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Figure 9
Gd-DO3A sites in lysozyme and afamin. The top panel shows the arrangement of the Gd-DO3A sites in a high-resolution model of lysozyme (PDB entry 1h87; Girard et al., 2003BB17), in which the Gd pair forms a crystal contact involving hydrophobic interaction of the DO3A methyl groups with Trp62 of one molecule and Trp123 of a symmetry mate. A similar arrangement of the Gd ions exists in afamin, where two of the strongest difference peaks (inset) appear in the central hydrophobic binding cleft. The placed Gd atoms refined with an occupancy of between 0.9 and 0.7, and the distance between them is also 6.1 Å, as in the lysozyme model, with sufficient space in the binding site to accommodate the DO3A crowns of the Gd-DO3A complexes. The bottom centre panel shows mFoDFc positive OMIT difference electron density displayed at a 2.5σ level in green and 2mFoDFc density displayed at 0.8σ in blue. The DO3A crowns are not refined but are placed in an orientation corresponding to that in PDB entry 1h87. The methyl groups of the placed DO3A crowns face towards a phenylalanine lining the bottom (left side of the figure) of the binding pocket, resembling the interactions observed in PDB entry 1h87. A similar interaction can be proposed for the third Gd site located at a crystal contact in afamin (bottom right). The top figure was produced with ICM-Pro from Molsoft (Abagyan et al., 2006BB1) and the electron-density figures were produced with Coot (Emsley et al., 2010BB14).

Journal logoSTRUCTURAL
ISSN: 2059-7983
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