5WBD

Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins - N49A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins.

Mann, S.I.Heinisch, T.Ward, T.R.Borovik, A.S.

(2017) J Am Chem Soc 139: 17289-17292

  • DOI: https://doi.org/10.1021/jacs.7b10452
  • Primary Citation of Related Structures:  
    5WBA, 5WBB, 5WBD, 6ANX

  • PubMed Abstract: 

    Copper-hydroperoxido species (Cu II -OOH) have been proposed to be key intermediates in biological and synthetic oxidations. Using biotin-streptavidin (Sav) technology, artificial copper proteins have been developed to stabilize a Cu II -OOH complex in solution and in crystallo. Stability is achieved because the Sav host provides a local environment around the Cu-OOH that includes a network of hydrogen bonds to the hydroperoxido ligand. Systematic deletions of individual hydrogen bonds to the Cu-OOH complex were accomplished using different Sav variants and demonstrated that stability is achieved with a single hydrogen bond to the proximal O-atom of the hydroperoxido ligand: changing this interaction to only include the distal O-atom produced a reactive variant that oxidized an external substrate.


  • Organizational Affiliation

    Department of Chemistry, University of California , 1102 Natural Science II, Irvine, California 92697, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Streptavidin159Streptomyces avidiniiMutation(s): 1 
UniProt
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22629
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SI7
Query on SI7

Download Ideal Coordinates CCD File 
B [auth A][N-(2-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](hydroxy)copper
C26 H36 Cu N6 O3 S
VJQJBNZBGSOUKA-HRKQCRCBSA-M
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.51α = 90
b = 57.51β = 90
c = 174.81γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM50781-21S1

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description