Coagulation Factor IX is positioned at the merging point of the intrinsic and extrinsic blood coagulation cascade. Activated Factor IX (FIXa) serves to trigger the amplification of coagulation via formation of the Xase complex that involves Factor IXa, its substrate; Factor X (FX), and cofactor Factor VIIIa (FVIIIa) on the surface of activated platelets. Within the Xase complex the substrate turnover by Factor IXa is dramatically enhanced a million-fold, however, the mechanistic and structural basis remains poorly understood. We have combined a multi-faceted approach using enzymatic, biophysical and crystallographic methods to evaluate a key set of activity enhanced FIXa variants. We demonstrate a delicately balanced, bidirectional network driven by essential molecular interactions in multiple regions of the Factor IXa molecule, most interestingly through long range communication through the Ile212-Ile213 motif unique to FIXa. The network further consists of compensatory brakes (Tyr99, Phe174, Gln192) and accelerators (V16, I213) which together allow for a subtle fine tuning of enzymatic activity. When compared across methodologies, we observed that trends in enzymatic activity were paralleled by thermal stability measurements and identified a positive correlation between increased catalytic activity and increased thermal stability of Factor IXa variants. It therefore becomes reasonable to suggest that in the native FIXa molecule, these structural elements are likely modulated by the physiological cofactor and substrate in a positive manner to achieve the dramatic augmentation in Factor IXa activity observed in the Xase complex.