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Vanadium in PDB 7ady: Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein

Enzymatic activity of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein

All present enzymatic activity of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein:
1.18.6.1;

Protein crystallography data

The structure of Co-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein, PDB code: 7ady 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) 46.66 / 1.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.576, 80.027, 107.200, 83.99, 72.48, 75.03
R / Rfree (%) 12.1 / 14.1

Other elements in 7ady:

The structure of Co-Removed State of 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-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein (pdb code 7ady). 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-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein, PDB code: 7ady:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 7ady

Go back to Vanadium Binding Sites List in 7ady
Vanadium binding site 1 out of 2 in the Co-Removed State of 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-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V501

b:7.8
occ:1.00
V1 A:D6N501 0.0 7.8 1.0
O5 A:HCA502 2.1 7.6 1.0
O7 A:HCA502 2.1 7.6 1.0
ND1 A:HIS423 2.3 7.6 1.0
S4B A:D6N501 2.3 7.9 1.0
S1B A:D6N501 2.4 8.2 1.0
S3B A:D6N501 2.4 8.7 1.0
FE5 A:D6N501 2.7 7.9 1.0
FE7 A:D6N501 2.8 8.0 1.0
FE6 A:D6N501 2.8 8.2 1.0
C7 A:HCA502 3.0 7.8 1.0
C3 A:HCA502 3.1 8.1 1.0
CE1 A:HIS423 3.2 8.3 1.0
CG A:HIS423 3.4 7.8 1.0
CX A:D6N501 3.6 8.7 1.0
CB A:HIS423 3.8 7.8 1.0
C2 A:HCA502 4.0 8.0 1.0
O6 A:HCA502 4.2 8.4 1.0
O A:HOH845 4.2 9.5 1.0
O2 A:BCT503 4.3 9.3 1.0
C4 A:HCA502 4.3 7.5 1.0
O1 A:HCA502 4.3 10.0 1.0
NE2 A:HIS423 4.4 8.6 1.0
C5 A:HCA502 4.4 8.8 1.0
CD2 A:HIS423 4.4 8.3 1.0
CA A:HIS423 4.5 7.7 1.0
NZ A:LYS83 4.7 10.0 1.0
C1 A:HCA502 4.8 8.6 1.0
NZ A:LYS361 4.8 20.4 1.0
O A:HOH607 4.8 8.7 1.0
S5A A:D6N501 4.9 8.7 1.0

Vanadium binding site 2 out of 2 in 7ady

Go back to Vanadium Binding Sites List in 7ady
Vanadium binding site 2 out of 2 in the Co-Removed State of 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-Removed State of the Active Site of Vanadium Nitrogenase Vfe Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
D:V501

b:6.5
occ:1.00
V1 D:D6N501 0.0 6.5 1.0
O6 D:HCA502 2.1 6.6 1.0
O7 D:HCA502 2.2 6.3 1.0
ND1 D:HIS423 2.3 6.6 1.0
S4B D:D6N501 2.3 6.9 1.0
S1B D:D6N501 2.4 6.9 1.0
S3B D:D6N501 2.4 7.3 1.0
FE5 D:D6N501 2.7 6.8 1.0
FE7 D:D6N501 2.8 6.8 1.0
FE6 D:D6N501 2.8 6.9 1.0
C7 D:HCA502 3.0 6.5 1.0
C3 D:HCA502 3.1 6.6 1.0
CE1 D:HIS423 3.2 7.3 1.0
CG D:HIS423 3.4 6.7 1.0
CX D:D6N501 3.7 6.7 1.0
CB D:HIS423 3.8 7.0 1.0
C2 D:HCA502 4.0 6.6 1.0
O5 D:HCA502 4.1 7.4 1.0
O D:HOH847 4.2 8.5 1.0
C4 D:HCA502 4.3 6.5 1.0
O1 D:BCT503 4.3 7.4 1.0
O2 D:HCA502 4.3 8.2 1.0
C5 D:HCA502 4.4 7.3 1.0
NE2 D:HIS423 4.4 7.4 1.0
CD2 D:HIS423 4.5 7.5 1.0
CA D:HIS423 4.5 6.7 1.0
NZ D:LYS83 4.7 8.7 1.0
C1 D:HCA502 4.7 7.0 1.0
O D:HOH610 4.8 6.9 1.0
NZ D:LYS361 4.8 16.7 1.0
S5A D:D6N501 4.9 7.4 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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