Transcription terminators trigger the dissociation of RNA polymerase elongation complexes and the release of RNA products at specific DNA template positions. The mechanism by which these signals alter the catalytic properties of the highly processive elongation transcription complexes is unclear. Here, we propose that intrinsic terminators impede transcript elongation by promoting a misarrangement of reactants and catalytic effectors within the active site of T7 RNA polymerase. In effect, a productive catalytic coordination network can be readily restored when Mg2+ effectors are replaced by the more “relaxing” Mn2+ ions, leading to transcript elongation beyond the termination point. This Mn2+-dependent incorporation of additional nucleotides occurs within unstable transcription complexes that ultimately dissociate at positions downstream from the normal termination site. Thus, Mn2+ coordination in the polymerase active center can compensate for the disruptive but limited perturbation of the catalytic arrangement of reactants that accompany larger structural changes of the transcription complex triggered by termination signals. These results provide evidence that the geometry of the catalytic coordination network within the active site is a crucial component of RNA polymerase catalysis. Limited variations of the active site architecture are sufficient to confer tight control of the RNA polymerase function and, thus, may ubiquitously benefit signals regulating transcription.