FIGURE 4.

Connection degree in the PcrA-DNA complex. The connection degree measures the number of neighbors within a cut-off distance for all residues and prosthetic groups in a protein. For the PcrA-DNA complex in its substrate (ATP bound) and its product (no ATP/ADP bound) state, a residue network was constructed with its nodes composed of C_α atoms from amino acids, as well as phosphorus (P) atoms from nucleotides, as explained in the text. PcrA-DNA complexes are shown in cartoon (protein) and licorice (DNA) format, colored according to the connection degree: blue represents a high degree whereas red represents a low degree. It can be recognized that the highest connection degree (123 connection degree), corresponding to the most densely connected region, occurs at the site of ATP-γ phosphate in the substrate state. Histograms displaying the distribution of the connection degrees for the PcrA-DNA complexes in both substrate and product state are also shown.