Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.32 kDa 
• Atom Count: 2198 
• Residue Count: 257 
• Unique protein chains: 1

1H4N

H94N CARBONIC ANHYDRASE II COMPLEXED WITH TRIS

• DOI: 10.2210/pdb1H4N/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1997-05-29 Released: 1997-09-17 
• Deposition Author(s): Lesburg, C.A., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.154 
• R-Value Observed: 0.154 

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

• PubMed: 9398308 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CARBONIC ANHYDRASE II	A	259	Homo sapiens	Mutation(s): 1  Gene Names: CAII, CA2 EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens) Go to UniProtKB:  P00918
NIH Common Fund Data Resources
PHAROS  P00918 GTEx  ENSG00000104267

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	A	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
TRS	Ki :  12000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.207 
• R-Value Work: 0.154 
• R-Value Observed: 0.154 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.7	α = 90
b = 41.7	β = 104.6
c = 73	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-05-29 
• Released Date: 1997-09-17 
Deposition Author(s): Lesburg, C.A., Christianson, D.W.

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