Buried ligands

The cluster is coordinated at the tip of the cluster binding subdomain. Fe" (Fe-2) is close to the surface of the protein with its histidine ligands fully exposed to the solvent, whereas Fe " (Fe-1) is buried within the protein and surrounded by the three loops forming the cluster binding subdomain. However, in NDO the histidine ligands are not solvent accessible, but buried at the interface between the Rieske domain and the catalytic domain both histidine ligands form hydrogen bonds with acidic side chains in the catalytic site close to the catalytic iron. 

In the following years, the percent buried volume, % has emerged as a standard and intuitive parameter able to describe reasonably well the steric properties of NHCs [75]. The is the fraction of the volume of the fust coordination sphere around the metal occupied by a given ligand, see Fig. 1.17 [75]. 

Various spectroscopic methods have been used to probe the nature of the copper centers in the members of the blue copper oxidase family of proteins (e.g. see ref. 13). Prior to the X-ray determination of the structure of ascorbate oxidase in 1989, similarities in the EPR and UV-vis absorption spectra for the blue multi-copper oxidases including laccase and ceruloplasmin had been observed [14] and a number of general conclusions made for the copper centers in ceruloplasmin as shown in Table 1 [13,15]. It was known that six copper atoms were nondialyzable and not available to chelation directly by dithiocarbamate and these coppers were assumed to be tightly bound and/or buried in the protein. Two of the coppers have absorbance maxima around 610 nm and these were interpreted as blue type I coppers with cysteine and histidine ligands, and responsible for the pronounced color of the protein. However, they are not equivalent and one of them, thought to be involved in enzymatic activity, is reduced and reoxidized at a faster rate than the second (e.g. see ref. 16). There was general concurrence that there are two type HI... 

Substituent effects hae been observed in a series of substituted malonato complexes (167). The 9Be resonance frequencies move to higher field as the basicity of the ligand increases, as can be seen in Table XI. Quadrupolar broadening is considerable in complexes of the hydrolyzed trimer, so much so that unless a species of this sort is present in high concentration relative to the others, its signal may be buried in the baseline noise. The tetrahedron is significantly distorted from Td symmetry in these compounds. 

Fig. 8. Lck SH2 domain-peptide complex (Ac-cmF-Glu-Glu-Ile-OH, 12) revealing the twopronged plug engaging a two-holed socket 1 binding mode, reminiscent of the majority of SH2 domains (Protein Databank entry code 1BHF.PDB [118]). The protein is depicted in a Connolly surface mode, the ligand is given in a ball-and-stick representation. The cmF residue is deeply buried in its binding pocket (left)...

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