Crystal Structure of a Tris-thiolate Zn(II)S3O Complex in a de Novo Three-stranded Coiled Coil Peptide

Experimental Data Snapshot

  • Resolution: 1.89 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

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A Crystallographic Examination of Predisposition versus Preorganization in de Novo Designed Metalloproteins.

Ruckthong, L.Zastrow, M.L.Stuckey, J.A.Pecoraro, V.L.

(2016) J Am Chem Soc 138: 11979-11988

  • DOI: https://doi.org/10.1021/jacs.6b07165
  • Primary Citation of Related Structures:  
    5K92, 5KB0, 5KB1, 5KB2

  • PubMed Abstract: 

    Preorganization and predisposition are important molecular recognition concepts exploited by nature to obtain site-specific and selective metal binding to proteins. While native structures containing an MS3 core are often unavailable in both apo- and holo-forms, one can use designed three-stranded coiled coils (3SCCs) containing tris-thiolate sites to evaluate these concepts. We show that the preferred metal geometry dictates the degree to which the cysteine rotamers change upon metal complexation. The Cys ligands in the apo-form are preorganized for binding trigonal pyramidal species (Pb(II)S3 and As(III)S3) in an endo conformation oriented toward the 3SCC C-termini, whereas the cysteines are predisposed for trigonal planar Hg(II)S3 and 4-coordinate Zn(II)S3O structures, requiring significant thiol rotation for metal binding. This study allows assessment of the importance of protein fold and side-chain reorientation for achieving metal selectivity in human retrotransposons and metalloregulatory proteins.

  • Organizational Affiliation

    Department of Chemistry, ‡Biophysics Program, and §Life Sciences Institute, University of Michigan , Ann Arbor, Michigan 48109, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zn(II)(H2O)(GRAND Coil Ser-L12AL16C)3-36synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.89 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.853α = 90
b = 37.853β = 90
c = 141.072γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesES012236

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references, Derived calculations