User:Jacob Holt/Sandbox 1: Difference between revisions

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=== Ligand Binding Pocket and Histidine Coordination ===

The ligand binding pocket is a narrow tunnel that extends approximately 24 Å into the mostly hydrophobic interior of the protein. The ligand is stabilized by bending into a kinked conformation which creates a tight fit in the binding pocket tunnel, and by a hydrogen bond that occurs between the <scene name='87/877552/W258/2'>W 258</scene> side chain and the acyl carbonyl<ref name="Bai" />. The kink in the tunnel is formed by the conserved residues, <scene name='87/877552/Desaturation_site/9'>T 257 and W 149</scene> which are stabilized by the hydrogen bond shared with Q143<ref name="Bai" />. There are <scene name='87/877552/Substrate_orientation_w_fe/5'>two Fe2+ ions</scene> that interact with the substrate; the Fe2+ ions are coordinated by <scene name='87/877552/Histidine_coordination/8'>9 invariant histidine residues</scene>. <scene name='87/877552/Substrate_oreintation_fe_90deg/3'>When rotated 90 degrees</scene> the ligand is seen to be in a eclipsed position, indicating it is in its post-reaction form. One metal ion is coordinated by 4 histidines residues and a water molecule, and the other metal ion is coordinated by 5 histidine residues<ref name="Bai" />. The histidine residues position the metal ions 6.4 Å apart<ref name="Bai" />.

The ligand binding pocket is a narrow tunnel that extends approximately 24 Å into the mostly hydrophobic interior of the protein. The ligand is stabilized by bending into a kinked conformation which creates a tight fit in the binding pocket tunnel, and by a hydrogen bond that occurs between the <scene name='87/877552/W258/3'>W 258</scene> side chain and the acyl carbonyl<ref name="Bai" />. The kink in the tunnel is formed by the conserved residues, <scene name='87/877552/Desaturation_site/10'>T 257 and W 149</scene> which are stabilized by the hydrogen bond shared with Q143<ref name="Bai" />. There are <scene name='87/877552/Substrate_orientation_w_fe/5'>two Fe2+ ions</scene> that interact with the substrate; the Fe2+ ions are coordinated by <scene name='87/877552/Histidine_coordination/8'>9 invariant histidine residues</scene>. <scene name='87/877552/Substrate_oreintation_fe_90deg/3'>When rotated 90 degrees</scene> the ligand is seen to be in a eclipsed position, indicating it is in its post-reaction form. One metal ion is coordinated by 4 histidines residues and a water molecule, and the other metal ion is coordinated by 5 histidine residues<ref name="Bai" />. The histidine residues position the metal ions 6.4 Å apart<ref name="Bai" />.

=== Desaturation Site ===

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=== Active Site Cap ===

The two conserved residues of the active site cap are <scene name='87/877552/Active_site_cap/6'>Y 104 and G 287</scene>. These two residues form a hydrogen bond creating a ~~ridged~~ barrier at the end of the active site to keep the ligand from moving during the reaction<ref name="Bai" />. The active site cap is also used in determining the substrate length when entering the active site<ref name="Bai" />.

The two conserved residues of the active site cap are <scene name='87/877552/Active_site_cap/6'>Y 104 and G 287</scene>. These two residues form a hydrogen bond creating a rigid barrier at the end of the active site to keep the ligand from moving during the reaction<ref name="Bai" />. The active site cap is also used in determining the substrate length when entering the active site<ref name="Bai" />.

=== Catalytic Molecule ===

@@ Line 44: / Line 44: @@
 === Ligand Binding Pocket and Histidine Coordination ===
-The ligand binding pocket is a narrow tunnel that extends approximately 24 Å into the mostly hydrophobic interior of the protein. The ligand is stabilized by bending into a kinked conformation which creates a tight fit in the binding pocket tunnel, and by a hydrogen bond that occurs between the <scene name='87/877552/W258/2'>W 258</scene> side chain and the acyl carbonyl<ref name="Bai" />. The kink in the tunnel is formed by the conserved residues, <scene name='87/877552/Desaturation_site/9'>T 257 and W 149</scene> which are stabilized by the hydrogen bond shared with Q143<ref name="Bai" />. There are <scene name='87/877552/Substrate_orientation_w_fe/5'>two Fe2+ ions</scene> that interact with the substrate; the Fe2+ ions are coordinated by <scene name='87/877552/Histidine_coordination/8'>9 invariant histidine residues</scene>.  <scene name='87/877552/Substrate_oreintation_fe_90deg/3'>When rotated 90 degrees</scene> the ligand is seen to be in a eclipsed position, indicating it is in its post-reaction form.  One metal ion is coordinated by 4 histidines residues and a water molecule, and the other metal ion is coordinated by 5 histidine residues<ref name="Bai" />.  The histidine residues position the metal ions 6.4 Å apart<ref name="Bai" />.
+The ligand binding pocket is a narrow tunnel that extends approximately 24 Å into the mostly hydrophobic interior of the protein. The ligand is stabilized by bending into a kinked conformation which creates a tight fit in the binding pocket tunnel, and by a hydrogen bond that occurs between the <scene name='87/877552/W258/3'>W 258</scene> side chain and the acyl carbonyl<ref name="Bai" />. The kink in the tunnel is formed by the conserved residues, <scene name='87/877552/Desaturation_site/10'>T 257 and W 149</scene> which are stabilized by the hydrogen bond shared with Q143<ref name="Bai" />. There are <scene name='87/877552/Substrate_orientation_w_fe/5'>two Fe2+ ions</scene> that interact with the substrate; the Fe2+ ions are coordinated by <scene name='87/877552/Histidine_coordination/8'>9 invariant histidine residues</scene>.  <scene name='87/877552/Substrate_oreintation_fe_90deg/3'>When rotated 90 degrees</scene> the ligand is seen to be in a eclipsed position, indicating it is in its post-reaction form.  One metal ion is coordinated by 4 histidines residues and a water molecule, and the other metal ion is coordinated by 5 histidine residues<ref name="Bai" />.  The histidine residues position the metal ions 6.4 Å apart<ref name="Bai" />.
 === Desaturation Site ===
@@ Line 50: / Line 50: @@
 === Active Site Cap ===
-The two conserved residues of the active site cap are <scene name='87/877552/Active_site_cap/6'>Y 104 and G 287</scene>.  These two residues form a hydrogen bond creating a ridged barrier at the end of the active site to keep the ligand from moving during the reaction<ref name="Bai" />.  The active site cap is also used in determining the substrate length when entering the active site<ref name="Bai" />.
+The two conserved residues of the active site cap are <scene name='87/877552/Active_site_cap/6'>Y 104 and G 287</scene>.  These two residues form a hydrogen bond creating a rigid barrier at the end of the active site to keep the ligand from moving during the reaction<ref name="Bai" />.  The active site cap is also used in determining the substrate length when entering the active site<ref name="Bai" />.
 === Catalytic Molecule ===