Figure - PMC

Skip to main content

View full-text article in PMC

. Author manuscript; available in PMC: 2020 May 28.

Published in final edited form as: J Chem Inf Model. 2018 Sep 10;59(5):2264–2273. doi: 10.1021/acs.jcim.8b00427

Figure 1: — (A) Cartoon view of the protein, labeling features of interest including loops 1 (light blue), 3 (blue), 5 (green), and 7 (yellow), the substrate oligonucleotide (purple), and the catalytic zinc (orange). (B) Numbering system used to identify atoms in nucleotides. R=DNA (C) Geometry of C2’ endo sugar pucker taken from the starting configuration of the dC simulation, and (D) C3’ endo sugar pucker taken from the second rC simulation. (E) Sugar pucker of the target C, measured in both A3B-dC and (F) A3B-rC simulations. In rC simulation replicate 2, the RNA transitions from a C2’ endo (DNA-preferred) to a C3’ endo (RNA-preferred) sugar pucker. (G) RMSD of target C compared to its initial pose in A3Bctd-DNA (black) and A3Bctd- DNA-rC (red) simulations.

Figure 1: — (A) Cartoon view of the protein, labeling features of interest including loops 1 (light blue), 3 (blue), 5 (green), and 7 (yellow), the substrate oligonucleotide (purple), and the catalytic zinc (orange). (B) Numbering system used to identify atoms in nucleotides. R=DNA (C) Geometry of C2’ endo sugar pucker taken from the starting configuration of the dC simulation, and (D) C3’ endo sugar pucker taken from the second rC simulation. (E) Sugar pucker of the target C, measured in both A3B-dC and (F) A3B-rC simulations. In rC simulation replicate 2, the RNA transitions from a C2’ endo (DNA-preferred) to a C3’ endo (RNA-preferred) sugar pucker. (G) RMSD of target C compared to its initial pose in A3Bctd-DNA (black) and A3Bctd- DNA-rC (red) simulations.