4FIK

Human carbonic anhydrase II H64A complexed with thioxolone hydrolysis products

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.117 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Synchrotron Radiation Provides a Plausible Explanation for the Generation of a Free Radical Adduct of Thioxolone in Mutant Carbonic Anhydrase II.

Sippel, K.H., Genis, C., Govindasamy, L., Agbandje-McKenna, M., Kiddle, J.J., Tripp, B.C., McKenna, R.

(2010) J Phys Chem Lett 1: 2898-2902

  • DOI: 10.1021/jz100954h
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Thioxolone acts as a prodrug in the presence of carbonic anhydrase II (CA II), whereby the molecule is cleaved by thioester hydrolysis to the carbonic anhydrase inhibitor, 4-mercaptobenzene-1,3-diol (TH0). Thioxolone was soaked into the proton transf ...

    Thioxolone acts as a prodrug in the presence of carbonic anhydrase II (CA II), whereby the molecule is cleaved by thioester hydrolysis to the carbonic anhydrase inhibitor, 4-mercaptobenzene-1,3-diol (TH0). Thioxolone was soaked into the proton transfer mutant H64A of CA II in an effort to capture a reaction intermediate via X-ray crystallography. Structure determination of the 1.2 Å resolution data revealed the TH0 had been modified to a 4,4'-disulfanediyldibenzene-1,3-diol, a product of crystallization conditions, and a zinc ligated 2,4-dihydroxybenzenesulfenic acid, most likely induced by radiation damage. Neither ligand was likely a result of an enzymatic mechanism.

    Related Citations: 
    • Inhibition of Carbonic Anhydrase II by Thioxolone: A Mechanistic and Structural Study
      Barrese, A.A., Genis, C., Fisher, S.Z., Orwenyo, J.N., Kumara, M.T., Dutta, S.K., Phillips, E., Kiddle, J.J., Tu, C., Silverman, D.N., Govindasamy, L., Agbandje-McKenna, M., McKenna, R., Tripp, B.C.
      (2008) Biochemistry 47: 3174
    Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, P.O. Box 100245, College of Medicine, University of Florida, Gainesville, Florida 32610.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2A260Homo sapiensMutation(s): 1 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918
GTEx  ENSG00000104267
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D2S
Query on D2S
Download CCD File 
A
4,4'-disulfanediyldibenzene-1,3-diol
C12 H10 O4 S2
DCHQLQXIXWXHFP-UHFFFAOYSA-N		 Ligand Interaction
TH7
Query on TH7
Download CCD File 
A
2,4-dihydroxybenzenesulfenic acid
C6 H6 O3 S
LJXFZIAMAZBGDO-UHFFFAOYSA-N		 Ligand Interaction
TH0
Query on TH0
Download CCD File 
A
4-MERCAPTOBENZENE-1,3-DIOL
C6 H6 O2 S
XFTQIEMOLHJTFV-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.117 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.37α = 90
b = 41.38β = 104.1
c = 72.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description