The ternary complex of Escherichia coli adenylate kinase (ECAK) with its substrates adenosine monophosphate (AMP) and Mg-ATP, which catalyzes the reversible transfer of a phosphoryl group between adenosine triphosphate (ATP) and AMP, was studied using molecular dynamics. The starting structure for the simulation was assembled from the crystal structures of ECAK complexed with the bisubstrate analog diadenosine pentaphosphate (AP5A) and of Bacillus stearothermophilus adenylate kinase complexed with AP5A, Mg2+, and 4 coordinated water molecules, and by deleting 1 phosphate group from AP5A. The interactions of ECAK residues with the various moieties of ATP and AMP were compared to those inferred from NMR, X-ray crystallography, site-directed mutagenesis, and enzyme kinetic studies. The simulation supports the hypothesis that hydrogen bonds between AMP's adenine and the protein are at the origin of the high nucleoside monophosphate (NMP) specificity of AK. The ATP adenine and ribose moieties are only loosely bound to the protein, while the ATP phosphates are strongly bound to surrounding residues. The coordination sphere of Mg2+, consisting of 4 waters and oxygens of the ATP β- and γ-phosphates, stays approximately octahedral during the simulation. The important role of the conserved Lys13 in the P loop in stabilizing the active site by bridging the ATP and AMP phosphates is evident. The influence of Mg2+, of its coordination waters, and of surrounding charged residues in maintaining the geometry and distances of the AMP α-phosphate and ATP β- and γ-phosphates is sufficient to support an associative reaction mechanism for phosphoryl transfer. Proteins 2005. © 2004 Wiley-Liss, Inc.