NMR Structure of the ZFY-6T[Y10F] Zinc Finger

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 52 
  • Conformers Submitted: 25 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


The hidden thermodynamics of a zinc finger.

Lachenmann, M.J.Ladbury, J.E.Phillips, N.B.Narayana, N.Qian, X.Weiss, M.A.

(2002) J Mol Biol 316: 969-989

  • DOI: https://doi.org/10.1006/jmbi.2001.5335
  • Primary Citation of Related Structures:  
    1KLR, 1KLS

  • PubMed Abstract: 

    The Zn finger provides a model for studies of protein structure and stability. Its core contains a conserved phenylalanine residue adjoining three architectural elements: a beta-hairpin, an alpha-helix and a tetrahedral Zn(2+)-binding site. Here, we demonstrate that the consensus Phe is not required for high-affinity Zn(2+) binding but contributes to the specification of a precise DNA-binding surface. Substitution of Phe by leucine in a ZFY peptide permits Zn(2+)-dependent folding. Although a native-like structure is retained, structural fluctuations lead to attenuation of selected nuclear Overhauser enhancements and accelerated amide proton exchange. Surprisingly, wild-type Zn affinity is maintained by entropy-enthalpy compensation (EEC): a hidden entropy penalty (TDeltaDeltaS 7kcal/mol) is balanced by enhanced enthalpy of association (DeltaDeltaH -7kcal/mol) at 25 degrees C. Because the variant is less well ordered than the Phe-anchored domain, the net change in entropy is opposite to the apparent change in configurational entropy. By analogy to the thermodynamics of organometallic complexation, we propose that EEC arises from differences in solvent reorganization. Exclusion of Leu among biological sequences suggests an evolutionary constraint on the dynamics of a Zn finger.

  • Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4935, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UniProt & NIH Common Fund Data Resources
Find proteins for P08048 (Homo sapiens)
Explore P08048 
Go to UniProtKB:  P08048
PHAROS:  P08048
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08048
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 52 
  • Conformers Submitted: 25 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Data collection, Database references, Derived calculations