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Figure 5
The substrate-binding pocket of DAD. (a) A stereoview of the omit map for the active-site region of the protein showing the positive difference electron density for the unknown ligand(s) contoured at 3.0 r.m.s. Our interpretation of this density as an iron-bound carbonate and a cryoprotectant molecule, glycerol, is shown along with the iron-binding histidines and other residues in the vicinity. A more complete view of the active-site residues and putative ligands with their refined electron density, contoured at 1.0 r.m.s., is shown in (b). Both ligands fit the electron density satisfactorily, make reasonable hydrogen bonds and refine reasonably well. The dative bonds to the iron ion and the hydrogen bonds made by the putative glycerol and carbonate moieties (dark green) are shown as yellow dashed lines in (c). The glycerol makes hydrogen bonds to the putative carbonate and to Ser49, Trp61 and Asp63, which are conserved residues. (d) shows more details of the iron ligands along with the electron density for the putative carbonate and glycerol. The refined 2FoFc map is shown in pale blue contoured at the same level as in (b) and the residual FoFc positive difference density, contoured at 2.5 r.m.s., is shown in dark blue. There is a feature of difference density connected with the iron and pointing in the direction of Glu108 which may represent the binding site of diatomic oxygen. Where shown, dative-bond or hydrogen-bond lengths are in Å.

Journal logoBIOLOGICAL
ISSN: 1399-0047
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