Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 4-mer -A4 

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

Macromolecule Content

• Total Structure Weight: 233860.78 
• Atom Count: 16381 
• Residue Count: 2030 
• Unique protein chains: 2

4TKU

Reactivated Nitrogenase MoFe-protein from A. vinelandii

• DOI: 10.2210/pdb4TKU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Azotobacter vinelandii


• Deposited: 2014-05-27 Released: 2014-10-01 
• Deposition Author(s): Spatzal, T., Perez, K., Einsle, O., Howard, J.B., Rees, D.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 0.142 
• R-Value Work: 0.132 

Literature

Ligand binding to the FeMo-cofactor: structures of CO-bound and reactivated nitrogenase.

Spatzal, T., Perez, K.A., Einsle, O., Howard, J.B., Rees, D.C.

(2014) Science 345: 1620-1623

• PubMed: 25258081 
• DOI: 10.1126/science.1256679
• Primary Citation of Related Structures:  
  4TKV


• PubMed Abstract: 
  

The mechanism of nitrogenase remains enigmatic, with a major unresolved issue concerning how inhibitors and substrates bind to the active site. We report a crystal structure of carbon monoxide (CO)-inhibited nitrogenase molybdenum-iron (MoFe)-protein at 1.50 angstrom resolution, which reveals a CO molecule bridging Fe2 and Fe6 of the FeMo-cofactor. The μ2 binding geometry is achieved by replacing a belt-sulfur atom (S2B) and highlights the generation of a reactive iron species uncovered by the displacement of sulfur. The CO inhibition is fully reversible as established by regain of enzyme activity and reappearance of S2B in the 1.43 angstrom resolution structure of the reactivated enzyme. The substantial and reversible reorganization of the FeMo-cofactor accompanying CO binding was unanticipated and provides insights into a catalytically competent state of nitrogenase.

---

Organizational Affiliation: 

Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, MailCode 114-96, California Institute of Technology, Pasadena, CA 91125, USA. [e-mail] [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Nitrogenase molybdenum-iron protein alpha chain	A, C	492	Azotobacter vinelandii	Mutation(s): 0  Gene Names: nifD EC: 1.18.6.1
Find proteins for P07328 (Azotobacter vinelandii) Go to UniProtKB:  P07328

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Nitrogenase molybdenum-iron protein beta chain	B, D	523	Azotobacter vinelandii	Mutation(s): 0  Gene Names: nifK EC: 1.18.6.1
Find proteins for P07329 (Azotobacter vinelandii) Go to UniProtKB:  P07329

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A, C	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
FE2	B, D	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
IMD	A, B, C, D	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ICS	A, C	iron-sulfur-molybdenum cluster with interstitial carbon C Fe7 Mo S9 DDQFAOMIVKLFON-UHFFFAOYSA-N
CLF	B, D	FE(8)-S(7) CLUSTER Fe8 S7 JKVMXLBGZBULKV-DHHOTQGYAO
HCA	A, C	3-HYDROXY-3-CARBOXY-ADIPIC ACID C7 H10 O7 XKJVEVRQMLKSMO-SSDOTTSWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 0.142 
• R-Value Work: 0.132 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 80.941	α = 90.00
b = 130.785	β = 110.58
c = 107.005	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-05-27 
• Released Date: 2014-10-01 
• Deposition Author(s): Spatzal, T., Perez, K., Einsle, O., Howard, J.B., Rees, D.C.

Revision History 

• Version 1.0: 2014-10-01
  Type: Initial release
• Version 1.1: 2014-10-15
  Type: Database references