Sandbox GGC4

Mitochondrial cytochrome c oxidase is an important aspect of an aerobic cellular respiration. The structure shows an overall view of the mitochondrial cytochrome c oxidase. It consist of all proteins including the alpa 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 been selected at the oxidized side of the structure but 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.<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>