 | Acta Crystallographica Section F Acta Crystallographica Section F STRUCTURAL BIOLOGY COMMUNICATIONS |
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![[Figure 3]](en5472fig3mag.jpg)
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Figure 3
Extra density in the active site of CrpaA.01119.a.A1/TIM. (a) A close-up of the active-site loop (red) of CrpaA.01119.a.A1/TIM and the extra blob of density shown in the same colours as in Fig. 2 ![[link]](../../../../../../logos/arrows/f_arr.gif) . The structure of TIM from T. brucei in complex with 2-phosphoglycerate (2PG) is superimposed (PDB entry 4tim
) and shown in light-grey ribbons, with the cofactors shown as colored sticks. The active-site loop of CrpaA.01119.a.A1/TIM is in the open conformation, while the active-site loop of ligand-bound TIM from T. brucei is closed. The extra density in the CrpaA.01119.a.A1/TIM structure, shown as σA-weighted Fo − Fc density contoured at 3σ, almost superimposes with the phosphate group of 2PG in T. brucei TIM, but extends in a different direction. (b) A stereo figure of the 2PG-binding environment in T. brucei TIM (PDB entry 4tim
) shown in the same orientation as in (a). 2PG is bound to the protein by a tight hydrogen-bond network. Residues to the right of the ligand are part of the closed active-site loop, which is in the closed conformation. (c) A stereo figure of the ligand-binding environment in P. falciparum TIM (PDB entry 1o5x
) shown in the same orientation as in (b). The 2PG ligand is cleaved, possibly as a consequence of radiation damage, to 2-oxoglycerate (3PY) and metaphosphate (PO3). The active-site loop is in the open conformation. (d) A stereo figure of the environment of the unidentified electron density in CrpaA.01119.a.A1 together with the σA-weighted OMIT 2Fo − Fc electron density at 1σ in blue and the σA OMIT Fo − Fc electron density at ±3σ in green/red. One protein molecule is shown with green C atoms and the crystallographic symmetry mate is shown with purple C atoms. The unidentified electron-density blob is in proximity to the phosphate group of 2PG in T. brucei TIM; however, the glycerate group of 2PG does not match the density. While the hydrogen-bonding partners of 2PG to the left in (b) are conserved compared with CrpaA.01119.a.A1/TIM, the different conformations of the active-site loop render the binding environment to the right significantly different. The unidentified electron-density blob also superimposes with the metaphosphate in P. falciparum TIM. The right part of the extra electron density has a somewhat tetrahedral shape. However, a tentatively modelled sulfate ion (ball-and-stick model) together with a water molecule make only very few interactions with the protein. Refinement indicates that sulfate would only be at low occupancy. |
![[Figure 3]](en5472fig3.jpg)
| STRUCTURAL BIOLOGY COMMUNICATIONS |
ISSN: 2053-230X
