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The differences between the mutant structures were tested by refining with interchanged starting models.
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The mutant structures also show more or less similar architecture with regard to the domain, but, there is significant difference in the GGEEF turn between β1 and β2.
b Following submission, the server will model the mutant structures and perform docking simulations.
The mutant structures were generated in a four-step procedure.
We minimized the energies of the proteins both before and after the mutation and then used the mutant structures to re-run PRISM [ 35, 36] and model the new interaction between the mutant target and its partner.
Greater fluctuation in Rg in mutant (T854A) structure suggested structural alteration in the mutant structure.
The higher the RMSD value is, the greater the deviation will be between the native and mutant structures.
We represent this as a vector of ones and zeroes, and compute the correlation coefficient between the WT and mutant structures.
Thus, the only significant difference between the wild-type and mutant structures is that the PfLDH-W107fA specificity loop is found in the open conformation, consistent with weaker binding of substrate.
This table also lists the distances in the wt-KaiC and mutant structures between the γ-phosphorus of ATP and either the Cα positions or selected side chain atoms [i.e. P (pThr, pSer), Oγ (Thr), Cβ (Ala), Cγ (Asp, Asn), or Cδ (Glu)] of residues 432, 431 and 426.
An additional remarkable variation in the T254 mutant structures compared to wild type is observed in the peptide bond between His256 and Lys257.
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