6GNL

Zr(IV)-substituted Keggin directly binding to the side chain of Hen Egg-White Lysozyme (HEWL)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Direct observation of the ZrIVinteraction with the carboxamide bond in a noncovalent complex between Hen Egg White Lysozyme and a Zr-substituted Keggin polyoxometalate.

Vandebroek, L.Van Meervelt, L.Parac-Vogt, T.N.

(2018) Acta Crystallogr C Struct Chem 74: 1348-1354

  • DOI: 10.1107/S2053229618010690

  • PubMed Abstract: 
  • The successful cocrystallization of the noncovalent complex formed between (Et <sub>2 </sub>NH <sub>2 </sub>) <sub>8 </sub>[{α-PW <sub>11 </sub>O <sub>39 </sub>Zr-(μ-OH)(H <sub>2 </sub>O)} <sub>2 </sub>]·7H <sub>2 </sub>O Keggin polyoxometalate (2) a ...

    The successful cocrystallization of the noncovalent complex formed between (Et 2 NH 2 ) 8 [{α-PW 11 O 39 Zr-(μ-OH)(H 2 O)} 2 ]·7H 2 O Keggin polyoxometalate (2) and Hen Egg White Lysozyme (HEWL) protein is reported. The resulting structural model revealed interaction between monomeric [Zr(PW 11 O 39 )] 4- (1), which is a postulated catalytically active species, and the protein in two positions in the asymmetric unit. The first position (occupancy 36%) confirms the previously observed binding sites on the protein surface, whereas the second position (occupancy 14%) provides novel insights into the hydrolytic mechanisms of Zr IV -substituted polyoxometalates. The new interaction site occurs at the Asn65 residue, which is directly next to the Asp66-Gly67 peptide bond that was identified recently as a cleavage site in the polyoxometalate-catalysed hydrolysis of HEWL. Furthermore, in this newly discovered binding site, the monomeric polyoxometalate 1 is observed to bind directly to the side chain of the Asn65 residue. This binding of Zr IV as a Lewis-acid metal to the carbonyl O atom of the Asn65 side chain is very similar to the intermediate state proposed in density functional theory (DFT) studies in which Zr IV activates the peptide bond via interaction with its carbonyl O atom, and can be thus regarded as a model for interaction between Zr IV and a peptide bond.


    Organizational Affiliation

    Department of Chemistry, KU Leuven, Celestijnenlaan 200F box 2404, Leuven 3001, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZKG
Query on ZKG

Download SDF File 
Download CCD File 
A
ZIRCONIUM(IV) PHOSPHOTUNGSTATE KEGGIN
O39 P W11 Zr
NBVITJPYFSGCOJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.147 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.701α = 90.00
b = 77.701β = 90.00
c = 37.866γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PHASERphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-11-14
    Type: Data collection, Database references