4ZFP

A new crystal structure for the adduct formed in the reaction between AuSac2, a cytotoxic homoleptic gold(I) compound with the saccharinate ligand, and the model protein hen egg white lysozyme

• PDB DOI: https://doi.org/10.2210/pdb4ZFP/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2015-04-21 Released: 2015-06-24 
• Deposition Author(s): Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.235 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 

Literature

Structural evidences for a secondary gold binding site in the hydrophobic box of lysozyme.

Ferraro, G., Massai, L., Messori, L., Cinellu, M.A., Merlino, A.

(2015) Biometals 28: 745-754

• PubMed: 26054833 
• DOI: https://doi.org/10.1007/s10534-015-9863-7
• Primary Citation of Related Structures:  
  4ZFP


• PubMed Abstract: 
  

  A new crystal structure is reported here for the adduct formed in the reaction between NH4 [Au(Sac)2], AuSac2, a cytotoxic homoleptic gold(I) complex with the saccharinate ligand, and the model protein hen egg white lysozyme. To produce this adduct, AuSac2 breaks down and releases both saccharinate ligands. The resulting Au(I) ions bind the protein to ND1 and NE2 atoms of His15 but also to SD atom of the zero-solvent accessible Met105 side chain, which is located in the protein hydrophobic box. The unexpected existence of this secondary gold(I) binding site is confirmed by spectroscopic and spectrometric measurements in solution.

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Organizational Affiliation: 

Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126, Naples, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.36 kDa 
• Atom Count: 1,175 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AU	I [auth A], J [auth A], K [auth A]	GOLD ION Au ZBKIUFWVEIBQRT-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.235 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.584	α = 90
b = 77.584	β = 90
c = 37.111	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-24 
Deposition Author(s): Merlino, A.

Revision History  

• Version 1.0: 2015-06-24
  Type: Initial release
  
• Version 1.1: 2015-07-08
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description