Metal binding sites in macromolecular structures

项目：大分子结构中的金属结合环境 翻译后摘要：金属离子在生物大分子的机制和结构中起着至关重要的作用， 包括生物化学反应的催化、电子传递、气体的结合和 核苷酸和其它多磷酸盐化合物。然而，最近一项对公共结构的调查显示， 沉积在PDB中的含金属蛋白质和核酸揭示了大量的错误鉴定的 和/或次优建模的金属结合位点。这促使创建了一个诊断工具 金属结合微环境模型，“CheckMyMetal”（CMM）网络服务器 (http：//csgid.org/csgid/metal_sites/），该软件可检测金属结构中的几何形状和其他不规则性 结合位点，并提醒研究人员在金属分配的潜在错误。作为CMM的生产版本， 已经获得了广泛的使用，研究界已经确定了未来发展的几个方向 主要兴趣：1）研究和验证大分子中不常见的重金属结合位点 结构; 2）建立服务器以提供高质量、经验证的金属结合位点的定制子集; 3） 开发工具，自动检测电子密度中可能的金属结合位点，并识别和添加 在晶体学模型建立和改进过程中最可几金属离子; 4）系统地编目 金属结合结构并检测新的金属结合基序。我们建议开发的工具包， CMM作为一个基础，包含几个模块，这些模块可以独立工作，也可以作为 结构建模、验证、解释和注释流水线。这项提案不仅是为了 结构生物学家在晶体学模型构建过程中建模和验证新结构， 改进，而且也为更广泛的观众-生物医学研究人员研究含金属的蛋白质和 核酸

Project: Metal binding environments in macromolecular structures Abstract: Metal ions play vital roles in both the mechanism and architecture of biological macromolecules, including the catalysis of biochemical reactions, electron transport, binding of gases, and stabilization of nucleotides and other polyphosphate compounds. However, a recent survey of publicly available structures of metal-containing proteins and nucleic acids deposited in the PDB revealed an abundance of misidentified and/or sub-optimally modeled metal binding sites. This prompted the creation of a diagnostic tool for the models of metal binding microenvironments, the "CheckMyMetal" (CMM) web server (http://csgid.org/csgid/metal_sites/), which detects geometric and other irregularities in structures of metal binding sites and alerts researchers to potential errors in metal assignment. As the production version of CMM has gained widespread usage, the research community has identified several directions for future development of major interest:1) investigate and validate uncommon heavy metal binding sites in macromolecular structures; 2) establish a server to provide customized subsets of high-quality, validated metal binding sites; 3) develop tools to automatically detect likely metal binding sites in electron density, and identify and add the most probable metal ion during crystallographic model building and refinement; and 4) systematically catalog metal binding architectures and detect new metal binding motifs. The toolkit we propose to develop, using CMM as a basis, contains several modules that will work either independently or as integrated steps in the structure modeling, validation, interpretation and annotation pipeline. This proposal was designed not only for structural biologists to model and validate new structures during crystallographic model building and refinement, but also for a broader audience—biomedical researchers studying metal-containing proteins and nucleic acids.