Figure 3.
Fig. 3. (a) Comparison of active site waters in E.
facieum VanA, which replace Lys-215 in E. coli DdlB. Magnesium
atoms are shown in gray with water molecules in red. The
structures of VanA and DdlB were superimposed and the relative
positions of waters in VanA and Lys-215 in DdlB compared. Water
475 in VanA takes an equivalent position to the side-chain
nitrogen of Lys-215 in DdlB. Hydrogen-bonding distances between
adjacent water molecules, magnesium atoms, and phosphate atoms
are not shown for clarity. Other water molecules, notably W371,
W569, and W574, coordinate with magnesium ions in the active
site of VanA. (b) A stereo representation and 2 F[o] F[c] map
showing the active-site residues in contact with the
phosphinophosphinate transition state intermediate. The map is
contoured at 1 by using
the final 2.5-Å resolution map. Residues in the immediate
vicinity of the transition state intermediate are marked. The
two magnesium ions that coordinate with the phosphate ion of the
intermediate and the -phosphate
of ADP are displayed in gray, and water molecules in this
vicinity are displayed in red. Water 475 in VanA takes an
equivalent position to the side-chain nitrogen of Lys-215 in
DdlB. Other water molecules, notably W371 and W574, coordinate
with magnesium ions in the active site of VanA. (c) Stereo
diagram of the hydrogen bonding interacts with and in the
vicinity of the phosphorylated phosphinate inhibitor in the
active site. The Glu-250, Lys-22, Tyr-4315, and His-244
hydrogen-bonding network is shown, making a 2.7-Å hydrogen
bond with the carboxylate oxygen of the inhibitor. This
carboxylate also hydrogen bonds to a conserved serine (316 in
VanA), which is not shown for clarity. The position of His-244
in our structure is such that it cannot make hydrogen-bonding
interactions with the Glu-16 and Ser-177, which are structurally
conserved in comparison to DdlB. The later two amino acids form
important interactions that anchor D-Ala in the first subsite,
an analogous situation to that found in DdlB.
F[c] map
showing the active-site residues in contact with the
phosphinophosphinate transition state intermediate. The map is
contoured at 1 
by using
the final 2.5-Å resolution map. Residues in the immediate
vicinity of the transition state intermediate are marked. The
two magnesium ions that coordinate with the phosphate ion of the
intermediate and the 
-phosphate
of ADP are displayed in gray, and water molecules in this
vicinity are displayed in red. Water 475 in VanA takes an
equivalent position to the side-chain nitrogen of Lys-215 in
DdlB. Other water molecules, notably W371 and W574, coordinate
with magnesium ions in the active site of VanA. (c) Stereo
diagram of the hydrogen bonding interacts with and in the
vicinity of the phosphorylated phosphinate inhibitor in the
active site. The Glu-250, Lys-22, Tyr-4315, and His-244
hydrogen-bonding network is shown, making a 2.7-Å hydrogen
bond with the carboxylate oxygen of the inhibitor. This
carboxylate also hydrogen bonds to a conserved serine (316 in
VanA), which is not shown for clarity. The position of His-244
in our structure is such that it cannot make hydrogen-bonding
interactions with the Glu-16 and Ser-177, which are structurally
conserved in comparison to DdlB. The later two amino acids form
important interactions that anchor D-Ala in the first subsite,
an analogous situation to that found in DdlB.