Sandbox Reserved 1069: Difference between revisions
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You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. | ||
== Structural Overview == | == Structural Overview == | ||
== | === Zinc Binding Sites === | ||
Each zinc promoter contains three zinc binding sites. There is an active site (Site A), and two cytoplasmic binding sites (Site B and C). It was found that only site A and C are conserved, while Site B does not have a relevant biological function to this protein. | |||
'''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. | |||
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. | 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. | ||
Revision as of 21:01, 17 March 2017
| This Sandbox is Reserved from 02/09/2015, through 05/31/2016 for use in the course "CH462: Biochemistry 2" taught by Geoffrey C. Hoops at the Butler University. This reservation includes Sandbox Reserved 1051 through Sandbox Reserved 1080. |
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This is a default text for your page '. Click above on edit this page' to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
Structural OverviewStructural Overview
Zinc Binding SitesZinc Binding Sites
Each zinc promoter contains three zinc binding sites. There is an active site (Site A), and two cytoplasmic binding sites (Site B and C). It was found that only site A and C are conserved, while Site B does not have a relevant biological function to this protein.
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.
This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
</StructureSection>
ReferencesReferences
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644