N-Zinclopedia: A database of predicted transition metal-binding sites and metalloenzymes
- 1Tel Aviv University
Abstract
Metal ions are among the most common enzymatic cofactors, yet metal utilization remains poorly mapped. Here, we present N-Zinclopedia, an atlas of predicted transition metal-binding sites and candidate metalloenzymes across protein fold space. N-Zinclopedia catalogs protein sites compatible with transition metal coordination, identified using ZincSight screening of protein structure model databases. We focused on previously uncharacterized domains and proteins, screening for transition metal-binding sites within over a million of these, spanning both poorly annotated and canonical folds. We also classified the predicted sites, using MAHOMES-II, as candidate catalytic or non-catalytic metal-binding sites. Experimental characterization of a previously unknown zinc binding site confirms that ZincSight can determine previously un-annotated zinc binding. N-Zinclopedia significantly expands the known landscape of metal utilization, providing numerous predictions that await experimental examination. N-Zinclopedia is available at: https://bentallab.github.io/nzinclopedia.
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BibTeX
@misc{mechtinger2026nzinclopedia,
title = {{N-Zinclopedia: A database of predicted transition metal-binding sites and metalloenzymes}},
author = {G. Mechtinger and G. Axel and L. Marcellino and A. M. Bowman and J. Slusky and N. Ben-Tal},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.18.759936},
url = {https://www.biorxiv.org/content/10.64898/2026.10.18.759936v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - N-Zinclopedia: A database of predicted transition metal-binding sites and metalloenzymes
AU - G. Mechtinger
AU - G. Axel
AU - L. Marcellino
AU - A. M. Bowman
AU - J. Slusky
AU - N. Ben-Tal
PY - 2026
DA - 2026/10/18
PB - bioRxiv
DO - 10.64898/2026.10.18.759936
UR - https://www.biorxiv.org/content/10.64898/2026.10.18.759936v1
AB - Metal ions are among the most common enzymatic cofactors, yet metal utilization remains poorly mapped. Here, we present N-Zinclopedia, an atlas of predicted transition metal-binding sites and candidate metalloenzymes across protein fold space. N-Zinclopedia catalogs protein sites compatible with transition metal coordination, identified using ZincSight screening of protein structure model databases. We focused on previously uncharacterized domains and proteins, screening for transition metal-binding sites within over a million of these, spanning both poorly annotated and canonical folds. We also classified the predicted sites, using MAHOMES-II, as candidate catalytic or non-catalytic metal-binding sites. Experimental characterization of a previously unknown zinc binding site confirms that ZincSight can determine previously un-annotated zinc binding. N-Zinclopedia significantly expands the known landscape of metal utilization, providing numerous predictions that await experimental examination. N-Zinclopedia is available at: https://bentallab.github.io/nzinclopedia.
ER -