Mg2+ ions block N-methyl-D-aspartate (NMDA) channels by entering the pore from either the extracellular or the cytoplasmic side of the membrane in a voltage-dependent manner. We have used these two different block phenomena to probe the structure of the subunits forming NMDA channels. We have made several amino acid substitutions downstream of the Q/R/N site in the TMII region of both NR1 and NR2A subunits. Mutant NR1 subunits were coexpressed with wild-type NR2A subunits and vice versa in Xenopus oocytes. We found that individually mutating the first two amino acid residues downstream to the Q/R/N site affects mostly the block by external Mg2+. Mutations Recently, a series of biochemical studies (14-17) have suggested that, instead of traversing the membrane, the region labeled TMII forms a loop, dipping in and out of the membrane from the internal side. Such pore loops have become a common structural motif in the case of the voltage-gated ion channels since they were first proposed for the Shaker potassium channel by Yellen et al. (18). They used tetraethylammonium (TEA), known to block potassium channels from both sides of the membrane, to probe the structure of a 20 amino acid stretch in the linker between the membrane spanning domains S5 and S6. Mutations on both ends of this "P region" were found to affect only the block by external TEA, whereas a mutation in the center of the P region selectively affected the internal TEA block.In the present study, we have used a similar approach to test whether the mutation of certain amino acid residues downstream of the Q/R/N site affects differentially the blocks produced by internal and external Mg2+. Again, the results suggest that permeation in the channel involves a pore loop.N-methyl-D-aspartate (NMDA) receptors form cation selective ion channels at excitatory synapses and can be distinguished from other glutamate-gated ion channels by their pharmacological and biophysical properties (1). The voltage dependence of the NMDA receptor channel, which is thought to play an important role in many physiological and pathophysiological processes, results from an extracellular Mg2+ block (2, 3), which increases markedly with hyperpolarization due to the binding of Mg2+ deep inside the pore (4, 5). Mg2+ ions can also block the NMDA channel from the cytoplasmic surface (6). Like the external Mg2+ block, the internal Mg2+ block is voltage dependent, but it increases with depolarization and the unblocking rate of internal Mg2+ is two orders of magnitude faster than that of external Mg2+. It has been proposed that external and internal Mg2+ bind to two different blocking sites within the channel pore (6, 7).The genes coding for the subunits of the NMDA receptor have recently been cloned, offering new opportunities for structure function studies (8-10). Functional channels are composed of the NR1 subunit and one or more members of the NR2 family. Site-directed mutagenesis rapidly identified an asparagine residue (N) as playing a key role in the external Mg2+ block (11...