Sandbox Reserved 1600: Difference between revisions

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[[Image:Hemes2.png|300 px|right|thumb|Figure 1. The active site of bd oxidase for ''Geobacillus thermodenitrificans''. Heme B558 (pink; left), Heme B595 (pink; right), and Heme D (green). Important residues shown in blue. Measurements are shown in Å.]]

The active site for bd oxidase in ''Geobacillus thermodenitrificans'' is located in subunit Cyd A. The site consists of three iron hemes: <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>, <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>, and <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> that are held together in a rigid triangular <scene name='83/838655/Hemes/8'>arrangement</scene> due to [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions].<ref name = ”Safarian” /> The <scene name='83/838655/Hemes_measurements/5'>length</scene> between each heme's central iron is relatively constant which serves to shuttle protons and electrons from one heme to another efficiently (Fig. 1). It is suggested that <scene name='83/838655/Bd_oxidase_heme_558/2'>Heme B558</scene> acts as an electron acceptor, orientated toward the extracellular side by <scene name='83/838655/Bdoxidase_structure_heme/4'>His 186, Met 325, and Lys 252</scene> (Fig. 1).<ref name = ”Safarian” /> With <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene> closest in proximity to the intracellular side, it is suggested it functions as the proton acceptor with two potential proton pathways. It is then proposed that both <scene name='83/838655/Bd_oxidase_heme_558/2'>Heme B558</scene> and <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene> shuttle their respective ions directly to <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene> based on this being the shortest pathway.

The active site for bd oxidase in ''Geobacillus thermodenitrificans'' is located in subunit Cyd A. The site consists of three iron hemes: <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>, <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>, and <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> that are held together in a rigid triangular <scene name='83/838655/Hemes/8'>arrangement</scene> due to [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions].<ref name = ”Safarian” /> The <scene name='83/838655/Hemes_measurements/5'>length</scene> between each heme's central iron is relatively constant which serves to shuttle protons and electrons from one heme to another efficiently (Fig. 1). It is suggested that <scene name='83/838655/Bd_oxidase_heme_558/2'>Heme B558</scene> acts as an electron acceptor, orientated toward the extracellular side by <scene name='83/838655/Bdoxidase_structure_heme/4'>His 186, Met 325, and Lys 252</scene> (Fig. 1).<ref name = ”Safarian” /> With <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> closest in proximity to the intracellular side, it is suggested it functions as the proton acceptor with two potential proton pathways. It is then proposed that both <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> and <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> shuttle their respective ions directly to <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> based on this being the shortest pathway.

==Potential Oxygen Entry Site==

<scene name='83/838655/Bd_oxidase_heme_d/1'>Heme D</scene> is the hypothesized spot for the <scene name='83/832926/Potential_oxygen_entry_site/1'>oxygen</scene> to enter the protein. Heme D (shown in green) is directly connected to the protein surface on CydA and contains a solvent accessible substrate channel. This channel and accessibility allow for oxygen to easily bind to Heme D and eventually be reduced to two H₂O molecules. This process requires a proton and electron source, both described in the later sections.

<scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> is the hypothesized spot for the <scene name='83/832926/Potential_oxygen_entry_site/1'>oxygen</scene> to enter the protein. Heme D (shown in green) is directly connected to the protein surface on CydA and contains a solvent accessible substrate channel. This channel and accessibility allow for oxygen to easily bind to Heme D and eventually be reduced to two H₂O molecules. This process requires a proton and electron source, both described in the later sections.

==Electron Source==

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@@ Line 19: / Line 19: @@
 [[Image:Hemes2.png|300 px|right|thumb|Figure 1. The active site of bd oxidase for ''Geobacillus thermodenitrificans''. Heme B558 (pink; left), Heme B595 (pink; right), and Heme D (green). Important residues shown in blue. Measurements are shown in Å.]]
-The active site for bd oxidase in ''Geobacillus thermodenitrificans'' is located in subunit Cyd A. The site consists of three iron hemes: <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>, <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>, and <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> that are held together in a rigid triangular <scene name='83/838655/Hemes/8'>arrangement</scene> due to [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions].<ref name = ”Safarian” /> The <scene name='83/838655/Hemes_measurements/5'>length</scene> between each heme's central iron is relatively constant which serves to shuttle protons and electrons from one heme to another efficiently (Fig. 1). It is suggested that <scene name='83/838655/Bd_oxidase_heme_558/2'>Heme B558</scene> acts as an electron acceptor, orientated toward the extracellular side by <scene name='83/838655/Bdoxidase_structure_heme/4'>His 186, Met 325, and Lys 252</scene> (Fig. 1).<ref name = ”Safarian” /> With <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene> closest in proximity to the intracellular side, it is suggested it functions as the proton acceptor with two potential proton pathways. It is then proposed that both <scene name='83/838655/Bd_oxidase_heme_558/2'>Heme B558</scene> and <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene> shuttle their respective ions directly to <scene name='83/838655/Bd_oxidase_heme_b_595/1'>Heme B595</scene> based on this being the shortest pathway.
+The active site for bd oxidase in ''Geobacillus thermodenitrificans'' is located in subunit Cyd A. The site consists of three iron hemes: <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>, <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>, and <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> that are held together in a rigid triangular <scene name='83/838655/Hemes/8'>arrangement</scene> due to [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions].<ref name = ”Safarian” /> The <scene name='83/838655/Hemes_measurements/5'>length</scene> between each heme's central iron is relatively constant which serves to shuttle protons and electrons from one heme to another efficiently (Fig. 1). It is suggested that <scene name='83/838655/Bd_oxidase_heme_558/2'>Heme B558</scene> acts as an electron acceptor, orientated toward the extracellular side by <scene name='83/838655/Bdoxidase_structure_heme/4'>His 186, Met 325, and Lys 252</scene> (Fig. 1).<ref name = ”Safarian” /> With <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> closest in proximity to the intracellular side, it is suggested it functions as the proton acceptor with two potential proton pathways. It is then proposed that both <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> and <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> shuttle their respective ions directly to <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> based on this being the shortest pathway.
 ==Potential Oxygen Entry Site==
-<scene name='83/838655/Bd_oxidase_heme_d/1'>Heme D</scene> is the hypothesized spot for the <scene name='83/832926/Potential_oxygen_entry_site/1'>oxygen</scene> to enter the protein. Heme D (shown in <font color='green'><b>green</b></font>) is directly connected to the protein surface on CydA and contains a solvent accessible substrate channel. This channel and accessibility allow for oxygen to easily bind to Heme D and eventually be reduced to two H₂O molecules. This process requires a proton and electron source, both described in the later sections.
+<scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> is the hypothesized spot for the <scene name='83/832926/Potential_oxygen_entry_site/1'>oxygen</scene> to enter the protein. Heme D (shown in <font color='green'><b>green</b></font>) is directly connected to the protein surface on CydA and contains a solvent accessible substrate channel. This channel and accessibility allow for oxygen to easily bind to Heme D and eventually be reduced to two H₂O molecules. This process requires a proton and electron source, both described in the later sections.
 ==Electron Source==