3KKX | pdb_00003kkx

Neutron structure of human carbonic anhydrase II

• PDB DOI: https://doi.org/10.2210/pdb3KKX/pdb

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


• Deposited: 2009-11-06 Released: 2010-01-12 
• Deposition Author(s): Fisher, S.Z., Langan, P.A.

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Experimental Data Snapshot

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.286 (Depositor) 
• R-Value Work: 
  0.275 (Depositor) 

Starting Model: experimental

Literature

Neutron structure of human carbonic anhydrase II: implications for proton transfer.

Fisher, S.Z., Kovalevsky, A.Y., Domsic, J.F., Mustyakimov, M., McKenna, R., Silverman, D.N., Langan, P.A.

(2010) Biochemistry 49: 415-421

• PubMed: 20025241 
• DOI: https://doi.org/10.1021/bi901995n
• Primary Citation Related Structures: 
  3KKX


• PubMed Abstract: 
  

  Human carbonic anhydrase II (HCA II) catalyzes the reversible hydration of carbon dioxide to form bicarbonate and a proton. Despite many high-resolution X-ray crystal structures, mutagenesis, and kinetic data, the structural details of the active site, especially the proton transfer pathway, are unclear. A large HCA II crystal was prepared at pH 9.0 and subjected to vapor H-D exchange to replace labile hydrogens with deuteriums. Neutron diffraction studies were conducted at the Protein Crystallography Station at Los Alamos National Laboratory. The structure to 2.0 A resolution reveals several interesting active site features: (1) the Zn-bound solvent appearing to be predominantly a D(2)O molecule, (2) the orientation and hydrogen bonding pattern of solvent molecules in the active site cavity, (3) the side chain of His64 being unprotonated (neutral) and predominantly in an inward conformation pointing toward the zinc, and (4) the phenolic side chain of Tyr7 appearing to be unprotonated. The implications of these details are discussed, and a proposed mechanism for proton transfer is presented.

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Organizational Affiliation: 
• Bioscience Division MS M888, Los Alamos National Laboratory, Los Alamos, New Mexico 87544, USA. [e-mail]

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: 29.35 kDa 
• Atom Count: 2,286 
• Modeled Residue Count: 258 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: CA2, HCA II 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: NEUTRON DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.286 (Depositor) 
• R-Value Work:  0.275 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.6	α = 90
b = 41.56	β = 104.56
c = 72.82	γ = 90

Software Package:

Software Name	Purpose
PCS	data collection
nCNS	refinement
d*TREK	data reduction
SCALA	data scaling
nCNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Fisher, S.Z., Langan, P.A.

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-04-25
  Changes: Data collection
• Version 1.3: 2018-06-20
  Changes: Data collection
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description