PDBsum entry 3ks3

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Lyase PDB id
Jmol PyMol
Protein chain
257 a.a. *
Waters ×483
* Residue conservation analysis
PDB id:
Name: Lyase
Title: High resolution structure of human carbonic anhydrase ii at 0.9 a
Structure: Carbonic anhydrase 2. Chain: a. Synonym: carbonic anhydrase ii, ca-ii, carbonate dehydratase ii, carbonic anhydrasE C, cac. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ca2. Expressed in: escherichia coli. Expression_system_taxid: 562.
0.90Å     R-factor:   0.138     R-free:   0.145
Authors: B.S.Avvaru
Key ref: B.S.Avvaru et al. (2010). A short, strong hydrogen bond in the active site of human carbonic anhydrase II. Biochemistry, 49, 249-251. PubMed id: 20000378
20-Nov-09     Release date:   26-Jan-10    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2
260 a.a.
257 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Carbonic anhydrase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
= CO(2)
+ H(2)O
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular space   11 terms 
  Biological process     angiotensin-mediated signaling pathway   22 terms 
  Biochemical function     protein binding     6 terms  


    Added reference    
Biochemistry 49:249-251 (2010)
PubMed id: 20000378  
A short, strong hydrogen bond in the active site of human carbonic anhydrase II.
B.S.Avvaru, C.U.Kim, K.H.Sippel, S.M.Gruner, M.Agbandje-McKenna, D.N.Silverman, R.McKenna.
The crystal structure of human carbonic anhydrase II (HCA II) obtained at 0.9 A resolution reveals that a water molecule, termed deep water, Dw, and bound in a hydrophobic pocket of the active site forms a short, strong hydrogen bond with the zinc-bound solvent molecule, a conclusion based on the observed oxygen-oxygen distance of 2.45 A. This water structure has similarities with hydrated hydroxide found in crystals of certain inorganic complexes. The energy required to displace Dw contributes in significant part to the weak binding of CO(2) in the enzyme-substrate complex, a weak binding that enhances k(cat) for the conversion of CO(2) into bicarbonate. In addition, this short, strong hydrogen bond is expected to contribute to the low pK(a) of the zinc-bound water and to promote proton transfer in catalysis.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21377464 J.A.Cuesta-Seijo, M.S.Borchert, J.C.Navarro-Poulsen, K.M.Schnorr, S.B.Mortensen, and L.Lo Leggio (2011).
Structure of a dimeric fungal α-type carbonic anhydrase.
  FEBS Lett, 585, 1042-1048.  
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