ne2. 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. 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 Oe1, H42 Nd1, H108 Ne2, and H112 Ne2. 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. 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). | ||