UgpG catalytic cavity. (a) UgpG transparent solvent-accessible surface around the catalytic cavity, with bound G1P (ball-and-stick) and catalytic H-bonding residues (sticks). On the left of G1P, there is enough space for an NTP molecule. The side chains, atoms of residues M109 and V204, and the main chains, atoms of residues Q105, D133, D134, and E191 were removed for clarity.(b) G1P H-bonding network with UgpG catalytic residues, where dashed lines represent proton-donor to proton-acceptor distances of up to 3.2 Å. (c) The Rmla-deoxythymidine complex structure 1H5R (36) with its H-bonding network. (d) A deoxythymidine molecule was manually fitted, using a molecular graphics workstation, into the empty UgpG catalytic cavity using the complex structure shown in panel c as a template. M109 is represented by its main-chain atoms only, for purposes of clarity. Carbon is represented in black, oxygen in white, nitrogen in light gray, and phosphorus in dark gray.