4E5Q

Human Carbonic Anhydrase II in complex with cyanate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7024 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Human carbonic anhydrase II-cyanate inhibitor complex: putting the debate to rest.

West, D.Pinard, M.A.Tu, C.Silverman, D.N.McKenna, R.

(2014) Acta Crystallogr F Struct Biol Commun 70: 1324-1327

  • DOI: 10.1107/S2053230X14018135
  • Primary Citation of Related Structures:  4QEF

  • PubMed Abstract: 
  • The binding of anions to carbonic anhydrase II (CA II) has been attributed to high affinity for the active-site zinc. An anion of interest is cyanate, for which contrasting binding modes have been reported in the literature. Previous spectroscopic da ...

    The binding of anions to carbonic anhydrase II (CA II) has been attributed to high affinity for the active-site zinc. An anion of interest is cyanate, for which contrasting binding modes have been reported in the literature. Previous spectroscopic data have shown cyanate behaving as an inhibitor, directly binding to the zinc, in contrast to previous crystallographic data that implied that cyanate acts as a substrate mimic that is not directly bound to the zinc but overlaps with the binding site of the substrate CO2. Wild-type and the V207I variant of CA II have been expressed and X-ray crystal structures of their cyanate complexes have been determined to 1.7 and 1.5 Å resolution, respectively. The rationale for the V207I CA II variant was its close proximity to the CO2-binding site. Both structures clearly show that the cyanate binds directly to the zinc. In addition, inhibition constants (∼40 µM) were measured using (18)O-exchange mass spectrometry for wild-type and V207I CA II and were similar to those determined previously (Supuran et al., 1997). Hence, it is concluded that under the conditions of these experiments the binding of cyanate to CA II is directly to the zinc, displacing the zinc-bound solvent molecule, and not in a site that overlaps with the CO2 substrate-binding site.


    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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
0NM
Query on 0NM

Download SDF File 
Download CCD File 
A
cyanic acid
C H N O
XLJMAIOERFSOGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7024 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.192α = 90.00
b = 41.010β = 104.51
c = 71.536γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
SCALEPACKdata scaling
PHENIXrefinement
CrystalCleardata collection
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-03-14 
  • Released Date: 2013-03-27 
  • Deposition Author(s): West, D., McKenna, R.

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2014-10-08
    Type: Database references
  • Version 1.2: 2014-10-22
    Type: Database references
  • Version 1.3: 2017-11-15
    Type: Refinement description