Recurring structural motifs

Fig. 17 Commonly recurring structural motifs, (a) the paddlewheel dimer of Cu05 square pyramids, (b) the tetrahedron of Zn04 tetrahedra sharing a central oxygen, and (c) the trigonal planar trimer of OO, octahedra sharing a central oxygen. Gray spheres denote carbon and red oxygen CuO,. ZnO-. and CrC>6 polyhedra are shown in dark blue, pale blue and green, respectively.

In recent years, as the size of the PDB has increased, database methods have continued to attract attention. With a larger database, recurring structural motifs have been classified for loop structures [111, 114, 116, 129, 134], including their sequence dependence. Database methods have been applied only for loops of up to 8 residues. Fidelis et al. [126] found that for loops of length greater than 7 there is not likely to be a segment in the PDB that corresponds to the correct loop conformations for the 58 protein they looked at. Some authors report that when the database contains a loop of similar structure to the target to be modeled, their methods perform well, with RMSD values around 1A or better. Otherwise they tend to fail [124, 127, 130]. 

The third recurring structural motif with non-amino-acid components found in metalloproteins is the metal-dithiolene unit found in molybdenum- and tungsten-containing oxidases or dehydrogenases (see Chapter 8.18). The dithiolene is typically a pterin derivative (often with phosphate and/or nucleotide appendages) and coordinated to Mo or W in a 1 1 or 2 1 stoichiometry (Figure 7)." These units usually function in two-electron redox reactions (cf 0x0 transfer ), shuttling between... 

Hub intermediate A key intermediate product in a convergent synthesis plan that appears more than once in the synthesis route the structure of this intermediate is the same as a recurring structural motif found in the final target product. 

Fig. Z 1,4 interactions at C-C-S-C and S-C-C-S units in gauche placement (left) a bracket unit, the recurring structural motif of ethyl-linked thiacrowns...

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