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Vanadium in PDB 7adr: Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein

Enzymatic activity of Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein

All present enzymatic activity of Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein:
1.18.6.1;

Protein crystallography data

The structure of Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein, PDB code: 7adr was solved by M.Rohde, K.Grunau, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.45 / 1.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.579, 79.934, 107.223, 84.11, 72.42, 75.19
R / Rfree (%) 10.2 / 11.7

Other elements in 7adr:

The structure of Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Iron (Fe) 32 atoms

Vanadium Binding Sites:

The binding sites of Vanadium atom in the Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein (pdb code 7adr). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein, PDB code: 7adr:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 7adr

Go back to Vanadium Binding Sites List in 7adr
Vanadium binding site 1 out of 2 in the Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V501

b:8.4
occ:1.00
V1 A:D6N501 0.0 8.4 1.0
O5 A:HCA502 2.1 8.1 1.0
O7 A:HCA502 2.1 8.4 1.0
ND1 A:HIS423 2.3 8.2 1.0
S4B A:D6N501 2.3 8.6 1.0
S1B A:D6N501 2.3 8.7 1.0
S3B A:D6N501 2.4 8.9 1.0
FE5 A:D6N501 2.7 8.5 1.0
FE7 A:D6N501 2.7 8.7 1.0
FE6 A:D6N501 2.8 8.8 1.0
C7 A:HCA502 3.0 8.6 1.0
C3 A:HCA502 3.1 8.6 1.0
CE1 A:HIS423 3.2 9.2 1.0
CG A:HIS423 3.4 8.8 1.0
CX A:D6N501 3.6 8.8 1.0
CB A:HIS423 3.8 8.9 1.0
C2 A:HCA502 4.0 8.9 1.0
O6 A:HCA502 4.2 9.7 1.0
O A:HOH845 4.2 10.4 1.0
C4 A:HCA502 4.3 8.8 1.0
O2 A:BCT503 4.3 9.3 1.0
O1 A:HCA502 4.3 10.1 1.0
C5 A:HCA502 4.4 9.3 1.0
NE2 A:HIS423 4.4 9.4 1.0
CD2 A:HIS423 4.5 9.3 1.0
CA A:HIS423 4.5 8.3 1.0
C A:CMO504 4.6 7.4 1.0
NZ A:LYS83 4.7 10.9 1.0
C1 A:HCA502 4.8 9.0 1.0
S5A A:D6N501 4.9 9.3 1.0

Vanadium binding site 2 out of 2 in 7adr

Go back to Vanadium Binding Sites List in 7adr
Vanadium binding site 2 out of 2 in the Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of Co Bound As Bridging Ligand at the Active Site of Vanadium Nitrogenase Vfe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:V501

b:7.0
occ:1.00
V1 D:D6N501 0.0 7.0 1.0
O6 D:HCA502 2.1 7.1 1.0
O7 D:HCA502 2.2 7.1 1.0
ND1 D:HIS423 2.3 7.3 1.0
S4B D:D6N501 2.3 7.3 1.0
S1B D:D6N501 2.4 7.3 1.0
S3B D:D6N501 2.4 7.5 1.0
FE5 D:D6N501 2.7 7.2 1.0
FE7 D:D6N501 2.7 7.3 1.0
FE6 D:D6N501 2.8 7.4 1.0
C7 D:HCA502 3.0 7.3 1.0
C3 D:HCA502 3.1 6.8 1.0
CE1 D:HIS423 3.2 7.6 1.0
CG D:HIS423 3.4 7.2 1.0
CX D:D6N501 3.6 7.0 1.0
CB D:HIS423 3.8 7.5 1.0
C2 D:HCA502 4.0 7.3 1.0
O5 D:HCA502 4.2 8.3 1.0
O D:HOH852 4.2 8.9 1.0
C4 D:HCA502 4.3 7.2 1.0
O1 D:BCT503 4.3 7.8 1.0
O2 D:HCA502 4.4 8.4 1.0
C5 D:HCA502 4.4 7.8 1.0
NE2 D:HIS423 4.4 8.0 1.0
CD2 D:HIS423 4.5 7.9 1.0
CA D:HIS423 4.5 7.5 1.0
C D:CMO504 4.6 6.0 1.0
NZ D:LYS83 4.7 9.3 1.0
C1 D:HCA502 4.8 7.4 1.0
S5A D:D6N501 4.9 8.0 1.0

Reference:

M.Rohde, K.Grunau, O.Einsle. Co Binding to the Fev Cofactor of Co-Reducing Vanadium Nitrogenase at Atomic Resolution. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 32915491
DOI: 10.1002/ANIE.202010790
Page generated: Wed Dec 16 02:32:17 2020

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