Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.86 kDa 
• Atom Count: 2375 
• Residue Count: 258 
• Unique protein chains: 1

2NNG

Structure of inhibitor binding to Carbonic Anhydrase II

• DOI: 10.2210/pdb2NNG/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-10-24 Released: 2007-05-08 
• Deposition Author(s): Christianson, D.W., Jude, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.165 
• R-Value Observed: 0.132 

Literature

Structural Analysis of Charge Discrimination in the Binding of Inhibitors to Human Carbonic Anhydrases I and II.

Srivastava, D.K., Jude, K.M., Banerjee, A.L., Haldar, M., Manokaran, S., Kooren, J., Mallik, S., Christianson, D.W.

(2007) J Am Chem Soc 129: 5528-5537

• PubMed: 17407288 
• DOI: 10.1021/ja068359w
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Despite the similarity in the active site pockets of carbonic anhydrase (CA) isozymes I and II, the binding affinities of benzenesulfonamide inhibitors are invariably higher with CA II as compared to CA I. To explore the structural basis of this molecular recognition phenomenon, we have designed and synthesized simple benzenesulfonamide inhibitors substituted at the para position with positively charged, negatively charged, and neutral functional groups, and we have determined the affinities and X-ray crystal structures of their enzyme complexes. The para-substituents are designed to bind in the midsection of the 15 A deep active site cleft, where interactions with enzyme residues and solvent molecules are possible. We find that a para-substituted positively charged amino group is more poorly tolerated in the active site of CA I compared with CA II. In contrast, a para-substituted negatively charged carboxylate substituent is tolerated equally well in the active sites of both CA isozymes. Notably, enzyme-inhibitor affinity increases upon neutralization of inhibitor charged groups by amidation or esterification. These results inform the design of short molecular linkers connecting the benzenesulfonamide group and a para-substituted tail group in "two-prong" CA inhibitors: an optimal linker segment will be electronically neutral, yet capable of engaging in at least some hydrogen bond interactions with protein residues and/or solvent. Microcalorimetric data reveal that inhibitor binding to CA I is enthalpically less favorable and entropically more favorable than inhibitor binding to CA II. This contrasting behavior may arise in part from differences in active site desolvation and the conformational entropy of inhibitor binding to each isozyme active site.

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Organizational Affiliation: 

Department of Chemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0  Gene Names: 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZYX	A	4-(2-AMINOETHYL)BENZENESULFONAMIDE C8 H12 N2 O2 S FXNSVEQMUYPYJS-UHFFFAOYSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CMH	A	L-PEPTIDE LINKING	C4 H9 Hg N O2 S		CYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ZYX	IC50:  3100   nM  BindingDB
ZYX	Kd:  4400   nM  Binding MOAD
ZYX	Ki:  37   nM  BindingDB
ZYX	Ki:  21000   nM  BindingDB
ZYX	Kd :  4400   nM  PDBBind
ZYX	Ki:  159   nM  BindingDB
ZYX	Ki:  160   nM  BindingDB
ZYX	Ki:  160000   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.165 
• R-Value Observed: 0.132 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.289	α = 90
b = 41.44	β = 104.56
c = 71.975	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-10-24 
• Released Date: 2007-05-08 
Deposition Author(s): Christianson, D.W., Jude, K.M.

Revision History 

• Version 1.0: 2007-05-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description