The interaction between two paramagnetic metal centers, a [3Fe-4S](+) cluster and a [NiFe] center, is investigated in the hydrogenase from Desulfovibrio vulgaris Miyazaki F by pulsed ELDOR (electron-electron double resonance). The distance between the metal centers is known from X-ray crystallography. The experimental dipolar spin-spin interaction deviates from the value expected for two point-dipoles located at the centers of the metal clusters. An extended spin-coupling model accounting for the spin coupling in the [3Fe-4S](+) cluster yields the observed interaction under the assumption of a particular magnetic coupling scheme for the three Fe ions. These results demonstrate that pulsed ELDOR can be used to gain insight into the inner structure of a multinuclear metal cluster.