Crystal structure topology

The Sema domain consisting of about 500 amino acids is characterized by highly conserved cysteine residues that form intramolecular disulfide bonds. Crystal structures have revealed that the Sema domain folds in the manner of the (3 propeller topology which is also found in integrins or the low-density lipoprotein (LDL) receptors. Sema domains are found in semaphorins, plexins and in the receptor tyrosine kinases Met and Ron. 

Tsirelson, V.G., Zou, P.F. and Bader, R.F.W. (1995) Topological definition of crystal structure determination of the bonded interactions in solid molecular chlorine, Ada Cryst., A51, 143-153. 

The structure of (+)-phomactin A was determined using both NMR and crystallographic methods (Fig. 8.1). Although the crystal structure is of low quality, it clearly revealed the unusual ABCD-tetracyclic topology as well as the absolute stereochemistry. Subsequently, nine additional phomactins were isolated from various fungal sources with many of them displaying anti-PAF activity [3-5] B [3], B1 [3], B2 [3], C [3] (or Sch 47918 [6]), D [3], E [4], F [4], G [4], and finally, H [5] (Fig. 8.2). 

In general, zeolites are crystalline aluminosilicates with microporous channels and/or cages in their structures. The first zeolitic minerals were discovered in 1756 by the Swedish mineralogist Cronstedt [3], Upon heating of the minerals, he observed the release of steam from the crystals and called this new class of minerals zeolites (Greek zeos = to boil, lithos = stone). Currently, about 160 different zeolite structure topologies are known [4] and many of them are found in natural zeolites. However, for catalytic applications only a small number of synthetic zeolites are used. Natural zeolites typically have many impurities and are therefore of limited use for catalytic applications. Synthetic zeolites can be obtained with exactly defined compositions, and desired particle sizes and shapes can be obtained by controlling the crystallization process. 

A few considerations about possible schemes of relationships between inorganic crystal structures based on a systematic construction of complex structural types by means of a few operations (symmetry operations, topological transformations) applied to some building units (point systems, clusters, rods, sheets), have been previously reported in 3.9.1, following criteria suggested, for instance, by Hyde and Andersson (1989) and by Zvyagin (1993). 

Table 2.2 summarizes basic crystallographic data for the iron oxides. Iron oxides, hydroxides and oxide hydroxides consist of arrays of Fe ions and 0 or OH ions. As the anions are much larger than the cations (the radius of the 0 ion is 0.14 nm, whereas those of Fe and Fe" are 0.065 and 0.082 nm, respectively), the arrangement of anions governs the crystal structure and the ease of topological interconversion between different iron oxides. Table 2.3 lists the atomic coordinates of the iron oxides. 

PH domains bind phosphatidyl inositol derivatives and, due to this property, are able to mediate membrane association of signal proteins. The PH domain of PL-C61 binds to phospholipids such as Ptd(Ins)P2 with high affinity and specificity. The crystal structure of the PH domain of PL-C81 with bound Ptd(Ins)P2 surprisingly has a very similar folding topology to the PTB domain that specifically binds phosphotyrosine-containing peptides (see 8.2.3 review Lemmon et al, 1996). The importance of this similarity is not understood. 

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