Binding of glutamate to ionotropic glutamate receptors occurs within a bilobate binding pocket built from conserved S1 and S2 domains. Using the crystal structure of the binding region of the (RS)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)-propionic acid (AMPA)-selective GluR2 subunit, we identified determinants of ligand selectivity and efficacy within the glutamate-binding pocket of the NR2B subunit of the N-methyl-D-aspartate (NMDA) receptor by site-directed mutagenesis. Electrophysiological analyses of mutated NR2B polypeptides revealed drastic effects on the affinity of L-glutamate but not of the co-agonist glycine. With seven out of 19 substitutions, we found differences in the potency of the full agonist L-glutamate and the partial agonist NMDA. In particular, substitutions located at the interface between the S1 and S2 domains resulted in changes of agonist efficacy, suggesting a role in transducing the ligand-binding signal. Inhibition by the competitive antagonist D-AP5 was highly sensitive to replacement of residues involved in stabilization of the closed conformation of the binding pocket, consistent with antagonists preventing closure of the binding pocket. In addition, we identified residues predicted to be important for liganding the methyl group of NMDA. Collectively our data describe specific side chain interactions that determine ligand efficacy and pharmacology at the glutamate site of the NMDA receptor.