The complete three-dimensional structure of the active site region of the human immunodeficiency virus type 1 (HIV-1) integrase (IN) is not unambiguously known. This region includes a flexible loop comprising residues 141-148 and the N-terminal portion of the helix alpha-4, which contains E152, the third catalytic residue, and Y143, which plays a secondary role in catalysis. Relatively high B-factors exist for most of the residues in the aforementioned region. The HIV-1 IN belongs to the polynucleotidyl transferase superfamily, whose members have been proposed to use two divalent metal ions for catalysis. Although only the position of the first metal ion has been determined crystallographically for the HIV-1 IN, we recently have proposed a binding site for the second metal ion. Based on this information, we have performed two 500-psec molecular dynamics simulations of the catalytic domain of the HIV-1 IN containing two Mg(2)+ ions. In one of the simulations, we included a dianionic phosphate group (HPO(4)(2)-) in the active site to mimic a portion of the DNA backbone of a substrate for the integration reaction. Electrostatics calculations and ionization state predictions were carried out on representative structures taken from the molecular dynamics simulations. Different conformational behaviors of the enzyme were observed, depending upon whether two Mg(2)+ ions were bound or two Mg(2)+ ions plus phosphate. The electrostatic calculations performed on the dynamical structures provide a further refinement about which regions of the catalytic domain of the HIV-1 IN may be involved in the DNA binding.