User:Cameron Evans/Sandbox 1: Difference between revisions

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GluDH makes non-coavalent and specific contacts with its substrates, cofactors and allosteric inhibitors.

~~For example, glutamate~~ and α-KG both bind via hydrogen bonding within the catalytic cleft between the two distinct clamping domains (~~see description above~~ in ~~prokaryotes)~~.

Glutamate and α-KG both bind via hydrogen bonding within the catalytic cleft between the two distinct clamping domains. Both make contact with K126, K90, S381, R211, and N349. However, α-KG binding is thought to be stabilized also by N374 (through a water molecule) and K114 and Glu by K114 in a different crystal structure.

~~Both make contact~~ with ~~K126~~, ~~K90~~, ~~S381~~, ~~R211~~, and ~~N349~~. ~~However~~, ~~α-KG binding is thought~~ to ~~be stabilized also by N374 (through a water molecule) and K114 and Glu by K114~~ in ~~a different crystal structure~~.

NADH, as it binds within the to the catalytic cleft, makes specific hydrogen bonds with D168, S170, E275, S276, N349, A326 and S327 in all crystal structures. Q250 contacts both NADPH and NADH, but not NAD+. Instead Q330 makes a similar contact to NAD+ in that region.

NADH, as it binds within the to the catalytic cleft, makes specific hydrogen bonds with D168, S170, E275, S276, N349, A326 and S327 in all crystal structures. Q250 contacts both NADPH and NADH, but not NAD+. Instead Q330 makes a similar contact to NAD+ in that region. <scene name='User:Cameron_Evans/Sandbox_1/Mammal_ligands_without_glu/2'>This scene~~</scene> roughly illustrates~~ the ~~binding pocket in which the dinucleotide cofactor sits. Directly above the cofactor is evident the space where~~ Glu ~~would sit~~.<~~ref name=1hwxyz~~ />

<scene name='User:Cameron_Evans/Sandbox_1/Mammal_ligands_without_glu/3'>This scene shows all of the specific interactions of boGluDH with Glu and NADH. </scene>

===Allosteric Interactions===

@@ Line 72: / Line 72: @@
 GluDH makes non-coavalent and specific contacts with its substrates, cofactors and allosteric inhibitors.
-For example, glutamate and α-KG both bind via hydrogen bonding within the catalytic cleft between the two distinct clamping domains (see description above in prokaryotes).
+Glutamate and α-KG both bind via hydrogen bonding within the catalytic cleft between the two distinct clamping domains. Both make contact with K126, K90, S381, R211, and N349. However, α-KG binding is thought to be stabilized also by N374 (through a water molecule) and K114 and Glu by K114 in a different crystal structure.
-Both make contact with K126, K90, S381, R211, and N349. However, α-KG binding is thought to be stabilized also by N374 (through a water molecule) and K114 and Glu by K114 in a different crystal structure.
+NADH, as it binds within the to the catalytic cleft, makes specific hydrogen bonds with D168, S170, E275, S276, N349, A326 and S327 in all crystal structures. Q250 contacts both NADPH and NADH, but not NAD+. Instead Q330 makes a similar contact to NAD+ in that region.
-NADH, as it binds within the to the catalytic cleft, makes specific hydrogen bonds with D168, S170, E275, S276, N349, A326 and S327 in all crystal structures. Q250 contacts both NADPH and NADH, but not NAD+. Instead Q330 makes a similar contact to NAD+ in that region. <scene name='User:Cameron_Evans/Sandbox_1/Mammal_ligands_without_glu/2'>This scene</scene> roughly illustrates the binding pocket in which the dinucleotide cofactor sits. Directly above the cofactor is evident the space where Glu would sit.<ref name=1hwxyz />
+<scene name='User:Cameron_Evans/Sandbox_1/Mammal_ligands_without_glu/3'>This scene shows all of the specific interactions of boGluDH with Glu and NADH. </scene>
 ===Allosteric Interactions===