A piece of a ligand and the side chain of a “gate-keeper” Phe occupy the same space with well-defined features observed for both (resolution is 1.7 A). It looks about 50:50. How do you refine both ligand and protein side chain in this case? A couple of phenixbb suggestions for dealing with ligand-ligand overlapping density have been considered. With the first suggestion, the two entities still clashed and moved apart off of their respective densities. The second suggestion is not applicable in this case since the other molecule is not a ligand but part of the protein but it was tested anyway. Although there was no bumping, the occupancies don’t add up, resulting in a big blob of negative density around the ligand piece.

Only two comments:

At that resolution, constrained group occupancy refinement should work reasonably well (provided you can model the 2 entities). Then you also do not have clashes between the molecules, because Occ(A)+Occ(B)=1, meaning when one (A) is there, the other one (B) is not. This works with refmac (external keyword file); if you need more sophisticated occupancy re/constraints SHELXL may offer more opportunities.
There is no necessity for the two NCS copies of the binding site to look exactly the same (non-equivalent). Maybe there is a good reason/story (accessibility, contacts etc) for one site to be occupied differently than the other one.

Best, BR

Modeling two molecules that occupy overlapping binding sites in a structure simply involves designating them as alternate conformers, with the same chain and residue number, and an occupancy that sums to 1.0. For example, if you have an AMP and an ADP that occupy the same binding site, you would define them as

AAMP B 501

BADP B 501

and initially set the occupancies for the atoms in each conformer to the ratio (50:50, 30:70, etc.) that you observe in the density.

Refinement in this manner is straightforward in PHENIX.

Diana

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