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. 2019 Nov 11;20(22):5644. doi: 10.3390/ijms20225644

Figure 5.

Figure 5

Molecular properties of the UPF1-AMPPNP model systems. (A) Substrate binding site residues of the UPF1 protein and studied mutations. RMSFs for wild-type UPF1, mutant models; apo-form and AMPPNP bound UPF1. (B) Individual residues of UPF1 contributing to the binding energy for AMPPNP, calculated by MM-PBSA. (C) Binding mode of AMPPNP to the UPF1 protein in different model systems, and UPF1 residues forming stable H-bonds with AMPPNP having occupancy ≥10%. (D) Binding conformation of AMPPNP with respect to the wild-type and mutated UPF1 (T499M, E637K, and E833K) obtained from the end of MDS.