Prior knowledge or freedom of interpretation? A critical look at a recently published classification of "novel" Zn binding sites

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2016-06, Vol.84 (6), p.770-776
• Main Authors: Raczynska, Joanna E, Wlodawer, Alexander, Jaskolski, Mariusz
• Format: Article
• Language: English
• Subjects: Animals; Binding Sites; crystal structure; Databases, Protein; Humans; Ligands; Metalloproteins - chemistry; Models, Molecular; Protein Conformation; protein data bank (PDB); stereochemistry; Stereoisomerism; Zinc - chemistry; Zn coordination
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.25024

ABSTRACT In a recently published article (Yao, Flight, Rouchka, and Moseley, Proteins 2015;83:1470–1487) the authors proposed novel Zn coordination patterns in protein structures, apparently discovered using an unprejudiced approach to the information collected in the Protein data Bank (PDB), which they advocated as superior to the prior‐knowledge‐informed paradigm. In our assessment of those propositions we demonstrate here that most, if not all, of the “new” coordination geometries are fictitious, as they are based on incorrectly interpreted protein crystal structures, which in themselves are often not error‐free. The flaws of interpretation include partial or wrong Zn sites, missed or wrong ligands, ignored crystal symmetry and ligands, etc. In conclusion, we warn against using this and similar meta‐analyses that ignore chemical and crystallographic knowledge, and emphasize the importance of safeguarding structural databases against bad apples. Proteins 2016; 84:770–776. © 2016 Wiley Periodicals, Inc.