2H4N

H94N CARBONIC ANHYDRASE II COMPLEXED WITH ACETAZOLAMIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Histidine --> carboxamide ligand substitutions in the zinc binding site of carbonic anhydrase II alter metal coordination geometry but retain catalytic activity.

Lesburg, C.A.Huang, C.Christianson, D.W.Fierke, C.A.

(1997) Biochemistry 36: 15780-15791

  • DOI: 10.1021/bi971296x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The catalytic zinc ion of human carbonic anhydrase II (CAII) is coordinated by three histidine ligands (H94, H96, and H119) and a hydroxide ion with tetrahedral geometry. Structural and functional analysis of variants in which the zinc ligands H94 an ...

    The catalytic zinc ion of human carbonic anhydrase II (CAII) is coordinated by three histidine ligands (H94, H96, and H119) and a hydroxide ion with tetrahedral geometry. Structural and functional analysis of variants in which the zinc ligands H94 and H119 are substituted with asparagine and glutamine, and comparison with results obtained with aspartate and glutamate substitutions indicate that the neutral ligand field provided by the protein optimizes the electrostatic environment for the catalytic function of the metal ion, including stabilization of bound anions. This is demonstrated by catalytic activity measurements for ester hydrolysis and CO2 hydration, as well as sulfonamide inhibitor affinity assays. High-resolution X-ray crystal structure determinations of H94N, H119N, and H119Q CAIIs reveal that the engineered carboxamide side chains coordinate to zinc with optimal stereochemistry. However, zinc coordination geometry remains tetrahedral only in H119Q CAII. Metal geometry changes to trigonal bipyramidal in H119N CAII due to the addition of a second water molecule to the zinc coordination polyhedron and also in H94N CAII due to the displacement of zinc-bound hydroxide by the bidentate coordination of a Tris molecule. Possibly, the bulky histidine imidazole ligands of the native enzyme play a role in disfavoring trigonal bipyramidal coordination geometry for zinc. Protein-metal affinity is significantly compromised by all histidine --> carboxamide ligand substitutions. Diminished affinity may result from significant movements (up to 1 A) of the metal ion from its position in the wild-type enzyme, as well as the associated, minor conformational changes of metal ligands and their neighboring residues.


    Organizational Affiliation

    Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CARBONIC ANHYDRASE II
A
259Homo sapiensMutation(s): 1 
Gene Names: CAIICA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AZM
Query on AZM

Download CCD File 
A
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE
C4 H6 N4 O3 S2
BZKPWHYZMXOIDC-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AZMKi:  3300   nM  BindingDB
AZMKi:  2150   nM  BindingDB
AZMKi:  2000   nM  BindingDB
AZMKi:  2100   nM  BindingDB
AZMKd:  1.5   nM  BindingDB
AZMIC50:  89.9000015258789   nM  BindingDB
AZMIC50:  16.200000762939453   nM  BindingDB
AZMKd:  46   nM  BindingDB
AZMIC50:  53.099998474121094   nM  BindingDB
AZMKd:  38   nM  BindingDB
AZMIC50:  69.69999694824219   nM  BindingDB
AZMIC50:  6   nM  BindingDB
AZMIC50:  110.27999877929688   nM  BindingDB
AZMKi:  10.100000381469727   nM  BindingDB
AZMIC50:  47.599998474121094   nM  BindingDB
AZMIC50:  48.099998474121094   nM  BindingDB
AZMKd:  6.800000190734863   nM  BindingDB
AZMKd:  0.07000000029802322   nM  BindingDB
AZMKi:  184   nM  BindingDB
AZMIC50:  10   nM  BindingDB
AZMIC50:  12   nM  BindingDB
AZMKd:  10   nM  BindingDB
AZMKi:  159   nM  BindingDB
AZMKi:  420   nM  BindingDB
AZMKi:  370   nM  BindingDB
AZMKi:  374   nM  BindingDB
AZMIC50:  20   nM  BindingDB
AZMIC50:  18.5   nM  BindingDB
AZMIC50:  24   nM  BindingDB
AZMIC50:  23   nM  BindingDB
AZMIC50:  13   nM  BindingDB
AZMKi:  250   nM  BindingDB
AZMIC50:  14   nM  BindingDB
AZMKi:  3.299999952316284   nM  BindingDB
AZMIC50:  0.47999998927116394   nM  BindingDB
AZMIC50:  15   nM  BindingDB
AZMKd:  18   nM  BindingDB
AZMKd:  17   nM  BindingDB
AZMIC50:  36   nM  BindingDB
AZMIC50:  37   nM  BindingDB
AZMIC50:  38   nM  BindingDB
AZMKi:  61   nM  BindingDB
AZMKi:  0.800000011920929   nM  BindingDB
AZMIC50:  25   nM  BindingDB
AZMIC50:  28   nM  BindingDB
AZMKi:  33   nM  BindingDB
AZMIC50:  29   nM  BindingDB
AZMKi:  0.3400000035762787   nM  BindingDB
AZMKd :  2   nM  PDBBind
AZMKi:  104   nM  BindingDB
AZMIC50:  68   nM  BindingDB
AZMKi:  2   nM  Binding MOAD
AZMIC50:  92.5   nM  BindingDB
AZMIC50:  98.30000305175781   nM  BindingDB
AZMIC50:  56.5   nM  BindingDB
AZMIC50:  63   nM  BindingDB
AZMKi:  25   nM  BindingDB
AZMKi:  12   nM  BindingDB
AZMIC50:  152   nM  BindingDB
AZMKi:  15   nM  BindingDB
AZMIC50:  77.80000305175781   nM  BindingDB
AZMIC50:  60.400001525878906   nM  BindingDB
AZMIC50:  48.900001525878906   nM  BindingDB
AZMKi:  11   nM  BindingDB
AZMKd:  0.05999999865889549   nM  BindingDB
AZMKi:  10   nM  BindingDB
AZMIC50:  124   nM  BindingDB
AZMKi:  25   nM  BindingDB
AZMIC50:  283   nM  BindingDB
AZMIC50:  285   nM  BindingDB
AZMIC50:  309   nM  BindingDB
AZMIC50:  351   nM  BindingDB
AZMKi:  4.900000095367432   nM  BindingDB
AZMIC50:  6.699999809265137   nM  BindingDB
AZMIC50:  362   nM  BindingDB
AZMIC50:  370   nM  BindingDB
AZMKi:  18   nM  BindingDB
AZMIC50:  220   nM  BindingDB
AZMIC50:  8.899999618530273   nM  BindingDB
AZMKi:  22   nM  BindingDB
AZMKi:  12.300000190734863   nM  BindingDB
AZMIC50:  440   nM  BindingDB
AZMIC50:  441   nM  BindingDB
AZMKi:  7   nM  BindingDB
AZMKd:  2.5999999046325684   nM  BindingDB
AZMIC50:  48.29999923706055   nM  BindingDB
AZMIC50:  2400   nM  BindingDB
AZMIC50:  2800   nM  BindingDB
AZMIC50:  34.29999923706055   nM  BindingDB
AZMIC50:  4500   nM  BindingDB
AZMIC50:  8.880000114440918   nM  BindingDB
AZMIC50:  4300   nM  BindingDB
AZMIC50:  68.5999984741211   nM  BindingDB
AZMIC50:  3800   nM  BindingDB
AZMKi:  40.810001373291016   nM  BindingDB
AZMIC50:  4020   nM  BindingDB
AZMIC50:  4100   nM  BindingDB
AZMIC50:  3900   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.7α = 90
b = 41.7β = 104.6
c = 73γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-09-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance