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User:Josey McKinley/Sandbox 1

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<scene name='87/877602/Hydrophillic_top/1'>Abbey's Scene</scene>
<scene name='87/877602/Hydrophillic_top/1'>Abbey's Scene</scene>
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== Active Site==
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Two structures of SCD known. One structure shows the substrate, water molecule, and zinc (4YMK). The second structure shows the product and iron (6WF2). For the pictures below, the structure is shown with two zinc ions in order to demonstrate how is <scene name='87/877627/Zn_and_water/1'>water</scene> coordination with the ions. Water is used in the mechanism, which is why we chose to use the structure with zinc to explain the active site.
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The two <scene name='87/877627/Just_zn/1'>zinc</scene>ions are 6.4 Angstroms apart. The ions sit above the kink in the active site. They are stabilized by the <scene name='87/877627/His_box2/1'>his box</scene>. The ion closest to C9 is 5.2 angstroms from it. This ion interacts with 4 histidines, H (list here) and one water molecule. The ion closest to C10 is 4.7 angstroms away from it. This ion interacts with 5 histidines, H (LIST HERE). These 9 total Histidine residues form a <scene name='87/877627/His_box2/1'>his box</scene>.The his box is used to stabilize the ions into the active site, forming a prosthetic group. The his box is highly conserved among the other isoforms of SCD. Other residues around the his box are used to hydrogen bond to the histidines to stabilize them. These residues include: <scene name='87/877627/E161/1'>E161</scene>,
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<scene name='87/877627/N261/1'>N261</scene>,
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<scene name='87/877627/D165/1'>D165</scene>, and
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<scene name='87/877627/E291/1'>E291</scene>
== References ==
== References ==

Revision as of 18:45, 6 April 2021

Contents

Stearoyl-CoA Desaturase 1 from Mus musculus

Stearoyl-CoA Desaturase 1- 4YMK

Drag the structure with the mouse to rotate

Active Site

Two structures of SCD known. One structure shows the substrate, water molecule, and zinc (4YMK). The second structure shows the product and iron (6WF2). For the pictures below, the structure is shown with two zinc ions in order to demonstrate how is coordination with the ions. Water is used in the mechanism, which is why we chose to use the structure with zinc to explain the active site. The two ions are 6.4 Angstroms apart. The ions sit above the kink in the active site. They are stabilized by the . The ion closest to C9 is 5.2 angstroms from it. This ion interacts with 4 histidines, H (list here) and one water molecule. The ion closest to C10 is 4.7 angstroms away from it. This ion interacts with 5 histidines, H (LIST HERE). These 9 total Histidine residues form a .The his box is used to stabilize the ions into the active site, forming a prosthetic group. The his box is highly conserved among the other isoforms of SCD. Other residues around the his box are used to hydrogen bond to the histidines to stabilize them. These residues include: , 

,
, and

References

[3]

  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
  3. ↑ Ransey E, Paredes E, Dey SK, Das SR, Heroux A, Macbeth MR. Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn(2+) /Mn(2+) heterobinucleation. FEBS Lett. 2017 Jul;591(13):2003-2010. doi: 10.1002/1873-3468.12677. Epub 2017, Jun 14. PMID:28504306 doi:http://dx.doi.org/10.1002/1873-3468.12677


Student Contributors

  • Josey McKinley
  • Abbey Wells
  • Anthony Durand

Proteopedia Page Contributors and Editors (what is this?)

Josey McKinley

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