Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I
Figure 14
The relative degree of rotation of the N-β-glycosyl bond for the template nucleotide in the 1LV5 simulation performed with Desmond using Charmm27 force field.
The torsion corresponds to an angle of roughly −90° when the nucleotide is in the active site and then changes to ∼0° when the N-β-glycosyl bond rotates moving the template nucleotide out of the active site entirely. Representative conformations of the nucleotide are shown at 130 ns and 400 ns to show the rotation. The torsion being measured is defined in the bottom right of the figure.