Fig. 2.
Conformation of palmitic acid in the chCD1–2-binding groove. (A) Side view of the final 2FoFc map (Fo, observed structure factors; Fc, calculated structure factors) map drawn as a blue mesh around the palmitic acid (yellow) and contoured at 0.8σ. The α2 helix is removed for clarity. Note that the ligand electron density is fairly weak, possibly reflecting less than full occupancy of the palmitate. One hydrogen bond (blue dashed line, 2.9Å) is formed between Arg-82 and the carboxyl group of palmitic acid. Several groove-forming residues are depicted as gray sticks. Met-74 (M74) and Val-75 (V75) are part of the A′ loop (see Fig. 1). (B) Top view (TCR view), looking down onto the slightly transparent molecular surface of the groove. Electrostatic surface potentials were calculated using the APBS program (49). Red is electronegative, and blue is electropositive (−30 to +30 kT/e). Important residues lining the entrance to the groove are labeled. The positive charge of Arg-82 (R82) is ideally situated to neutralize the negative charge of the carboxyl group of the bound palmitate.