Fig. 8. Water networks in the active site are displaced and used by fragments for bridging interactions.

(A) Water networks in the apo enzyme (P4₃ crystal form). Waters are shown as blue spheres, with electron density contoured at 5.0 σ (blue mesh) and 1.5 σ (blue surface). Hydrogen bonds are shown as dashed lines (distances are 2.6 to 3 Å). (B) Water networks in the Mac1-ADPr complex. ADPr is shown as cyan sticks. Conformational changes upon ADPr binding are highlighted with black arrows. (C) Comparison of crystallographic B-factors of water molecules in the catalytic site and adenosine site. The range and 95% confidence interval are shown. (D) Examples of the role of water networks in fragment binding. Left: ZINC340465 (PDB 5RSV) forms a single hydrogen bond to the protein (green dashed line) but forms five hydrogen bonds via water molecules. Right: Although few fragments of hydrogen bond directly to the backbone oxygen of Ala¹⁵⁴, several fragments interact with this residue via bridging water molecules (red dashed line) including ZINC89254160_N3 (PDB 5RSJ). (E) Plot showing all water molecules that lie within 3.5 Å of a noncarbon fragment atom. Water molecules are shown as blue spheres, with the major clusters circled. The cluster highlighted with a red arrow bridges fragments and the Ala¹⁵⁴ backbone oxygen.