Sandbox Reserved 1069: Difference between revisions

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'''Binding Site A'''

Binding site A is in the center of the transmembrane domain, attached and confined via residues from the TM2 and TM5 helices. The TM2 domain has Asp45 and Asp49, and the TM5 has His153 and Asp157. This site is the protein's active site, meaning that this is where the zinc is able to attach and eventually exit the cell via proton transport. This particular site has an ideal tetrahedron among its residues which is preferred for zinc, thus making it the perfect active site for zinc to bind.

It is important to note that the structure of this binding site is rigid because of the coordination of the zinc between the four residues. This rigidity is indicative that any slight shift on either of the helices will cause a drastic readjustment of the coordination of zinc. In addition, there are no outer-shell constraints to hold the residues in place, which means that with a readjustment of the molecule, there is no energy being expended to bind or release another zinc molecule. Therefore, the zinc is able to rapidly release and a new zinc can bind again with a simple reorientation or shift of the molecule. This rapid on off bind and release mechanism is the regulator of homeostatic levels of zinc in the cell.

It is important to note that the structure of this binding site is rigid because of the coordination of the zinc between the four residues. This rigidity is indicative that any slight shift on either of the helices will cause a drastic readjustment of the coordination of zinc. In addition, there are no outer-shell constraints to hold the residues in place, which means that with a readjustment of the molecule, there is no energy being expended to bind or release another zinc molecule. Therefore, the zinc is able to rapidly release and a new zinc can bind again with a simple reorientation or shift of the molecule. This rapid on off bind and release mechanism is the regulator of homeostatic levels of zinc in the cell. This regulation is so rapid in fact, it is significantly faster than other zinc exchange rate proteins- by several orders of magnitude.

'''Binding Site C'''

Binding site C has vastly opposite properties from what is seen in binding site A. It is located on the TM2-TM3 loop on the cytoplasmic membrane and between the two c-terminus domain interfaces. Here, there is a binuclear coordination of zinc between the Asp285 residue that bridges the zinc ions together and the four coordinating residues (His232, His248, His283 and His261). The Asp285 residue is conserved, meaning it does not have outer shell constraints. However, the four histidine residues all have outer shell constraints. These constraints consist of hydrogen bonds to the residues surrounding the binding site. These hydrogen bonds can form bidentate bonds, which means that the hydrogen bond attaches to a metal in two places. These bonds in turn create an extensive network of interactions at the CTD interface, and it is these interactions that allow for stability for the CTD-CTD association.

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

Sandbox Reserved 1069: Difference between revisions

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@@ Line 13: / Line 13: @@
 '''Binding Site A'''
 Binding site A is in the center of the transmembrane domain, attached and confined via residues from the TM2 and TM5 helices. The TM2 domain has Asp45 and Asp49, and the TM5 has His153 and Asp157. This site is the protein's active site, meaning that this is where the zinc is able to attach and eventually exit the cell via proton transport. This particular site has an ideal tetrahedron among its residues which is preferred for zinc, thus making it the perfect active site for zinc to bind.
-It is important to note that the structure of this binding site is rigid because of the coordination of the zinc between the four residues. This rigidity is indicative that any slight shift on either of the helices will cause a drastic readjustment of the coordination of zinc. In addition, there are no outer-shell constraints to hold the residues in place, which means that with a readjustment of the molecule, there is no energy being expended to bind or release another zinc molecule. Therefore, the zinc is able to rapidly release and a new zinc can bind again with a simple reorientation or shift of the molecule. This rapid on off bind and release mechanism is the regulator of homeostatic levels of zinc in the cell.
+It is important to note that the structure of this binding site is rigid because of the coordination of the zinc between the four residues. This rigidity is indicative that any slight shift on either of the helices will cause a drastic readjustment of the coordination of zinc. In addition, there are no outer-shell constraints to hold the residues in place, which means that with a readjustment of the molecule, there is no energy being expended to bind or release another zinc molecule. Therefore, the zinc is able to rapidly release and a new zinc can bind again with a simple reorientation or shift of the molecule. This rapid on off bind and release mechanism is the regulator of homeostatic levels of zinc in the cell. This regulation is so rapid in fact, it is significantly faster than other zinc exchange rate proteins- by several orders of magnitude.
+'''Binding Site C'''
+Binding site C has vastly opposite properties from what is seen in binding site A. It is located on the TM2-TM3 loop on the cytoplasmic membrane and between the two c-terminus domain interfaces. Here, there is a binuclear coordination of zinc between the Asp285 residue that bridges the zinc ions together and the four coordinating residues (His232, His248, His283 and His261). The Asp285 residue is conserved, meaning it does not have outer shell constraints. However, the four histidine residues all have outer shell constraints. These constraints consist of hydrogen bonds to the residues surrounding the binding site. These hydrogen bonds can form bidentate bonds, which means that the hydrogen bond attaches to a metal in two places. These bonds in turn create an extensive network of interactions at the CTD interface, and it is these interactions that allow for stability for the CTD-CTD association.
 This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.