Calmodulin: PDB 1CDM

Structure of bovine brain calmodulin, with the calmodulin-binding segment (target sequence) of calmodulin-dependent protein kinase II, solved by W. Meador & F. Quiocho, 1994.

Recommended display options:

Color chain to distinguish calmodulin from its target peptide.
Display as
ribbons or cartoon to show the largely a-helical structure of both proteins.
Note how calmodulin (blue) wraps around the target peptide (green).

Select hetero-ligand, display as spacefill, & color CPK to visualize Ca++.
Question: How many Ca++ ions are bound to calmodulin?
Drag the image, and observe the helix-loop-helix motif of each Ca++ binding site.

Type into the command line select met*a, enter, and then change display to spacefill, with color CPK, to view the cluster of methionine residues that forms a hydrophobic pocket at each end of calmodulin.
leu299 and change its display to view the position of a conserved hydrophobic residue in the target protein. This residue, which may be either Trp or Leu, is essential for sensitivity of some kinases to calmodulin.  

Now, to get a clearer view of one Ca++ binding site, select all, and then hide selected.
Type into the command line
select 1-40a, enter, and display as ribbons.
ca1 (calcium #1) & display as spacefill
select 20-26a, display as ball & stick, and color CPK. Hold down the shift while left-dragging to zoom in.

Identify amino acids that interact with Ca++. (Hint: May include anionic amino acids above).
Question: What atoms of what chemical groups interact with Ca++?

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