Journal:Acta Cryst D:S2059798323004175

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molecule bound with Asn37</scene>. A hydrogen bond is formed the main chain carbonyl oxygen of Ile16 and N2 atom of NAG (white dotted line). <scene name='96/965740/Nag_molecules_n65/2'>Two NAG molecules bound with Asn65</scene>. A hydrogen bond is formed between OD1 atom of <scene name='96/965740/Nag_molecules_n65/6'>Asp420 and N2 atom of NAG</scene> (white dotted line). A CH-pi interaction is formed between the <scene name='96/965740/Nag_molecules_n65/5'>phenyl group of Tyr595 and the D-glycopyranose ring of NAG</scene>.
molecule bound with Asn37</scene>. A hydrogen bond is formed the main chain carbonyl oxygen of Ile16 and N2 atom of NAG (white dotted line). <scene name='96/965740/Nag_molecules_n65/2'>Two NAG molecules bound with Asn65</scene>. A hydrogen bond is formed between OD1 atom of <scene name='96/965740/Nag_molecules_n65/6'>Asp420 and N2 atom of NAG</scene> (white dotted line). A CH-pi interaction is formed between the <scene name='96/965740/Nag_molecules_n65/5'>phenyl group of Tyr595 and the D-glycopyranose ring of NAG</scene>.
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Analysis of solvent tunnels highlighted the amino acids that are crucial for proton transfer into the trinuclear copper site. <scene name='96/965740/Ttlmco1_tunnels/10'>Graphical representation of TtLMCO1 tunnels</scene>. T2 and T3 tunnels are shown as red and blue spheres, respectively. Copper ions are shown as brown spheres and side chains of residues forming the tunnels as shown as wheat sticks. Docking simulations with substrates that are oxidized by ''Tt''LMCO1 provide evidence that substrate specificity of these metallo-proteins is not exclusively related to their redox potential but also on the architecture of the binding site and the side chain flexibility of specific amino acids. Also, our analysis points to a potential biological role of these biocatalysts, involving the production of pigments and other bioactive compounds in their natural hosts. <scene name='96/965740/Test/3'>TextToBeDisplayed</scene>
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Analysis of solvent tunnels highlighted the amino acids that are crucial for proton transfer into the trinuclear copper site. <scene name='96/965740/Ttlmco1_tunnels/10'>Graphical representation of TtLMCO1 tunnels</scene>. T2 and T3 tunnels are shown as red and blue spheres, respectively. Copper ions are shown as brown spheres and side chains of residues forming the tunnels as shown as wheat sticks. Docking simulations with substrates that are oxidized by ''Tt''LMCO1 provide evidence that substrate specificity of these metallo-proteins is not exclusively related to their redox potential but also on the architecture of the binding site and the side chain flexibility of specific amino acids. Graphical representation of docking simulation results for TtLMCO1:
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*<scene name='96/965740/Binding_pocket/6'>Ball-and-stick representation of the substrate
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binding pocket of TtLMCO1 with L-ascorbic acid</scene>.
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**<jmol>
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<jmolLink>
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<script> select (atomno=8866),(atomno=5677),(atomno=8862),(atomno=5678),(atomno=5851),(atomno=8279),(atomno=8863),(atomno=6993),(atomno=6994),(atomno=4642),(atomno=4645),(atomno=8864),(atomno=2475); selectionHalos ON;
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delay 0.5; selectionHalos OFF;</script>
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<text>Hydrogen bonds.</text>
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</jmolLink>
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</jmol>
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**<jmol>
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<jmolLink>
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<script> select (atomno=8861),(atomno=9003),(atomno=9000),(atomno=2468); selectionHalos ON;
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delay 0.5; selectionHalos OFF;</script>
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<text>Hydrophobic interactions.</text>
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</jmolLink>
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</jmol>
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*<scene name='96/965740/Binding_pocket/7'>Ball-and-stick representation of the substrate binding pocket of TtLMCO1 with 2,6-DMP</scene>.
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**<jmol>
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<jmolLink>
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<script> select (atomno=8872),(atomno=5678),(atomno=5851),(atomno=8279),(atomno=8856),(atomno=8860); selectionHalos ON;
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delay 0.5; selectionHalos OFF;</script>
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<text>Hydrogen bonds.</text>
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</jmolLink>
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</jmol>
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**<jmol>
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<jmolLink>
 +
<script> select (atomno=8873),(atomno=9003),(atomno=9001); selectionHalos ON;
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delay 0.5; selectionHalos OFF;</script>
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<text>Hydrophobic interactions.</text>
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</jmolLink>
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</jmol>
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**<jmol>
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<jmolLink>
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<script> select (atomno=9008),(atomno=9007); selectionHalos ON;
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delay 0.5; selectionHalos OFF;</script>
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<text>Pi-pi interactions.</text>
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</jmolLink>
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</jmol>
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*<scene name='96/965740/Binding_pocket/10'>Ball-and-stick representation of the substrate binding pocket of TtLMCO1 with ferulic acid.</scene>
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**<jmol>
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<jmolLink>
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<script> select (atomno=8877),(atomno=8879),(atomno=5678),(atomno=5851),(atomno=8279); selectionHalos ON;
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delay 0.5; selectionHalos OFF;</script>
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<text>Hydrogen bonds.</text>
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</jmolLink>
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</jmol>
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**<jmol>
 +
<jmolLink>
 +
<script> select (atomno=8857),(atomno=5818),(atomno=9002); selectionHalos ON;
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delay 0.5; selectionHalos OFF;</script>
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<text>Hydrophobic interactions.</text>
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</jmolLink>
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</jmol>
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**<jmol>
 +
<jmolLink>
 +
<script> select (atomno=9009),(atomno=9007); selectionHalos ON;
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delay 0.5; selectionHalos OFF;</script>
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<text>Pi-pi interactions.</text>
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</jmolLink>
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</jmol>
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*<scene name='96/965740/Binding_pocket/11'>Spacefill representation of the substrate binding pocket of TtLMCO1 with L-ascorbic acid</scene>. {{Template:ColorKey_Hydrophobic}}, {{Template:ColorKey_Polar}}
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*<scene name='96/965740/Binding_pocket/12'>Spacefill representation of the substrate binding pocket of TtLMCO1 with 2,6-DMP</scene>.
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*<scene name='96/965740/Binding_pocket/13'>Spacefill representation of the substrate binding pocket of TtLMCO1 with ferulic acid</scene>.
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Also, our analysis points to a potential biological role of these biocatalysts, involving the production of pigments and other bioactive compounds in their natural hosts.
<b>References</b><br>
<b>References</b><br>

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Alexander Berchansky, Jaime Prilusky

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