Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I
Figure 13
The distance between the side chain OH on Tyr714 and δ-C of Glu658 for the open (1L3S, red), ajar (3HP6, green), and closed (1LV5, blue) structured simulated using Desmond with the Charmm27 force field.
Tyr714 and Glu658 are not hydrogen bonded in the 1L3S PDB (corresponding to a distance of 6.3 Å) or during any of the 1L3S simulation. The two residues are hydrogen bonded in the initial 3HP6 and 1LV5 PDB structures (distance <4 Å), but the hydrogen bond is broken within first 5.0 ns of each simulation and does not reform. Note that this figure has been scaled to only the first 50 ns of simulation time to demonstrate the timing of the Tyr714-Glu658 hydrogen bond breaking.