Figure 3.
Figure 3 Molecular details of the 3D^pol nucleotide-binding site
illustrating how the buried N-terminus positions Asp238 for
interactions with the 2' OH group of the bound NTP. (A)
Superposition of three 3D^pol structures showing the selective
1.4
Å movement of Asp238 toward the active site when the N-terminus
is properly positioned. The original partial wild-type structure
is in pink, the 3D^pol 68/L446A/R455D
structure is in salmon, and the complete structure is colored by
atom type with carbons colored according to structural motifs as
in Figure 1C. Most side chains have been omitted for clarity and
residues 324 -332 of the active site (magenta) were used for the
superimpositions. (B) Electron density map and model of the GTP
molecule bound to 3D^pol with the 2' OH group making a 2.8 Å
long hydrogen bond with Asp238. The GTP makes bridging
interactions between the fingers and palm domains. The base is
staked on Arg174 from the ring finger, the ribose interacts with
Arg174 from the ring finger and Asp238 in the palm, and the
triphosphate interacts with Arg163 and Lys167 from the ring
finger and the backbone of the palm domain. The map is a 2.35 Å
resolution 2F[o] -F[c] simulated annealing (1500 K) composite
omit map contoured at 1.6 around
the rGTP molecule bound after soaking crystals in 10 mM GTP. (C)
Stereo view showing how the buried N-terminus of 3D^pol
positions Asp238 for rNTP interactions. The N-terminus forms
three hydrogen bonds with the carbonyl oxygens of residues 64,
239, and 241 (magenta bonds) that act to position Asp238 for
interaction with the 2' OH of rNTPs. The structures of the G1A
mutant (orange), D238A mutant (teal, only residues 238 -241 are
shown), and original partial structure without a buried
N-terminus (red) are superimposed using the active site.
1.4
Å movement of Asp238 toward the active site when the N-terminus
is properly positioned. The original partial wild-type structure
is in pink, the 3D^pol 
68/L446A/R455D
structure is in salmon, and the complete structure is colored by
atom type with carbons colored according to structural motifs as
in Figure 1C. Most side chains have been omitted for clarity and
residues 324 -332 of the active site (magenta) were used for the
superimpositions. (B) Electron density map and model of the GTP
molecule bound to 3D^pol with the 2' OH group making a 2.8 Å
long hydrogen bond with Asp238. The GTP makes bridging
interactions between the fingers and palm domains. The base is
staked on Arg174 from the ring finger, the ribose interacts with
Arg174 from the ring finger and Asp238 in the palm, and the
triphosphate interacts with Arg163 and Lys167 from the ring
finger and the backbone of the palm domain. The map is a 2.35 Å
resolution 2F[o] -F[c] simulated annealing (1500 K) composite
omit map contoured at 1.6 
around
the rGTP molecule bound after soaking crystals in 10 mM GTP. (C)
Stereo view showing how the buried N-terminus of 3D^pol
positions Asp238 for rNTP interactions. The N-terminus forms
three hydrogen bonds with the carbonyl oxygens of residues 64,
239, and 241 (magenta bonds) that act to position Asp238 for
interaction with the 2' OH of rNTPs. The structures of the G1A
mutant (orange), D238A mutant (teal, only residues 238 -241 are
shown), and original partial structure without a buried
N-terminus (red) are superimposed using the active site.