8OGD

Structure of zinc(II) double mutant human carbonic anhydrase II bound to thiocyanate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

Starting Model: experimental
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This is version 1.0 of the entry. See complete history


Literature

Elucidating the concentration-dependent effects of thiocyanate binding to carbonic anhydrase.

Silva, J.M.Cerofolini, L.Carvalho, A.L.Ravera, E.Fragai, M.Parigi, G.Macedo, A.L.Geraldes, C.F.G.C.Luchinat, C.

(2023) J Inorg Biochem 244: 112222-112222

  • DOI: https://doi.org/10.1016/j.jinorgbio.2023.112222
  • Primary Citation of Related Structures:  
    8OGD, 8OGE

  • PubMed Abstract: 

    Many proteins naturally carry metal centers, with a large share of them being in the active sites of several enzymes. Paramagnetic effects are a powerful source of structural information and, therefore, if the native metal is paramagnetic, or it can be functionally substituted with a paramagnetic one, paramagnetic effects can be used to study the metal sites, as well as the overall structure of the protein. One notable example is cobalt(II) substitution for zinc(II) in carbonic anhydrase. In this manuscript we investigate the effects of sodium thiocyanate on the chemical environment of the metal ion of the human carbonic anhydrase II. The electron paramagnetic resonance (EPR) titration of the cobalt(II) protein with thiocyanate shows that the EPR spectrum changes from A-type to C-type on passing from 1:1 to 1:1000-fold ligand excess. This indicates the occurrence of a change in the electronic structure, which may reflect a sizable change in the metal coordination environment in turn caused by a modification of the frozen solvent glass. However, paramagnetic nuclear magnetic resonance (NMR) data indicate that the metal coordination cage remains unperturbed even in 1:1000-fold ligand excess. This result proves that the C-type EPR spectrum observed at large ligand concentration should be ascribed to the low temperature at which EPR measurements are performed, which impacts on the structure of the protein when it is destabilized by a high concentration of a chaotropic agent.


  • Organizational Affiliation

    Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 2 
Gene Names: CA2
EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (PDB Primary Data)
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: 1.75 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.028α = 90
b = 41.333β = 104.427
c = 72.25γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
carelessdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--
Florence Instruct-ERIC CenterItaly--
Fundacao para a Ciencia e a TecnologiaPortugalUIDP/04378/2020
Fundacao para a Ciencia e a TecnologiaPortugalUIDB/04378/2020
Fundacao para a Ciencia e a TecnologiaPortugalLA/P/0140/2020
Fundacao para a Ciencia e a TecnologiaPortugalPD/BD/135180/2017
Fundacao para a Ciencia e a TecnologiaPortugalPD/00065/2013
Fundacao para a Ciencia e a TecnologiaPortugalRECI/BBB-BEP/0124/2012
Fundacao para a Ciencia e a TecnologiaPortugalROTEIRO/0031/2013PINFRA/22161/2016
Fundacao para a Ciencia e a TecnologiaPortugalUIDB/00313/2020
Fundacao para a Ciencia e a TecnologiaPortugalUIDP/00313/2020

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release