Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes
Fig 7
Distribution of charges surrounding the NTP during MD simulations.
(a) The plot shows the net charge of the Pol II (protein and nucleotides, y-axis) within certain radius (x-axis) of the NTP in the diffusion pathways through the main channel (dark grey) or the secondary channel (light grey). (b)-(d) The same as in (a) but for the charges of the nucleotides, positively-charged amino acids (a.a.) and negatively-charged a.a. around NTP, respectively.