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PDBsum entry 3ks3

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protein ligands metals links
Lyase PDB id
3ks3
Jmol PyMol
Contents
Protein chain
257 a.a. *
Ligands
GOL
Metals
_ZN
Waters ×483
* Residue conservation analysis
PDB id:
3ks3
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.
Resolution:
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
Date:
20-Nov-09     Release date:   26-Jan-10    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.1  - Carbonic anhydrase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
H(2)CO(3)
= 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.
 
  ABSTRACT  
 
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.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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