Figure 5.

Molecular dynamics simulations highlighting the role of Zn²⁺ in providing conformational stability to CDR3. A and B, representation of structure along the trajectory at different time points in the Zn²⁺-bound (A) and Zn²⁺-free (B) state. In the presence of Zn²⁺, CDR3 loop conformation is restrained, whereas in the absence of Zn²⁺, it becomes more mobile, which allows the His residue (involved in coordination to Zn²⁺) to flip outside. C and D, RMSD of residues in the CDR3 region over the course of trajectory in the presence of Zn²⁺ (C) and in the absence of Zn²⁺ (D). E and F, RMS flexibility of residues in the CDR3 region in Å/ns in the presence of Zn²⁺ (E) and in the absence of Zn²⁺ (F); only side-chain atoms were taken for calculation. Conformational flexibility of residues from 115 to 121 significantly increases in the absence of Zn²⁺ coordination.