The Active Site of Malate Synthase

    The active site of E. coli malate synthase G contains a Magnesium ion coordinated to two carboxylate groups --
Aspartate 455 and Glutamate 427 (numbering of the E.coli isozyme G; aka MSG).  In the crystal structure solved to 2.0 Angstroms resolution, a molecule of glyoxylate was observed coordinated to this Mg²⁺, as shown below.  The glyoxylate  molecule is also held in place by two hydrogen bonds to the amino nitrogens at the N-terminus of an a-helix (green), and by another hydrogen bond donated from Arginine 338 to the aldehyde carbonyl oxygen.  Two water molecules complete the octahedral coordination sphere of the magnesium ion.
    We believe that the free terminal nitrogen of the guanidinium group of Arg338, activates the carbonyl oxygen of the thioester bond within  the second substrate acetyl-CoA, while Aspartate 631 acts as the catalytic base, deprotonating the terminal methyl group to form the enolate ion, which can collapse to attack the carbonyl carbon of glyoxylate to form a carbon-carbon bond, resulting in a malyl-Coenzyme A intermediate.  This intermediate is then hydrolyzed to form the products: malate and coenzyme A.  For details,  see the biochemistry paper and pdb links on the previous page.  You can see the definition of the electron density for the magnesium binding site in an "omit map".