Structure Solve

As source of infonnation we use the Surface Structure Database [14], a critical compilation of surface structures solved in detail, covering the period to the end of 1997. It contains 1113 structural detenninations with, on average, two detenninations for each stmcture thus there are approximately 550 distinct solved stnictures available. 

Figiire Bl.21,6. figure Bl.21,7, figure Bl.21,8 aud flgrue B 1,21,9 show several of the more complex structures solved by LEED iu recent years. They exlribit various effects observed at surfaces ... 

Two metal sites were identified in the structure solved of the chimeiic AC5Ci AC2C2 adenylyl cyclase in complex with 3-L-2, 3 -dd-5 -ATP (cf. Figs. 5 and 7) One is... 

One of the few crystal structures solved for a metal complex of a heterocyclic thiosemicarbazone is bis(l-formylisoquinoline thiosemicarbazone) nickel(II) monohydrate, [Ni(21-H)2] (Fig. 5) [208]. The nickel(II) center was found to be NNS coordinated by two approximately planar thiosemicarbazone ligands. 

CO3 species was formed and the X-ray structure solved. It is thought that the carbonate species forms on reaction with water, which was problematic in the selected strategy, as water was produced in the formation of the dialkyl carbonates. Other problems included compound solubility and the stability of the monoalkyl carbonate complex. Van Eldik and co-workers also carried out a detailed kinetic study of the hydration of carbon dioxide and the dehydration of bicarbonate both in the presence and absence of the zinc complex of 1,5,9-triazacyclododecane (12[ane]N3). The zinc hydroxo form is shown to catalyze the hydration reaction and only the aquo complex catalyzes the dehydration of bicarbonate. Kinetic data including second order rate constants were discussed in reference to other model systems and the enzyme carbonic anhy-drase.459 The zinc complex of the tetraamine 1,4,7,10-tetraazacyclododecane (cyclen) was also studied as a catalyst for these reactions in aqueous solution and comparison of activity suggests formation of a bidentate bicarbonate intermediate inhibits the catalytic activity. Van Eldik concludes that a unidentate bicarbonate intermediate is most likely to the active species in the enzyme carbonic anhydrase.460... 

These solution NMR and X-ray crystallographic findings have been contradicted by X-ray structures solved by Rypniewski et al.32 The results show a reduced active site unchanged from the oxidized state and let these authors to propose a five-coordinate copper ion that exists throughout the oxidation and reduction process. In 2001 the Protein Data Bank listed 39 X-ray crystallographic and NMR solution structures for CuZnSOD, including oxidized, reduced, genetically modified, and other species with or without attached substrates or substrate mimics such as azide ion. The reader is advised to search the Protein Data Bank for additional and more up-to-date structural depositions and search the literature for further discussion of mechanism. 

The first STS structure solved was that of a pinosylvin-forming STS from Pinus sylvestris. Pine trees can by-pass the C4H reaction and directly produce the CoA thioester of cinnamate that allows this STS to utilize a non-substituted cinnamoyl-CoA starter in vz vo.11 However, when presented in vitro with p-coumaroyl-CoA, the enzyme proves to be comparable in activity to STS enzymes from organisms that utilize the para-substituted cinnamoyl starter. 

The partial structure of the adenovirus type 2 fiber shaft was the first /(-structured fibrous fold characterized at atomic detail. The shaft contains 15-residue sequence pseudo-repeats with an invariant glycine or proline and conserved hydrophobic amino acids (Fig. 3A Green et al., 1983). Unfolding studies led to the identification of a stable domain, consisting of amino acids 319-582, which was subcloned, expressed, and purified (Mitraki et al., 1999). Subsequently, it was crystallized, and its structure solved at 2.4-A resolution (van Raaij et al., 1999b). Its structure revealed a new fold, called the triple /(-spiral. ... 

Following myoglobin and lysozyme, bovine carboxypeptidase A was the third protein to have its 3-D structure solved at high resolution. The active site zinc is bound to His69, Glu72 and Hisl96 (Figure 12.4), and to a water molecule, which is displaced when a... 

The corresponding Cu(I) complex, [Cu(dpa)2] +, has been isolated and its structure solved. It maintains a tetrahedral geometry, though with a few significant variations in the structural parameters (Cu-N = 2.02 A dihedral angle between the two CuN2 planes = 73.3°).176... 

The monocation [Fe4S5(C5H5)4]+ has been isolated and its X-ray structure solved. As expected on the basis of the electrochemical reversibility of the 2 + /+ response, the geometry of the dication precursor is maintained, with only a slight lengthening of the bond lengths. 

In a similar way, Voigt-Martin et al. [14] have solved the structure of [9,9 -bianthryl]-10-carbonitrile in three dimensions using 150 unique diffraction intensities, and independently verified the result with model building and image simulation techniques. As before, the potential maps are difficult to interpret, and independent validation is an important part of the structure solving procedure. 

Other structures solved by the ME formalism include 4-dimethylamino-3-cyanobiphenyl [15] 2,6-bis(4-dimethylamino-benzylidene)-cyclohexanone... 

The structure of P pantotrophus (fomerly Thiospharea pantotropha, (3)) cytochrome cdi, the first of this type to have its crystal structure solved (4), shows that the enz5une is a homodimer of 567 aminoacid residues and each subunit contains both a c-type cytochrome center and a di heme center (Fig. 3). The di heme (Fig. 1) is unique to this class of enzyme and on that basis alone might be expected to be the catalytic site. The c-type cytochrome centers, which are defined by the covalent attachment of the heme to the polypeptide are usually, but... 

The rule of thumb for a successful application of molecular replacement is that the model should have a root-mean-square deviation (RMSD) on C-alpha coordinates 2.0-2.5 Angstroms with the target structure, corresponding to a sequence identity with the target of 25-35%. In practice, however, there are many more structures solved by MR in the PDB using models with sequence identity of 60% or higher than otherwise. 

Small molecule crystal structures solved through direct methods yield very accurate atomic positions... 

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