Conformational changes in citrate synthase

Here we can see open and closed conformation on the corresponding picture. The C atoms of the small domain in each subunit of the enzyme are green, and those of the large domain are purple. N, O, and S atoms in both domains are blue, red, and yellow. Upon binding oxaloacetate, the smaller domain undergoes an 18 degree rotation relative to the larger domain, which closes the cleft. This generates the acetyl CoA binding site. 

The X-ray structure of hen egg white (HEW) lysozyme

(a) The polypeptide chain is show with a bound (NAG)6 substrate (green). The positions of the backbone Ca atoms are indicated together with the side chains of the catalytic residues Asp 52 and Glu 35 (red) and those that form disulfide bonds (yellow). The substrate’s sugar rings are designated A, at its nonreducing end (right), through F, at its reducing end (left). Lysozyme catalyzes the hydrolysis of the glycosidic bond between residues D and E. Rings A, B, and C are observed in the X-ray structure of the complex of (NAG)3 with lysozyme; the positions of rings D, E, and F were inferred from model building studies.

 

(b) A ribbon diagram of lysozyme highlighting the protein’s secondary structure and indicating the positions of its catalytically important side chains.

(c) A computer-generated model showing the protein’s molecular envelope (purple) and Ca backbone (blue). The side chains of the catalytic residues, Asp 52 (above) and Glu 35 (below), are colored yellow. Note the enzyme’s prominent substrate-binding cleft.

The active site of human carbonic anhydrase

In the drawing, the light gray ligand to the Zn+2 indicates the probable fifth Zn+2 coordination site (not shown in 3D window). In the 3D window on the left, a Zn2+ ion and a water molecule are represented by magenta and red spheres, respectively. Arrow points toward the opening of the active site cavity. Spacefill representation is used to illustrate both solvent and reactant accessability to the active site. 

Glyceraldehyde-3-phosphate dehydrogenase

The two-domain protein glyceraldehyde-3-phosphate dehydrogenase. The first domain (red) binds NAD+ (yellow), and the second domain (green) binds glyceraldehyde-3-phosphate (not shown)

Substrate-induced conformational change on example of yeast hexokinase

Here we see a pace-filling model of a hexokinase subunit showing the prominent bilobal appearance of the free enzyme (the C atoms in the small lobe are shaded green, and those in the large lobe are light gray; the N and O atoms are blue and red).

While here is a model of the hexokinase complex with glucose (purple); the lobes have swung together to engulf the substrate.