Sandbox Reserved 895: Difference between revisions

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The main tunnel and its interior cavity contain two regions of strong residual electron density that is not accounted for by the atoms located in the protein. This suggest that the substrate would interact with these electron dense regions. Shown in '''Figure 5B''', the first electron dense region is linear with a triangular shape on one end, suggesting the presence of a linear molecule containing a terminal functional group with trigonal planar geometry (such as an ester in the retinyl esters or a carboxylic acid functional group in fatty acids). The triangular portion is in proximity to the iron ion and when positioned correctly fulfills one or both open coordination sites set forth by the octahedral geometry while the linear portion occupies the main tunnel. Also shown in '''Figure 5B''', the second electron dense region is linear and bent in shape which is located within the interior cavity of the protein. This region could be represented by a bound PEG 200 molecule or a string of partially ordered water molecule. However the electron dese region cannot accommodate an longer compound such as (Hydroxyethyloxy)tri(ethyloxy)octane (C8E4).

[[Image:RPE65_Figure5_Binding_Pocket.jpg|thumb|center|512 px|alt=Figure 5: RPE65 Binding Pocket| '''Figure 5:''' RPE65 iron ion binding pocket coordination sites (A) Stereoview of the iron cofactor and its ligand. Shown in orange is the iron ion, shown in red is a water molecule. The bond length interactions are shown in angstroms from the iron atom. (B) Stereoview of the residual electron density from the RPE65 active site. The green mesh represents an unbiased electron density map contoured at 3.5 σ. The numbers next to teh dash lines indicates bond length interactions measured in angstroms. <ref> DOI 19805034 </ref>]]

=== ''' [1.2.3] Proposed Enzymatic Mechanism of RPE65''' ===

Sandbox Reserved 895: Difference between revisions

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 The main tunnel and its interior cavity contain two regions of strong residual electron density that is not accounted for by the atoms located in the protein. This suggest that the substrate would interact with these electron dense regions. Shown in '''Figure 5B''', the first electron dense region is linear with a triangular shape on one end, suggesting the presence of a linear molecule containing a terminal functional group with trigonal planar geometry (such as an ester in the retinyl esters or a carboxylic acid functional group in fatty acids). The triangular portion is in proximity to the iron ion and when positioned correctly fulfills one or both open coordination sites set forth by the octahedral geometry while the linear portion occupies the main tunnel. Also shown in '''Figure 5B''', the second electron dense region is linear and bent in shape which is located within the interior cavity of the protein. This region could be represented by a bound PEG 200 molecule or a string of partially ordered water molecule. However the electron dese region cannot accommodate an longer compound such as (Hydroxyethyloxy)tri(ethyloxy)octane (C8E4).
-[[Image:RPE65_Figure5_Binding_Pocket.jpg|thumb|center|512 px|alt=Figure 5: RPE65 Binding Pocket| '''Figure 5:''' RPE65 Binding Pocket <ref> DOI 19805034 </ref>]]
+[[Image:RPE65_Figure5_Binding_Pocket.jpg|thumb|center|512 px|alt=Figure 5: RPE65 Binding Pocket| '''Figure 5:''' RPE65 iron ion binding pocket coordination sites (A) Stereoview of the iron cofactor and its ligand. Shown in orange is the iron ion, shown in red is a water molecule. The bond length interactions are shown in angstroms from the iron atom. (B) Stereoview of the residual electron density from the RPE65 active site. The green mesh represents an unbiased electron density map contoured at 3.5 σ. The numbers next to teh dash lines indicates bond length interactions measured in angstroms. <ref> DOI 19805034 </ref>]]
 === ''' [1.2.3] Proposed Enzymatic Mechanism of RPE65''' ===