1XEG

Crystal structure of human carbonic anhydrase II complexed with an acetate ion

• PDB DOI: https://doi.org/10.2210/pdb1XEG/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-09-10 Released: 2005-09-27 
• Deposition Author(s): Mazumdar, P.A., Kumaran, D., Das, A.K., Swaminathan, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.210 
• R-Value Work: 0.180 

Literature

A novel acetate-bound complex of human carbonic anhydrase II.

Mazumdar, P.A., Kumaran, D., Swaminathan, S., Das, A.K.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 163-166

• PubMed: 18323598 
• DOI: https://doi.org/10.1107/S1744309108002078
• Primary Citation of Related Structures:  
  1XEG


• PubMed Abstract: 
  

  The enzyme human carbonic anhydrase II (hCAII) crystallized in an acetate-bound complex belonging to space group P2(1)2(1)2(1), with unit-cell parameters a = 42.3, b = 71.8, c = 74.0 A. The structure was solved by the molecular-replacement method and refined to an R value of 0.18 and an R(free) of 0.21. The acetate molecule replaced the zinc-bound water molecule in the structure, differing from previous reports regarding the site of acetate binding. This mode of binding disrupts the hydrogen-bonded solvent network required for activity of the enzyme. This mode of inhibitor binding is a novel one that has not been observed previously.

---

Organizational Affiliation: 

Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.41 kDa 
• Atom Count: 2,307 
• Modelled Residue Count: 258 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase II	A	260	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.210 
• R-Value Work: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.312	α = 90
b = 71.749	β = 90
c = 74.01	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing
CNS	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Mazumdar, P.A., Kumaran, D., Das, A.K., Swaminathan, S.

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations