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 1.2 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: 10.1021/bi902007b
  • Structures With Same Primary Citation

  • 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-bo ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2A260Homo sapiensMutation(s): 0 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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: 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

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Entry History 

Deposition Data

  • Deposited Date: 2009-11-20 
  • Released Date: 2010-01-26 
    • Deposition Author(s): Avvaru, B.S.

Revision History 

  • 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