There are several formats to describe PDB structural data and I introduce them in this article. Each format file is available from the PDBj web site (Figure 1). The most historical format is PDB format (Figure 2). It is 80 columns fixed format and the included information is partial. Moreover it includes some free description sections and it is not suitable for computational processing. As it will be phased out in 2016, it is recommended to use the current canonical format PDBx/mmCIF (Figure 3). It is defined by the extension of STAR format, which can include flexible length of lines. wwPDB also provides XML translated format PDBML (Figure 4). One can use general XML purser for it, but the file size is larger than PDBx/mmCIF. In the PDBx/mmCIF and PDBML, two types of ids for items such as atoms and residues are defined. One is author-defined id, which is not always sequential and may include non-numerical strings. The other is defined by wwPDB, which follows the systematic rule.
Some iron(III) complexes, including [Fe2(μ-O)(nta)2(H2O)2]2– (1), [Fe2(μ-O)(edda)2(H2O)2] (2), and [Fe2(μ-O)(ida)2(H2O)4] (3), are considered to be carcinogens causing renal injuries according to the results of previous animal experiments, where nitrilotriacetate [(nta)3–], ethylenediamine-N,N'-diacetate [(edda)2–], and iminodiacetate [(ida)2–] are the chelating ligands (chelators). On the other hand, a similar iron(III) complex [Fe2(μ-O)(pac)2(H2O)2] (4) is not considered to be a carcinogen, where N-(2-pyridylmethyl) iminodiacetate [(pac)2–] is the chelating ligand. In order to clarify the differences in carcinogenicity, the structures of complexes 1–4 were investigated based on the density functional theory (DFT) method, because the structures of complexes had not been clarified in solution. As a result, two-point interaction with hydrogen peroxide or α-helix was found to be possible for carcinogenic iron(III) complexes 1 and 3, whereas the interaction was found to be impossible for non-carcinogenic iron(III) complex 4.
After the accident of Fukushima's nuclear power plant, soil contamination was caused by radioactive cesium. In this study, the new cesium-adsorbent: Cs1-xNaxMnII(CN)3 Prussian blue analogue was theoretically designed to solve the problem. In Prussian blue (iron cyano-compound), both water defect and iron vacancy are closely related to cesium-adsorption. On the other hand, in Cs1-xNaxMnII(CN)3, the cesium-adsorption mechanism is completely different. Hybrid Kohn-Sham DFT calculations were performed to investigate the cesium-adsorption mechanism. It was concluded that more stable and efficient cesium-adsorption can be realized by the ion exchange between counter cations (between sodium and cesium ions), under applied voltage.