Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 44.90 kDa 
• Atom Count: 3612 
• Residue Count: 396 
• Unique protein chains: 1

1XDC

Hydrogen Bonding in Human Manganese Superoxide Dismutase containing 3-Fluorotyrosine

• DOI: 10.2210/pdb1XDC/pdb

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


• Deposited: 2004-09-05 Released: 2005-03-22 
• Deposition Author(s): Ayala, I., Perry, J.J., Szczepanski, J., Cabelli, D.E., Tainer, J.A., Vala, M.T., Nick, H.S., Silverman, D.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.252 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Literature

Hydrogen bonding in human manganese superoxide dismutase containing 3-fluorotyrosine

Ayala, I., Perry, J.J., Szczepanski, J., Tainer, J.A., Vala, M.T., Nick, H.S., Silverman, D.N.

(2005) Biophys J 89: 4171-4179

• PubMed: 16150974 
• DOI: 10.1529/biophysj.105.060616
• Primary Citation of Related Structures:  
  1XDC, 1XIL


• PubMed Abstract: 
  

Incorporation of 3-fluorotyrosine and site-specific mutagenesis has been utilized with Fourier transform infrared (FTIR) spectroscopy and x-ray crystallography to elucidate active-site structure and the role of an active-site residue Tyr34 in human manganese superoxide dismutase (MnSOD). Calculated harmonic frequencies at the B3LYP/6-31G** level of theory for L-tyrosine and its 3-fluorine substituted analog are compared to experimental frequencies for vibrational mode assignments. Each of the nine tyrosine residues in each of the four subunits of the homotetramer of human MnSOD was replaced with 3-fluorotyrosine. The crystal structures of the unfluorinated and fluorinated wild-type MnSOD are nearly superimposable with the root mean-square deviation for 198 alpha-carbon atoms at 0.3 A. The FTIR data show distinct vibrational modes arising from 3-fluorotyrosine in MnSOD. Comparison of spectra for wild-type and Y34F MnSOD showed that the phenolic hydroxyl of Tyr34 is hydrogen bonded, acting as a proton donor in the active site. Comparison with crystal structures demonstrates that the hydroxyl of Tyr34 is a hydrogen bond donor to an adjacent water molecule; this confirms the participation of Tyr34 in a network of residues and water molecules that extends from the active site to the adjacent subunit.

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Organizational Affiliation: 

Department of Pharmacology, University of Florida, Gainesville, Florida 32610, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Mn], mitochondrial	A, B	198	Homo sapiens	Mutation(s): 9  Gene Names: SOD2 EC: 1.15.1.1
Find proteins for P04179 (Homo sapiens) Explore P04179  Go to UniProtKB:  P04179
NIH Common Fund Data Resources
PHAROS:  P04179 GTEx:  ENSG00000112096

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	A, B	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YOF	A,B	L-PEPTIDE LINKING	C9 H10 F N O3		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.252 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.036	α = 90
b = 75.419	β = 90
c = 67.818	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
XFIT	data reduction
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-09-05 
• Released Date: 2005-03-22 
Deposition Author(s): Ayala, I., Perry, J.J., Szczepanski, J., Cabelli, D.E., Tainer, J.A., Vala, M.T., Nick, H.S., Silverman, D.N.

Revision History 

• Version 1.0: 2005-03-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model