Sandbox Reserved 1640: Difference between revisions

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== Important amino acids ==

Focussing on <scene name='86/861622/Ligand_view/1'>UGB ligand</scene>, Some important Amino acids would be <scene name='86/861622/Serine_128/1'>Serine(128)</scene>, Threonine(126), and Tyrosine(149) I found in the article that Lysine(153) is part of the triad also. They are <scene name='86/861622/Catalytic_triad/1'>the catalytic amino acids</scene> in my enzyme.THR and TYR are Amphipathic. This means they have both hydrophilic and hydrophobic parts. Serine, Threonine, and Tyrosine are Polar. Polar hydrophilic amino acids are important in UGB ligand binding to the substrate. The interactions play an important role in "molecular recognition". Different polarity means that there is a different charge distribution among the amino acids. This becomes important for locating or identifying the accessible area to the substrate. I found that the rings on the end have a lot to do with binding. The key Amino acids for binding from the website and the article are Pro, Gly, and Arg. which you can also see in figure 2D. When I used the RCSB website I saw that the sugar rings were intertwined. These key amino acids are important because they participate in hydrogen bonding. The 4th carbon engages the residues in the triad. The 2nd carbon with the OH attached to it and the 3rd carbon with the OH is hydrogen-bonded to ARG-185 and PRO-85. The 5th carbon on the carboxylate interacts with the THr-126, Ser-127, and the Ser-128. With the hydrogen bonding happening at the site, the negative charges are what drive the strained backbone. The sugar cavity has 3 water in it and they overlap the 3’-OH,4’-OH, and 5’- carbonate groups.

Focussing on <scene name='86/861622/Ligand_view/1'>UGB ligand</scene>, Some important Amino acids would be <scene name='86/861622/Serine_128/1'>Serine(128)</scene>, Threonine(126), and Tyrosine(149) I found in the article that Lysine(153) is part of the triad also. They are <scene name='86/861622/Catalytic_triad/1'>the catalytic amino acids</scene> in my enzyme.THR and TYR are Amphipathic. This means they have both hydrophilic and hydrophobic parts. Serine, Threonine, and Tyrosine are Polar. Polar hydrophilic amino acids are important in UGB ligand binding to the substrate. The interactions play an important role in "molecular recognition". Different polarity means that there is a different charge distribution among the amino acids. This becomes important for locating or identifying the accessible area to the substrate. I found that the rings on the end have a lot to do with binding. The key Amino acids for binding from the website and the article are Pro, Gly, and Arg. which you can also see in figure 2D. When I used the RCSB website I saw that the sugar rings were intertwined. These key amino acids are important because they participate in hydrogen bonding. The 4th carbon engages the residues in the triad. The 2nd carbon with the OH attached to it and the 3rd carbon with the OH is hydrogen-bonded to ARG-185 and PRO-85. The 5th carbon on the carboxylate interacts with the THr-126, Ser-127, and the Ser-128. With the hydrogen bonding happening at the site, the negative charges are what drive the strained backbone. The sugar cavity has 3 water in it and they overlap the 3’-OH,4’-OH, and 5’- carbonate groups. I also learned about disordered loops at the binding site. When You see the crystal structure through the X-ray. there is a blur and it means that the 2 loops are changing.So there ends up being no defined electron density.

== Structural highlights ==

Sandbox Reserved 1640: Difference between revisions

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 == Important amino acids ==
-Focussing on <scene name='86/861622/Ligand_view/1'>UGB ligand</scene>, Some important Amino acids would be <scene name='86/861622/Serine_128/1'>Serine(128)</scene>, Threonine(126), and Tyrosine(149) I found in the article that Lysine(153) is part of the triad also. They are <scene name='86/861622/Catalytic_triad/1'>the catalytic amino acids</scene> in my enzyme.THR and TYR are Amphipathic. This means they have both hydrophilic and hydrophobic parts. Serine, Threonine, and Tyrosine are Polar. Polar hydrophilic amino acids are important in UGB ligand binding to the substrate. The interactions play an important role in "molecular recognition". Different polarity means that there is a different charge distribution among the amino acids. This becomes important for locating or identifying the accessible area to the substrate. I found that the rings on the end have a lot to do with binding.  The key Amino acids for binding from the website and the article are Pro, Gly, and Arg. which you can also see in figure 2D. When I used the RCSB website I saw that the sugar rings were intertwined. These key amino acids are important because they participate in hydrogen bonding. The 4th carbon engages the residues in the triad. The 2nd carbon with the OH attached to it and the 3rd carbon with the OH is hydrogen-bonded to ARG-185 and PRO-85. The 5th carbon on the carboxylate interacts with the THr-126, Ser-127, and the Ser-128. With the hydrogen bonding happening at the site, the negative charges are what drive the strained backbone. The sugar cavity has 3 water in it and they overlap the 3’-OH,4’-OH, and 5’- carbonate groups.
+Focussing on <scene name='86/861622/Ligand_view/1'>UGB ligand</scene>, Some important Amino acids would be <scene name='86/861622/Serine_128/1'>Serine(128)</scene>, Threonine(126), and Tyrosine(149) I found in the article that Lysine(153) is part of the triad also. They are <scene name='86/861622/Catalytic_triad/1'>the catalytic amino acids</scene> in my enzyme.THR and TYR are Amphipathic. This means they have both hydrophilic and hydrophobic parts. Serine, Threonine, and Tyrosine are Polar. Polar hydrophilic amino acids are important in UGB ligand binding to the substrate. The interactions play an important role in "molecular recognition". Different polarity means that there is a different charge distribution among the amino acids. This becomes important for locating or identifying the accessible area to the substrate. I found that the rings on the end have a lot to do with binding.  The key Amino acids for binding from the website and the article are Pro, Gly, and Arg. which you can also see in figure 2D. When I used the RCSB website I saw that the sugar rings were intertwined. These key amino acids are important because they participate in hydrogen bonding. The 4th carbon engages the residues in the triad. The 2nd carbon with the OH attached to it and the 3rd carbon with the OH is hydrogen-bonded to ARG-185 and PRO-85. The 5th carbon on the carboxylate interacts with the THr-126, Ser-127, and the Ser-128. With the hydrogen bonding happening at the site, the negative charges are what drive the strained backbone. The sugar cavity has 3 water in it and they overlap the 3’-OH,4’-OH, and 5’- carbonate groups. I also learned about disordered loops at the binding site. When You see the crystal structure through the X-ray. there is a blur and it means that the 2 loops are changing.So there ends up being no defined electron density.
 == Structural highlights ==