3KIG

Mutant carbonic anhydrase II in complex with an azide and an alkyne

• PDB DOI: https://doi.org/10.2210/pdb3KIG/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-11-02 Released: 2010-11-17 
• Deposition Author(s): Schulze-Wischeler, J., Niehage, N.U., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.191 
• R-Value Work: 0.133 
• R-Value Observed: 0.127 

Literature

Stereo- and Regioselective Azide/Alkyne Cycloadditions in Carbonic Anhydrase II via Tethering, Monitored by Crystallography and Mass Spectrometry.

Schulze Wischeler, J., Sun, D., Sandner, N.U., Linne, U., Heine, A., Koert, U., Klebe, G.

(2011) Chemistry 17: 5842-5851

• PubMed: 21506176 
• DOI: https://doi.org/10.1002/chem.201002437
• Primary Citation of Related Structures:  
  3KIG, 3KNE


• PubMed Abstract: 
  

  The carbonic anhydrase II mutant His64Cys was prepared and applied to tethered alkyne/azide cycloaddition reactions. The azide component could be tethered to the enzyme surface through a disulfide bridge, while the alkyne component was reversibly coordinated through a sulfonamide anchor to the zinc ion in the original catalytic center of the enzyme. The incipient orientation of the reactants in the binding site and of the formed triazole product were characterized by crystallography. The reaction progression could be monitored by HPLC-MS analysis.

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Organizational Affiliation: 

Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.34 kDa 
• Atom Count: 2,318 
• Modelled Residue Count: 257 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	265	Homo sapiens	Mutation(s): 1  Gene Names: CA2 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DA4	D [auth A]	3-ethynylbenzenesulfonamide C8 H7 N O2 S WGEWFHNQCHZZMF-UHFFFAOYSA-N
DA9	C [auth A], E [auth A]	2-azido-N-(2-sulfanylethyl)ethanamide C4 H8 N4 O S JSHBGIMPVAGZMY-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DA4	PDBBind:  3KIG	IC50: 245 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.191 
• R-Value Work: 0.133 
• R-Value Observed: 0.127 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.4	α = 90
b = 41.4	β = 104.1
c = 72.3	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
CNS	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-17 
Deposition Author(s): Schulze-Wischeler, J., Niehage, N.U., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2010-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.4: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.5: 2024-02-21
  Changes: Data collection