Sandbox Reserved 1125: Difference between revisions
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=== Ca2+ interactions === | === Ca2+ interactions === | ||
[[Image:CA_pocket_interaction.gif | thumb| | [[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 mostly have a structural function, stabilizing the catalytic domain. | ||
The residues involved in the Ca996 interactions (coordinate bonds) are <scene name='71/719866/Ca2_interactions/1'>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/1'>two Gly residues (169 and 171) next to two Asp residues (137 and 173)</scene>. | ||
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==== Zn999 : the catalytic zinc ==== | ==== Zn999 : the catalytic zinc ==== | ||
It is involved in the catalytic activity and is situated at the bottom of the active-site. In a publication [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC394940/?page=2] which studies the catalytic domain of MMP8 thanks to the Pro-Leu-Gly-hydroxylamine inhibitor, this ion is penta-coordinated with: His197, His201 and His207 of MMP8 and with the carbonyl and the hydroxyl oxygen of the hydroxamic acid moiety of the inhibitor. On this <scene name='71/719866/Zn999_interactions/2'>link</scene> you can only see the 3 His of MMP8 with the Zn999. The fourth ligand of the catalytic zinc is a water molecule. | It is involved in the catalytic activity and is situated at the bottom of the active-site. In a publication [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC394940/?page=2] which studies the catalytic domain of MMP8 thanks to the Pro-Leu-Gly-hydroxylamine inhibitor, this ion is penta-coordinated with: His197, His201 and His207 of MMP8 and with the carbonyl and the hydroxyl oxygen of the hydroxamic acid moiety of the inhibitor. On this <scene name='71/719866/Zn999_interactions/2'>link</scene> you can only see the 3 His of MMP8 with the Zn999. The fourth ligand of the catalytic zinc is a water molecule. | ||
[[Image:ZN pocket interaction.gif | thumb| | [[Image:ZN pocket interaction.gif | thumb|ZN999 pocket interaction]] | ||
==== Zn998 : the structural zinc ==== | ==== Zn998 : the structural zinc ==== | ||
The residues involved in the Zn998 interactions are <scene name='71/719866/Zn998/1'>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's good to know that W Bode and al.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC394940/?page=2] were unable to exchange or remove this Zinc in their crystals, which is suggesting that there is a tight interaction with MMP-8. | The residues involved in the Zn998 interactions are <scene name='71/719866/Zn998/1'>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's good to know that W Bode and al.[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC394940/?page=2] were unable to exchange or remove this Zinc in their crystals, which is suggesting that there is a tight interaction with MMP-8. | ||
