Well, the water near the backbone of residue 61 is the worst bump. And this is
inconvenient as the calcium that is bound 'next door' is crucial for stability
and regulation of this molecule.
I have no idea how this can have happenen, but I can make a guess. In the old days, building a molecule in electron density was a giant endeavour. One of the problems was placing water in density that seems probable for water. For a long time a small program was used that put in the PDB file (in the early stages of density fitting) a water molecule close to every Cα so that when a water needed to be placed in density there always was one nearby to move it into that density. This reflected the famous quote by the famous crystallographer Jan Drenth that "the structure is solved once the R-factor is below 20 and you have one water molecule per residue".
I guess that they simply forgot to remove one water that was not need and thus stayed close to the Cα.