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Sandbox GGC4

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=Cytochrome c oxidase=
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==Name of your molecule==
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<StructureSection load='1V54' size='340' side='right' caption='Caption for this structure' scene='75/752268/Intro1/2'>
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<StructureSection load='1V54' size='340' side='right' caption='Caption for this structure' scene=''>
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This is a default text for your page '''Sandbox GGC4'''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
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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.
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== Function ==
== Function ==
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The Aspartate residue (Asp-51) in bovine heart cytochrome c oxidase plays a role in the redox-proton pumping.
 
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Cytochrome c oxidase in mitochondrial also play a key role in the use of four protons, that translocate across the membrane, and uses ATP synthase for ATP synthesis.
 
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The proton-pumping at the heme-copper functions in the transfer of energy for respiratory chains in eukaryotes and prokaryotes.
 
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<scene name='75/752268/Intro1/2'>Front view of cytochrome c oxidase.</scene>
 
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== Disease==
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== Disease ==
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There are some genetic disorders related to the dysfunction of cytochrome c oxidase that includes:
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Leigh Syndrome,
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== Relevance ==
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Anemia, and
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Cardiomyopathy
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== Structural highlights ==
== Structural highlights ==
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Mitochondrial cytochrome c oxidase is an important aspect of an aerobic cellular respiration, in which the amount of dioxygen is reduced to form water during pumping of proton at the inner membrane of the mitochondrial. The structure shows an overall view of the mitochondrial cytochrome c oxidase. It consists of all proteins including the alpha protein, side chains and water except the nucleic acid. The ligand and non-standard residues included in this structure are Magnesium ion, sodium ion,Heme a, Copper(ii) ion, Formyl group and Phosphothreonine.<scene name="75/752268/Intro1/2">Oxidize-Reduced Inter membrane side</scene> The second structure describes the oxidize state of the mitochondrial with limited side chains (A and B). All the proteins were selected at the oxidized side of the structure. The main idea was to identify the heme a [HEA] of cytochrome c-oxidase, which is the element that causes pumping of the proton. Again all proteins, all atoms with a limited residue numbers and limit chains of A and B for the oxidize side of the Cytochrome c oxidase were selected. The side chains and residues were labelled. Water was then added between residues [Y]440 and [Y]371, labeled it. The Aspartate residue (Asp-51) labeled in the oxidized state shows a proton-pumping occurring at that site and also a hydrogen bonding connection with the channels, where water molecules are located.<scene name='75/752268/Introduction_5b/1'>Heme a element and hydrogen bonding</scene> of the protein. The next scene shows the distance measured between the water and the residue [Ser]205, [Y]440 , and [Y]371 <scene name='75/752268/Introduction_5c/1'>Bond distances between HOH and limited residues </scene>. The final structure view describes about the Reduced state of the cytochrome c oxidase, the main focus was on the Copper (ii) ion [Cu] and the low-spin heme a [HEA] to the reduction site which is located on the inner membrane of the mitochondrial. The limited residues shown in this structure includes TGL, Sodium ion [NA], and Magnesium ion [MG] at the side chain N, which were labeled and the distance between CU and HEA were also measured<scene name='75/752268/Introduction_7/1'>Cu and Heme a Bond distance </scene>
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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.
</StructureSection>
</StructureSection>
== References ==
== References ==
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<ref>PMID:14673090 </ref>
 
<references/>
<references/>

Revision as of 19:04, 23 February 2018

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Caption for this structure

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References

  1. ↑ 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
  2. ↑ 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
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