Hello again all,
We have a molybdopterin active site cofactor. It is a
single molybdenum atom, with 2 oxygens and 1 sulfur as
ligands, and coordinated to a pterin ring via 2 more
sulfur atoms. The geometry of the molybdenum is very
roughly square pyramidal.
The issue that we are having involves the connectivity
of the cofactor. The refinement wants to connect the
sulfur ligand to the oxygen ligands, in addition to
their respective connections to the molybdenum, and it
wants only a single sulfur off the pterin ring
connected, not to the molybdenum, but to the sulfur
ligand. I have tried playing with the pdb file, but I
am basically just unsure as to how best to get the
connectivity the way it should be. Is there a way to
do this in COOT?
Thank you.
Jim
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