8BPU | pdb_00008bpu

X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(D-p-FPhF)(O2CCH3)3] (Structure 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 
    0.289 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.233 (DCC) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Effect of Equatorial Ligand Substitution on the Reactivity with Proteins of Paddlewheel Diruthenium Complexes: Structural Studies.

Teran, A.Ferraro, G.Sanchez-Pelaez, A.E.Herrero, S.Merlino, A.

(2023) Inorg Chem 62: 670-674

  • DOI: https://doi.org/10.1021/acs.inorgchem.2c04103
  • Primary Citation Related Structures: 
    8BPH, 8BPJ, 8BPU, 8BQM

  • PubMed Abstract: 

    The paddlewheel [Ru 2 Cl(O 2 CCH 3 ) 4 ] complex was previously reported to react with the model protein hen egg white lysozyme (HEWL), forming adducts with two diruthenium moieties bound to Asp101 and Asp119 side chains upon the release of one acetate. To study the effect of the equatorial ligands on the reactivity with proteins of diruthenium compounds, X-ray structures of the adducts formed when HEWL reacts with [Ru 2 Cl(D- p -FPhF)(O 2 CCH 3 ) 3 ] [D- p -FPhF = N , N '-bis(4-fluorophenyl)formamidinate] under different conditions were solved. [Ru 2 Cl(D- p -FPhF)(O 2 CCH 3 ) 3 ] is bonded through their equatorial positions to the Asp side chains. Protein binding occurs cis or trans to D- p -FPhF. Lys or Arg side chains or even main-chain carbonyl groups can coordinate to the diruthenium core at the axial site. Data help to understand the reactivity of paddlewheel diruthenium complexes with proteins, providing useful information for the design of new artificial diruthenium-containing metalloenzymes with potential applications in the fields of catalysis, biomedicine, and biotechnology.


  • Organizational Affiliation
    • Departamento de Química Inorgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid E-28040, Spain.

Macromolecule Content 

  • Total Structure Weight: 15.73 kDa 
  • Atom Count: 1,135 
  • Modeled Residue Count: 129 
  • Deposited Residue Count: 129 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LysozymeA [auth AAA]129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R2I
(Subject of Investigation/LOI)

Query on R2I



Download:Ideal Coordinates CCD File
D [auth AAA]9,11-bis(4-fluorophenyl)-2,4,6,8-tetraoxa-9,11-diaza-1$l^{4},5$l^{4}-diruthenatricyclo[3.3.3.0^{1,5}]undecane
C15 H14 F2 N2 O4 Ru2
TVQMJLRZOPYFSZ-UHFFFAOYSA-N
R2U
(Subject of Investigation/LOI)

Query on R2U



Download:Ideal Coordinates CCD File
E [auth AAA],
F [auth AAA]
Ru2-(OH)6 cluster
H6 O6 Ru2
AOQXTNLYRQGSLC-UHFFFAOYSA-H
EPE

Query on EPE



Download:Ideal Coordinates CCD File
C [auth AAA]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
B [auth AAA]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free:  0.289 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.233 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.36α = 90
b = 78.36β = 90
c = 37.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection
  • Version 1.2: 2024-02-14
    Changes: Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary