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Vanadium in PDB 6fea: A. Vinelandii Vanadium Nitrogenase, Turnover State

Enzymatic activity of A. Vinelandii Vanadium Nitrogenase, Turnover State

All present enzymatic activity of A. Vinelandii Vanadium Nitrogenase, Turnover State:
1.18.6.1;

Protein crystallography data

The structure of A. Vinelandii Vanadium Nitrogenase, Turnover State, PDB code: 6fea was solved by D.Sippel, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 102.12 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.610, 79.750, 107.160, 84.05, 72.44, 75.25
R / Rfree (%) 11.7 / 14.5

Other elements in 6fea:

The structure of A. Vinelandii Vanadium Nitrogenase, Turnover State also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Zinc (Zn) 2 atoms
Iron (Fe) 32 atoms

Vanadium Binding Sites:

The binding sites of Vanadium atom in the A. Vinelandii Vanadium Nitrogenase, Turnover State (pdb code 6fea). This binding sites where shown within 5.0 Angstroms radius around Vanadium atom.
In total 2 binding sites of Vanadium where determined in the A. Vinelandii Vanadium Nitrogenase, Turnover State, PDB code: 6fea:
Jump to Vanadium binding site number: 1; 2;

Vanadium binding site 1 out of 2 in 6fea

Go back to Vanadium Binding Sites List in 6fea
Vanadium binding site 1 out of 2 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 1 of A. Vinelandii Vanadium Nitrogenase, Turnover State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:V502

b:8.6
occ:1.00
V1 A:D6N502 0.0 8.6 1.0
O5 A:HCA501 2.1 8.4 1.0
O7 A:HCA501 2.1 8.5 1.0
ND1 A:HIS423 2.2 8.2 1.0
S4B A:D6N502 2.3 8.6 1.0
S1B A:D6N502 2.4 9.0 1.0
S3B A:D6N502 2.4 9.2 1.0
FE5 A:D6N502 2.7 8.8 1.0
FE7 A:D6N502 2.8 9.1 1.0
FE6 A:D6N502 2.8 9.3 1.0
C7 A:HCA501 2.9 8.1 1.0
C3 A:HCA501 3.1 8.0 1.0
CE1 A:HIS423 3.1 9.0 1.0
CG A:HIS423 3.4 8.6 1.0
CX A:D6N502 3.7 8.8 1.0
CB A:HIS423 3.8 8.5 1.0
C2 A:HCA501 4.0 8.9 1.0
O6 A:HCA501 4.1 9.9 1.0
O A:HOH788 4.1 10.0 1.0
C4 A:HCA501 4.3 8.6 1.0
O2 A:CO3503 4.3 9.2 1.0
O1 A:HCA501 4.3 10.7 1.0
C5 A:HCA501 4.4 10.0 1.0
NE2 A:HIS423 4.4 8.5 1.0
CD2 A:HIS423 4.5 9.0 1.0
CA A:HIS423 4.5 8.5 1.0
NZ A:LYS83 4.7 11.5 1.0
N2B A:D6N502 4.8 6.9 1.0
C1 A:HCA501 4.8 9.8 1.0
S5A A:D6N502 4.9 9.4 1.0
NZ A:LYS361 4.9 21.9 1.0

Vanadium binding site 2 out of 2 in 6fea

Go back to Vanadium Binding Sites List in 6fea
Vanadium binding site 2 out of 2 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

A full contact list of Vanadium with other atoms in the V binding site number 2 of A. Vinelandii Vanadium Nitrogenase, Turnover State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:V501

b:7.4
occ:1.00
V1 D:D6N501 0.0 7.4 1.0
O6 D:HCA502 2.1 7.0 1.0
O7 D:HCA502 2.2 7.2 1.0
ND1 D:HIS423 2.3 6.9 1.0
S4B D:D6N501 2.3 7.6 1.0
S1B D:D6N501 2.4 7.8 1.0
S3B D:D6N501 2.4 8.2 1.0
FE5 D:D6N501 2.7 7.5 1.0
FE7 D:D6N501 2.8 7.8 1.0
FE6 D:D6N501 2.8 7.9 1.0
C7 D:HCA502 2.9 7.8 1.0
C3 D:HCA502 3.1 6.5 1.0
CE1 D:HIS423 3.2 7.5 1.0
CG D:HIS423 3.4 7.3 1.0
CX D:D6N501 3.6 7.2 1.0
CB D:HIS423 3.8 7.7 1.0
C2 D:HCA502 4.0 7.5 1.0
O5 D:HCA502 4.2 8.4 1.0
O D:HOH845 4.2 9.2 1.0
O1 D:CO3503 4.3 7.5 1.0
C4 D:HCA502 4.3 7.6 1.0
O2 D:HCA502 4.3 9.2 1.0
NE2 D:HIS423 4.4 8.2 1.0
C5 D:HCA502 4.4 8.0 1.0
CD2 D:HIS423 4.5 8.1 1.0
CA D:HIS423 4.5 7.6 1.0
NZ D:LYS83 4.7 10.0 1.0
C1 D:HCA502 4.8 7.9 1.0
N2B D:D6N501 4.8 5.6 1.0
S5A D:D6N501 4.9 8.2 1.0
NZ D:LYS361 4.9 20.2 1.0

Reference:

D.Sippel, M.Rohde, J.Netzer, C.Trncik, J.Gies, K.Grunau, I.Djurdjevic, L.Decamps, S.L.A.Andrade, O.Einsle. A Bound Reaction Intermediate Sheds Light on the Mechanism of Nitrogenase. Science V. 359 1484 2018.
ISSN: ESSN 1095-9203
PubMed: 29599235
DOI: 10.1126/SCIENCE.AAR2765
Page generated: Wed Dec 16 02:31:45 2020

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