6LV4

Co- Carbonic Anhydrase II pH 11.0 20 atm CO2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.113 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Elucidating the role of metal ions in carbonic anhydrase catalysis.

Kim, J.K.Lee, C.Lim, S.W.Adhikari, A.Andring, J.T.McKenna, R.Ghim, C.M.Kim, C.U.

(2020) Nat Commun 11: 4557-4557

  • DOI: https://doi.org/10.1038/s41467-020-18425-5
  • Primary Citation of Related Structures:  
    6LUU, 6LUV, 6LUW, 6LUX, 6LUY, 6LUZ, 6LV1, 6LV2, 6LV3, 6LV4, 6LV5, 6LV6, 6LV7, 6LV8, 6LV9, 6LVA

  • PubMed Abstract: 

    Why metalloenzymes often show dramatic changes in their catalytic activity when subjected to chemically similar but non-native metal substitutions is a long-standing puzzle. Here, we report on the catalytic roles of metal ions in a model metalloenzyme system, human carbonic anhydrase II (CA II). Through a comparative study on the intermediate states of the zinc-bound native CA II and non-native metal-substituted CA IIs, we demonstrate that the characteristic metal ion coordination geometries (tetrahedral for Zn 2+ , tetrahedral to octahedral conversion for Co 2+ , octahedral for Ni 2+ , and trigonal bipyramidal for Cu 2+ ) directly modulate the catalytic efficacy. In addition, we reveal that the metal ions have a long-range (~10 Å) electrostatic effect on restructuring water network in the active site. Our study provides evidence that the metal ions in metalloenzymes have a crucial impact on the catalytic mechanism beyond their primary chemical properties.


  • Organizational Affiliation

    Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.


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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT (Subject of Investigation/LOI)
Query on BCT

Download Ideal Coordinates CCD File 
E [auth A]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CO (Subject of Investigation/LOI)
Query on CO

Download Ideal Coordinates CCD File 
D [auth A]COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
CO2 (Subject of Investigation/LOI)
Query on CO2

Download Ideal Coordinates CCD File 
B [auth A],
F [auth A]
CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.113 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.358α = 90
b = 41.458β = 104.02
c = 72.307γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2019R1A2C1004274

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description