7ADR

CO bound as bridging ligand at the active site of vanadium nitrogenase VFe protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.117 
  • R-Value Work: 0.102 
  • R-Value Observed: 0.102 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

CO Binding to the FeV Cofactor of CO-Reducing Vanadium Nitrogenase at Atomic Resolution.

Rohde, M.Grunau, K.Einsle, O.

(2020) Angew Chem Int Ed Engl 59: 23626-23630

  • DOI: https://doi.org/10.1002/anie.202010790
  • Primary Citation of Related Structures:  
    7ADR, 7ADY

  • PubMed Abstract: 

    Nitrogenases reduce N 2 , the most abundant element in Earth's atmosphere that is otherwise resistant to chemical conversions due to its stable triple bond. Vanadium nitrogenase stands out in that it additionally processes carbon monoxide, a known inhibitor of the reduction of all substrates other than H + . The reduction of CO leads to the formation of hydrocarbon products, holding the potential for biotechnological applications in analogy to the industrial Fischer-Tropsch process. Here we report the most highly resolved structure of vanadium nitrogenase to date at 1.0 Å resolution, with CO bound to the active site cofactor after catalytic turnover. CO bridges iron ions Fe2 and Fe6, replacing sulfide S2B, in a binding mode that is in line with previous reports on the CO complex of molybdenum nitrogenase. We discuss the structural consequences of continued turnover when CO is removed, which involve the replacement of CO possibly by OH - , the movement of Q176 D and K361 D , the return of sulfide and the emergence of two additional water molecules that are absent in the CO-bound state.


  • Organizational Affiliation

    Institut für Biochemie, Fakultät für Chemie und Pharmazie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg im Breisgau, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase vanadium-iron protein alpha chain
A, D
474Azotobacter vinelandiiMutation(s): 0 
Gene Names: vnfD
EC: 1.18.6.1
UniProt
Find proteins for P16855 (Azotobacter vinelandii)
Explore P16855 
Go to UniProtKB:  P16855
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16855
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase vanadium-iron protein beta chain
B, E
475Azotobacter vinelandiiMutation(s): 0 
Gene Names: vnfK
EC: 1.18.6.1
UniProt
Find proteins for P16856 (Azotobacter vinelandii)
Explore P16856 
Go to UniProtKB:  P16856
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16856
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nitrogenase vanadium-iron protein delta chain
C, F
113Azotobacter vinelandiiMutation(s): 0 
Gene Names: vnfG
EC: 1.18.6.1
UniProt
Find proteins for P16857 (Azotobacter vinelandii)
Explore P16857 
Go to UniProtKB:  P16857
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16857
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D6N (Subject of Investigation/LOI)
Query on D6N

Download Ideal Coordinates CCD File 
G [auth A],
U [auth D]
FeV
C Fe7 N S7 V
YNVNIECPQFRAMK-UHFFFAOYSA-N
CLF
Query on CLF

Download Ideal Coordinates CCD File 
M [auth B],
Z [auth E]
FE(8)-S(7) CLUSTER
Fe8 S7
JKVMXLBGZBULKV-UHFFFAOYSA-N
HCA
Query on HCA

Download Ideal Coordinates CCD File 
H [auth A],
V [auth D]
3-HYDROXY-3-CARBOXY-ADIPIC ACID
C7 H10 O7
XKJVEVRQMLKSMO-SSDOTTSWSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
Y [auth D]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
DA [auth E]
FA [auth F]
AA [auth E],
BA [auth E],
CA [auth E],
DA [auth E],
FA [auth F],
P [auth B],
Q [auth B],
R [auth B],
T [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
I [auth A],
W [auth D]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CMO (Subject of Investigation/LOI)
Query on CMO

Download Ideal Coordinates CCD File 
J [auth A],
X [auth D]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
EA [auth F],
N [auth B],
O [auth B],
S [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.117 
  • R-Value Work: 0.102 
  • R-Value Observed: 0.102 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.579α = 84.11
b = 79.934β = 72.42
c = 107.223γ = 75.19
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Germany310656

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description