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. Author manuscript; available in PMC: 2023 May 15.
Published in final edited form as: J Comput Chem. 2022 Mar 24;43(13):906–916. doi: 10.1002/jcc.26846

Figure 5.

Figure 5

(a) The distances of OD1-OG and Mg2+-OG at the catalytic site of HRAS·SOS·HRasGDP·Mg2+ during the MD simulations. The inset shows that Ser17 and Asp57 drift away from the Mg2+ ion. (b) The distances of OD1-OG and O-N at the catalytic site of HRAS·SOS·HRas during the MD simulation. The inset shows the H-bond network formed by Ser17, Asp57 and Ala59. (c) The distances of OD1-OG, OD2-OW1 and Mg2+-OG at the catalytic site of HRAS·SOS·HRasGTP·Mg2+ during the MD simulation. The inset shows the stable coordination of Mg2+ to Ser17, Asp57, GTP and the H2O molecules. (d) The least-square fitted conformations of the catalytic HRasGDP·Mg2+, HRas and HRasGTP·Mg2+ in complexes to the reference structure 3L8Z, with the calculated RMSD values of 0.672, 0.666 and 0.827 Å, respectively.