A less-biased analysis of metalloproteins reveals novel zinc coordination geometries

Sen Yao, Robert M. Flight, Eric C. Rouchka, Hunter N.B. Moseley

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


Zinc metalloproteins are involved in many biological processes and play crucial biochemical roles across all domains of life. Local structure around the zinc ion, especially the coordination geometry (CG), is dictated by the protein sequence and is often directly related to the function of the protein. Current methodologies in characterizing zinc metalloproteins' CG consider only previously reported CG models based mainly on nonbiological chemical context. Exceptions to these canonical CG models are either misclassified or discarded as "outliers." Thus, we developed a less-biased method that directly handles potential exceptions without pre-assuming any CG model. Our study shows that numerous exceptions could actually be further classified and that new CG models are needed to characterize them. Also, these new CG models are cross-validated by strong correlation between independent structural and functional annotation distance metrics, which is partially lost if these new CGs models are ignored. Furthermore, these new CG models exhibit functional propensities distinct from the canonical CG models.

Original languageEnglish
Pages (from-to)1470-1487
Number of pages18
JournalProteins: Structure, Function and Bioinformatics
Issue number8
StatePublished - Aug 1 2015

Bibliographical note

Publisher Copyright:
© 2015 Wiley Periodicals, Inc.


  • 3D structure
  • Bidentation
  • Carboxylate shift
  • Compressed angle
  • Structural bioinformatics
  • Structure-function relationship

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology


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