Figure 4.
Fig. 4. Structure of Fab Q425. (A) Overall structure. The
Q425:Ba^2+ complex is shown in ribbon representation, with Ba^2+
ion in red, heavy chain in orange, and light chain in blue.
Contoured in green at 6 is the rigid-body
difference Fourier (Ba^2+ vs. EDTA; see details in Materials and
Methods), marking the position of the Ba^2+ ion. (B) Q425:Ca^2+
structure, showing details of the Ca^2+ binding site. A close-up
of the Q425-calcium binding site is shown in an orientation
related to A by a 90° rotation around a horizontal axis. The
Ca^2+ ion is colored purple, oxygen atoms are colored red,
nitrogen atoms are in dark blue, carbon atoms of the heavy chain
are in yellow, and carbon atoms of the light chain are in blue.
Coordinating ligands are side-chain oxygens from Asn (residue
100a from the CDR H3), Asp (residue 32 from the CDR L1), and Glu
(residue 50 from the CDR L2), as well as the backbone carbonyl
of residue 92 (in the CDR L3). Ligand distances are shown in
Å. (C) Q425:EDTA structure, showing details of the same
site shown in B but in the presence of 10 mM EDTA.
is the rigid-body
difference Fourier (Ba^2+ vs. EDTA; see details in Materials and
Methods), marking the position of the Ba^2+ ion. (B) Q425:Ca^2+
structure, showing details of the Ca^2+ binding site. A close-up
of the Q425-calcium binding site is shown in an orientation
related to A by a 90° rotation around a horizontal axis. The
Ca^2+ ion is colored purple, oxygen atoms are colored red,
nitrogen atoms are in dark blue, carbon atoms of the heavy chain
are in yellow, and carbon atoms of the light chain are in blue.
Coordinating ligands are side-chain oxygens from Asn (residue
100a from the CDR H3), Asp (residue 32 from the CDR L1), and Glu
(residue 50 from the CDR L2), as well as the backbone carbonyl
of residue 92 (in the CDR L3). Ligand distances are shown in
Å. (C) Q425:EDTA structure, showing details of the same
site shown in B but in the presence of 10 mM EDTA.