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Figure 3.
FIG. 3. Identification of the nucleophile water. A,
simulated annealed omit electron density map, restricted to
exclusively show the exact position of the catalytic water
molecule in the wild type dUTPase:  ,  -imino-dUTP:Mg2+
structure. The figure also shows the hydrogen-bonding network
involving the phosphate chain in this complex structure. In
addition to the catalytic water, Mg2+-coordinating waters, W1,
W2, W4, W15, and W21, also participate in the primary
hydrogen-bonding interactions. B, superimposed structures of
wild type (dark tones) and Asp90  Asn mutant (light tones)
dUTPase: , -imino-dUTP:Mg2+
complexes. Note that the only remarkable difference between the
superimposed structures is the disappearance of W[cat] from the
mutant complex. Atomic color code: carbon, dark/light gray;
oxygen, dark/light red (pink); phosphorus, dark/light orange
(yellow); nitrogen, dark/light blue; magnesium, dark/light
purple. C, superimposed structures of Asp90 Asn mutant dUTPase:
dUTP:Mg2+ (dark tones) and Asp90 Asn mutant dUTPase: , -imino-dUTP:Mg2+ (light
tones) complexes. Note the close identity in the positions of
the nucleotide ligands. D, apoenzyme retains a water closely
corresponding to the W[cat] position. 3-Fold superimposition of
the apoenzyme (green carbons and water, otherwise standard atom
coloring), enzyme-substrate (dark tones), and enzyme-product
(light tones) structures. Note the position of the catalytic
water from the apoenzyme to the enzyme-substrate and
enzyme-product complexes. E, F, and G, simulated annealed omit
electron density maps for the substrates in wild type E. coli
dUTPase: , -imino-dUTP:Mg2+, the
Asp90 Asn E. coli dUTPase:
,
-imino-dUTP: Mg2+, and
the Asp90 Asn E. coli
dUTPase:dUTP:Mg2+ structures, respectively. Maps are restricted
to show the nucleotide ligand, the Mg2+, the three water
molecules coordinating to the metal ion, as well as the
catalytic water, if present.
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