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Figure 4.
Figure 4 Conformation of the nucleotide substrate in NDPK, T7
DNA polymerase and HIV reverse transcriptase. d4T triphosphate
from the NDPK complex in Figure 2B is shown in atom-type
coloured bonds superimposed onto (A) dideoxyGTP in the ternary
complex with bacteriophage T7 DNA polymerase–DNA (PDB file
1T7P) and (B) deoxyTTP in the ternary complex with HIV reverse
transcriptase–DNA (PDB file 1RTD). Least-square fitting was
performed on atom N1 of the base and common atoms in the sugar
and the  -phosphate.
In T7 polymerase and reverse transcriptase, relevant active site
residues, DNA and the ligand are in blue bonds, and blue spheres
represent two Mg^2+ ions bound. In NDPK, the red sphere is the
single Mg^2+ ion bound to d4T triphosphate. It is located <1
Å away from one of the two Mg^2+ of the polymerases.
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