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Updated: Sep 12, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware
Published on: December 25, 2021
Coordination Geometry Tuning in a Single-Atom Nanozyme to Mimic Metalloenzymes with Nonplanar Active Site
Hyesung Lee1, Changjoon Keum2, Choah Kwon3
1Department of Chemical and Biomolecular Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
Abstract:
Single-atom nanozymes (SAzymes) have been developed to mimic metalloenzymes by modulating their coordination environment. However, the impact of the coordination geometry at the metal center on the catalytic activity of the SAzymes, particularly those with nonplanar active site configurations, has been minimally explored. Here, the effects of the geometric configuration of the Zn-N4 active sites on the catalytic activity of the carbonic anhydrase (CA)-mimetic SAzymes are reported. CA-mimetic SAzymes with Zn-N4 active sites in tetrahedral, distorted tetrahedral, and square-planar configurations are prepared by simple temperature-controlled carbonization of ZIF-8. The SAzyme with the distorted tetrahedral Zn-N4 configuration displays superior catalytic CO2 hydration activity, attributed to increased Lewis acidity. Density functional theory (DFT) calculations reveal a pronounced Zn-OH affinity and localized electron accumulation at the distorted tetrahedral Zn site. These results demonstrate the critical role of precise geometric tuning in enhancing SAzyme efficacy and can be used to facilitate potential avenues for optimizing metal active centers in enzyme mimetics.
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