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Magnesium 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:

Zinc (Zn) 2 atoms
Vanadium (V) 2 atoms
Iron (Fe) 32 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the A. Vinelandii Vanadium Nitrogenase, Turnover State (pdb code 6fea). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the A. Vinelandii Vanadium Nitrogenase, Turnover State, PDB code: 6fea:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6fea

Go back to Magnesium Binding Sites List in 6fea
Magnesium binding site 1 out of 4 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A. Vinelandii Vanadium Nitrogenase, Turnover State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:10.8
occ:1.00
OE2 B:GLU70 2.0 12.0 1.0
O B:HOH678 2.0 12.5 1.0
OD2 E:ASP314 2.1 12.7 1.0
O E:HOH678 2.1 11.0 1.0
O B:HOH817 2.1 12.2 1.0
O E:HOH977 2.1 12.5 1.0
CD B:GLU70 3.2 11.9 1.0
CG E:ASP314 3.2 12.0 1.0
CB E:ASP314 3.9 9.6 1.0
CG B:GLU70 3.9 10.3 1.0
O B:LYS69 4.1 9.3 1.0
NZ A:LYS413 4.1 12.1 1.0
NZ A:LYS414 4.1 14.3 1.0
OE1 B:GLU70 4.1 15.5 1.0
O A:HOH865 4.1 14.6 1.0
O B:HOH676 4.1 12.8 1.0
OD2 E:ASP318 4.1 11.5 1.0
OD1 B:ASP222 4.2 13.2 1.0
O B:SER223 4.2 11.2 1.0
OH B:TYR437 4.2 14.9 1.0
OD1 E:ASP314 4.2 13.5 1.0
O B:PHE68 4.4 11.4 1.0
O E:ASP314 4.6 10.2 1.0
C E:ASP314 4.6 8.8 1.0
C B:LYS69 4.8 9.0 1.0
N B:SER223 4.8 11.5 1.0
CA E:ASP314 4.8 9.7 1.0
N E:ALA315 4.9 9.0 1.0
CB B:LYS69 5.0 10.7 1.0
O B:HOH957 5.0 30.7 1.0

Magnesium binding site 2 out of 4 in 6fea

Go back to Magnesium Binding Sites List in 6fea
Magnesium binding site 2 out of 4 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A. Vinelandii Vanadium Nitrogenase, Turnover State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:9.8
occ:1.00
OE2 E:GLU70 2.0 10.9 1.0
O E:HOH691 2.0 11.6 1.0
OD2 B:ASP314 2.1 12.0 1.0
O B:HOH685 2.1 10.3 1.0
O E:HOH844 2.1 11.5 1.0
O B:HOH973 2.1 11.6 1.0
CG B:ASP314 3.2 12.2 1.0
CD E:GLU70 3.2 10.6 1.0
CB B:ASP314 3.9 10.2 1.0
CG E:GLU70 3.9 9.9 1.0
O E:LYS69 4.0 8.9 1.0
NZ D:LYS414 4.1 11.6 1.0
NZ D:LYS413 4.1 11.8 1.0
OE1 E:GLU70 4.1 13.4 1.0
O D:HOH887 4.1 13.1 1.0
O E:HOH661 4.1 12.3 1.0
OD2 B:ASP318 4.1 10.6 1.0
OD1 B:ASP314 4.2 12.9 1.0
OD1 E:ASP222 4.2 12.5 1.0
O E:SER223 4.2 11.1 1.0
OH E:TYR437 4.2 13.4 1.0
O E:PHE68 4.5 9.8 1.0
O B:ASP314 4.6 9.9 1.0
C B:ASP314 4.6 9.5 1.0
N E:SER223 4.8 10.4 1.0
C E:LYS69 4.8 7.8 1.0
CA B:ASP314 4.8 9.4 1.0
N B:ALA315 4.9 9.0 1.0
CB E:LYS69 5.0 10.4 1.0

Magnesium binding site 3 out of 4 in 6fea

Go back to Magnesium Binding Sites List in 6fea
Magnesium binding site 3 out of 4 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A. Vinelandii Vanadium Nitrogenase, Turnover State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:17.4
occ:1.00
O C:HOH448 2.0 17.1 1.0
O C:HOH456 2.0 19.8 1.0
O C:HOH318 2.0 17.1 1.0
O C:HOH476 2.1 19.0 1.0
O C:HOH344 2.1 16.7 1.0
O A:HOH904 2.1 15.9 1.0
OE1 C:GLU14 4.0 17.6 1.0
O A:HOH795 4.1 22.6 1.0
O A:HOH796 4.2 17.0 1.0
O C:HOH458 4.2 19.6 1.0
O A:HOH890 4.2 17.3 1.0
O A:HOH1179 4.2 27.6 1.0
O C:HOH459 4.3 25.4 1.0
OE2 C:GLU15 4.4 20.7 1.0
O C:HOH444 4.4 19.8 1.0
O C:HOH460 4.5 29.1 1.0
O C:ALA11 4.6 13.9 1.0
CB C:ALA11 4.6 16.7 1.0
O A:ALA373 4.7 13.0 1.0
CA C:ALA11 4.8 14.9 1.0
CD C:GLU14 4.8 14.9 1.0
CG C:GLU14 4.8 16.8 1.0
CB C:GLU14 4.9 14.0 1.0
O A:HOH923 4.9 21.4 1.0
O C:HOH387 4.9 24.6 1.0
CB C:GLU15 4.9 17.6 1.0

Magnesium binding site 4 out of 4 in 6fea

Go back to Magnesium Binding Sites List in 6fea
Magnesium binding site 4 out of 4 in the A. Vinelandii Vanadium Nitrogenase, Turnover State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A. Vinelandii Vanadium Nitrogenase, Turnover State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:15.7
occ:1.00
O F:HOH449 2.0 18.3 1.0
O F:HOH315 2.1 15.1 1.0
O F:HOH442 2.1 17.3 1.0
O D:HOH870 2.1 15.6 1.0
O F:HOH334 2.1 14.8 1.0
O F:HOH422 2.1 15.8 1.0
OE1 F:GLU14 4.0 16.8 1.0
O D:HOH811 4.1 20.6 1.0
O D:HOH819 4.2 15.1 1.0
O D:HOH1168 4.2 28.2 1.0
O D:HOH859 4.2 15.0 1.0
O F:HOH441 4.2 18.7 1.0
OE2 F:GLU15 4.3 20.7 1.0
O F:HOH440 4.4 24.7 1.0
O F:HOH426 4.4 16.4 1.0
O F:HOH439 4.5 30.6 1.0
O F:ALA11 4.6 14.0 1.0
O D:ALA373 4.6 11.2 1.0
CD F:GLU14 4.7 15.7 1.0
CB F:ALA11 4.7 18.5 1.0
CG F:GLU14 4.8 14.8 1.0
CA F:ALA11 4.8 15.4 1.0
O D:HOH902 4.9 18.1 1.0
CB F:GLU14 4.9 13.2 1.0
O D:HOH864 5.0 23.7 1.0
CB F:GLU15 5.0 17.0 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: Mon Dec 14 22:41:29 2020

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