Abriata Luciano A
Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1223-31. doi: 10.1107/S0907444912026054. Epub 2012 Aug 18.
An updated picture of the ligand sets and copper-ligand atom bond lengths in proteins is presented which takes advantage of (i) the approximately twofold increase in the number of entries for copper-containing proteins in the PDB since the last study of this kind, especially benefiting from the recent incorporation of the structures of proteins involved in copper homeostasis, and (ii) a preliminary classification of copper sites based on their structural, electronic and functional features. This classification allowed the calculation of reliable target copper-ligand distances for several bonds that were not available in previous work and that are in good agreement with EXAFS data and the known chemistry of these sites. The analysis presented here further disclosed an artifactual dependence of the average of the reported Cu-NHis bond lengths on structure resolution, highlighting the importance of taking this into account when computing target distances even from high-resolution structures. Finally, a relationship between the two Cu-O distances in bidentate carboxylates is disclosed, similar to that reported previously for other metal ions.
本文展示了蛋白质中配体集和铜-配体原子键长的最新情况，这得益于：(i) 自上次此类研究以来，蛋白质数据银行（PDB）中含铜蛋白质条目的数量增加了约两倍，尤其受益于最近纳入的参与铜稳态的蛋白质结构；(ii) 根据铜位点的结构、电子和功能特征进行的初步分类。这种分类使得能够计算出先前工作中无法获得的几个键的可靠目标铜-配体距离，这些距离与扩展X射线吸收精细结构（EXAFS）数据以及这些位点的已知化学性质高度一致。此处的分析进一步揭示了报告的Cu-NHis键长平均值对结构分辨率的人为依赖性，突出了即使从高分辨率结构计算目标距离时考虑这一点的重要性。最后，揭示了双齿羧酸盐中两个Cu-O距离之间的关系，类似于先前报道的其他金属离子的情况。
