3KON

Crystal structure of cobalt (II) human carbonic anhydrase II at pH 11.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Comparison of solution and crystal properties of Co(II)-substituted human carbonic anhydrase II.

Avvaru, B.S.Arenas, D.J.Tu, C.Tanner, D.B.McKenna, R.Silverman, D.N.

(2010) Arch.Biochem.Biophys. 502: 53-59

  • DOI: 10.1016/j.abb.2010.07.010
  • Primary Citation of Related Structures:  3KOI, 3KOK

  • PubMed Abstract: 
  • The visible absorption of crystals of Co(II)-substituted human carbonic anhydrase II (Co(II)-HCA II) were measured over a pH range of 6.0-11.0 giving an estimate of pK(a) 8.4 for the ionization of the metal-bound water in the crystal. This is higher ...

    The visible absorption of crystals of Co(II)-substituted human carbonic anhydrase II (Co(II)-HCA II) were measured over a pH range of 6.0-11.0 giving an estimate of pK(a) 8.4 for the ionization of the metal-bound water in the crystal. This is higher by about 1.2 pK(a) units than the pK(a) near 7.2 for Co(II)-CA II in solution. This effect is attributed to a nonspecific ionic strength effect of 1.4M citrate in the precipitant solution used in the crystal growth. A pK(a) of 8.3 for the aqueous ligand of the cobalt was measured for Co(II)-HCA II in solution containing 0.8M citrate. Citrate is not an inhibitor of the catalytic activity of Co(II)-HCA II and was not observed in crystal structures. The X-ray structures at 1.5-1.6A resolution of Co(II)-HCA II were determined for crystals prepared at pH 6.0, 8.5 and 11.0 and revealed no conformational changes of amino-acid side chains as a result of the use of citrate. However, the studies of Co(II)-HCA II did reveal a change in metal coordination from tetrahedral at pH 11 to a coordination consistent with a mixed population of both tetrahedral and penta-coordinate at pH 8.5 to an octahedral geometry characteristic of the oxidized enzyme Co(III)-HCA II at pH 6.0.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo sapiensGene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to Gene View: CA2
Go to UniProtKB:  P00918
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.292α = 90.00
b = 41.212β = 104.25
c = 72.253γ = 90.00
Software Package:
Software NamePurpose
SHELXmodel building
CrystalCleardata collection
HKL-2000data scaling
SHELXphasing
HKL-2000data reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-11-13 
  • Released Date: 2010-08-25 
  • Deposition Author(s): Avvaru, B.S.

Revision History 

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance