3KS3

High resolution structure of Human Carbonic Anhydrase II at 0.9 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.138 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A short, strong hydrogen bond in the active site of human carbonic anhydrase II.

Avvaru, B.S.Kim, C.U.Sippel, K.H.Gruner, S.M.Agbandje-McKenna, M.Silverman, D.N.McKenna, R.

(2010) Biochemistry 49: 249-251

  • DOI: https://doi.org/10.1021/bi902007b
  • Primary Citation of Related Structures:  
    3KS3

  • PubMed Abstract: 

    The crystal structure of human carbonic anhydrase II (HCA II) obtained at 0.9 A resolution reveals that a water molecule, termed deep water, Dw, and bound in a hydrophobic pocket of the active site forms a short, strong hydrogen bond with the zinc-bound solvent molecule, a conclusion based on the observed oxygen-oxygen distance of 2.45 A. This water structure has similarities with hydrated hydroxide found in crystals of certain inorganic complexes. The energy required to displace Dw contributes in significant part to the weak binding of CO(2) in the enzyme-substrate complex, a weak binding that enhances k(cat) for the conversion of CO(2) into bicarbonate. In addition, this short, strong hydrogen bond is expected to contribute to the low pK(a) of the zinc-bound water and to promote proton transfer in catalysis.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Universityof Florida, Gainesville, Florida 32610, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens)
Explore P00918 
Go to UniProtKB:  P00918
PHAROS:  P00918
GTEx:  ENSG00000104267 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.354α = 90
b = 41.359β = 104.42
c = 72.308γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2010-01-26 
  • Deposition Author(s): Avvaru, B.S.

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations