Sandbox Reserved 1125: Difference between revisions

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Moreover, this pocket is rich in hydrophobic amino acids, what is suitable for binding to the substrates of MMP-8.
Moreover, this pocket is rich in hydrophobic amino acids, what is suitable for binding to the substrates of MMP-8.


[[Image:CA_pocket_interaction.gif | thumb|CA996 pocket interaction]]
==== Ca2+ interactions ====
==== Ca2+ interactions ====
[[Image:CA_pocket_interaction.gif | thumb|CA996 pocket interaction]]This enzyme binds 3 Ca ions, 2 of them in the catalytic domain, which are packed against the top of the beta sheet and have mostly a structural function, stabilizing the catalytic domain.<ref name="X-ray"/>
This enzyme binds 3 Ca ions, 2 of them in the catalytic domain, which are packed against the top of the beta sheet and have mostly a structural function, stabilizing the catalytic domain.<ref name="X-ray"/>
The residues involved in the Ca996 interactions (coordinate bonds) are <scene name='71/719866/Ca2_interactions/3'>two Gly residues (169 and 171) next to two Asp residues (137 and 173)</scene>.
The residues involved in the Ca996 interactions (coordinate bonds) are <scene name='71/719866/Ca2_interactions/3'>two Gly residues (169 and 171) next to two Asp residues (137 and 173)</scene>.


==== Zn2+ interactions ====
The zinc-binding motif HEXGHXXGXXH presents in the catalytic domain is characteristic for the protease activity of MMP-8.
===== Zn999 : the catalytic zinc =====
It is involved in the catalytic activity and is situated at the bottom of the active-site. This ion is penta-coordinated with: His197, His201 and His207 of MMP-8 and probably (according to the mechanism model described bellow) with a Gly residue of the substrate and a water molecule. On this <scene name='71/719866/Zn999_interactions/5'>link</scene> you can only see the 3 His of MMP-8 with the Zn999.
[[Image:ZN pocket interaction.gif | thumb|ZN998 pocket interaction]]
===== Zn998 : the structural zinc =====
The residues involved in the Zn998 interactions are <scene name='71/719866/Zn998/2'>an Asp residue (149) next to three His residues (147, 162 and 175)</scene>. The glutamic acid adjacent to the first histidine is essential for catalysis. It should be noted that scientists were unable to exchange or remove this Zinc in their crystals, which is suggesting that there is a tight interaction with MMP-8.<ref name="X-ray"/>




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==== Zn2+ interactions ====
The zinc-binding motif HEXGHXXGXXH presents in the catalytic domain is characteristic for the protease activity of MMP-8.
[[Image:ZN pocket interaction.gif | thumb|ZN998 pocket interaction]]
===== Zn999 : the catalytic zinc =====
It is involved in the catalytic activity and is situated at the bottom of the active-site. This ion is penta-coordinated with: His197, His201 and His207 of MMP-8 and probably (according to the mechanism model described bellow) with a Gly residue of the substrate and a water molecule. On this <scene name='71/719866/Zn999_interactions/5'>link</scene> you can only see the 3 His of MMP-8 with the Zn999.
===== Zn998 : the structural zinc =====
The residues involved in the Zn998 interactions are <scene name='71/719866/Zn998/2'>an Asp residue (149) next to three His residues (147, 162 and 175)</scene>. The glutamic acid adjacent to the first histidine is essential for catalysis. It should be noted that scientists were unable to exchange or remove this Zinc in their crystals, which is suggesting that there is a tight interaction with MMP-8.<ref name="X-ray"/>


=== Hinge domain ===
=== Hinge domain ===
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