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Magnesium in PDB 5n6y: Azotobacter Vinelandii Vanadium Nitrogenase

Enzymatic activity of Azotobacter Vinelandii Vanadium Nitrogenase

All present enzymatic activity of Azotobacter Vinelandii Vanadium Nitrogenase:
1.18.6.1;

Protein crystallography data

The structure of Azotobacter Vinelandii Vanadium Nitrogenase, PDB code: 5n6y 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) 102.04 / 1.35
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 75.250, 79.790, 106.970, 84.06, 72.62, 75.15
R / Rfree (%) 10.9 / 14.6

Other elements in 5n6y:

The structure of Azotobacter Vinelandii Vanadium Nitrogenase also contains other interesting chemical elements:

Iron (Fe) 30 atoms
Vanadium (V) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Azotobacter Vinelandii Vanadium Nitrogenase (pdb code 5n6y). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Azotobacter Vinelandii Vanadium Nitrogenase, PDB code: 5n6y:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5n6y

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Magnesium binding site 1 out of 4 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg502

b:15.0
occ:1.00
O B:HOH685 2.0 15.4 1.0
OE2 B:GLU70 2.0 17.2 1.0
OD2 E:ASP314 2.1 19.0 1.0
O B:HOH801 2.1 17.3 1.0
O E:HOH652 2.1 15.1 1.0
O E:HOH944 2.1 16.2 1.0
CD B:GLU70 3.2 17.3 1.0
CG E:ASP314 3.2 16.0 1.0
CG B:GLU70 3.9 14.8 1.0
CB E:ASP314 4.0 12.7 1.0
O B:LYS69 4.0 12.3 1.0
OE1 B:GLU70 4.1 20.0 1.0
O A:HOH814 4.1 24.4 1.0
OD2 E:ASP318 4.1 15.8 1.0
NZ A:LYS413 4.1 18.9 1.0
O B:HOH626 4.1 18.6 1.0
OH B:TYR437 4.2 22.1 1.0
OD1 B:ASP222 4.2 18.3 1.0
NZ A:LYS414 4.2 19.8 1.0
OD1 E:ASP314 4.2 20.3 1.0
O B:SER223 4.2 15.0 1.0
O B:PHE68 4.4 13.7 1.0
O E:ASP314 4.6 12.2 1.0
C E:ASP314 4.7 12.1 1.0
C B:LYS69 4.8 10.9 1.0
N B:SER223 4.8 15.4 1.0
O B:HOH943 4.9 42.0 1.0
CA E:ASP314 4.9 11.7 1.0
N E:ALA315 5.0 10.9 1.0

Magnesium binding site 2 out of 4 in 5n6y

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Magnesium binding site 2 out of 4 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Azotobacter Vinelandii Vanadium Nitrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg503

b:13.5
occ:1.00
OE2 E:GLU70 2.0 15.3 1.0
O E:HOH650 2.0 15.1 1.0
O B:HOH661 2.0 14.8 1.0
OD2 B:ASP314 2.0 17.6 1.0
O E:HOH752 2.1 16.8 1.0
O B:HOH888 2.1 15.7 1.0
CD E:GLU70 3.2 15.0 1.0
CG B:ASP314 3.2 18.5 1.0
CG E:GLU70 3.9 12.7 1.0
CB B:ASP314 4.0 12.3 1.0
O E:LYS69 4.0 11.7 1.0
NZ D:LYS414 4.1 17.9 1.0
OD2 B:ASP318 4.1 14.8 1.0
O D:HOH809 4.1 22.3 1.0
OE1 E:GLU70 4.1 19.1 1.0
O E:HOH646 4.1 17.7 1.0
OD1 E:ASP222 4.1 17.9 1.0
OD1 B:ASP314 4.2 19.3 1.0
NZ D:LYS413 4.2 17.6 1.0
OH E:TYR437 4.2 20.5 1.0
O E:SER223 4.2 13.3 1.0
O E:PHE68 4.4 13.2 1.0
O B:ASP314 4.6 12.3 1.0
C B:ASP314 4.7 12.7 1.0
N E:SER223 4.8 15.3 1.0
C E:LYS69 4.8 10.3 1.0
O E:HOH926 4.9 36.1 1.0
CA B:ASP314 5.0 12.5 1.0
CB E:LYS69 5.0 12.4 1.0

Magnesium binding site 3 out of 4 in 5n6y

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Magnesium binding site 3 out of 4 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

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

b:22.3
occ:1.00
O C:HOH310 2.0 21.1 1.0
O C:HOH410 2.1 23.3 1.0
O C:HOH339 2.1 19.2 1.0
O A:HOH868 2.1 20.2 1.0
O C:HOH401 2.1 22.3 1.0
O C:HOH419 2.1 23.4 1.0
OE1 C:GLU14 3.9 24.1 1.0
O C:HOH409 4.1 24.8 1.0
O A:HOH777 4.1 22.3 1.0
O A:HOH895 4.2 20.8 1.0
O C:HOH406 4.3 33.2 1.0
O A:HOH620 4.3 30.5 1.0
OE1 C:GLU15 4.4 27.0 1.0
O C:HOH400 4.5 25.3 1.0
O C:ALA11 4.5 17.5 1.0
O C:HOH412 4.6 35.8 1.0
CB C:ALA11 4.6 19.4 1.0
O A:ALA373 4.6 15.5 1.0
CA C:ALA11 4.7 15.8 1.0
CD C:GLU14 4.7 19.8 1.0
CB C:GLU14 4.8 16.7 1.0
CG C:GLU14 4.9 18.3 1.0
O A:HOH881 4.9 28.7 1.0
O C:HOH366 4.9 32.1 1.0
CB C:GLU15 4.9 23.1 1.0

Magnesium binding site 4 out of 4 in 5n6y

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Magnesium binding site 4 out of 4 in the Azotobacter Vinelandii Vanadium Nitrogenase


Mono view


Stereo pair view

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

b:22.3
occ:1.00
O F:HOH311 2.0 19.4 1.0
O D:HOH842 2.1 21.6 1.0
O F:HOH320 2.1 17.9 1.0
O F:HOH420 2.1 24.4 1.0
O F:HOH418 2.1 24.8 1.0
O F:HOH403 2.2 21.3 1.0
OE2 F:GLU14 3.9 23.0 1.0
O D:HOH785 4.2 21.0 1.0
O F:HOH415 4.2 25.3 1.0
O D:HOH819 4.2 20.6 1.0
O D:HOH677 4.3 35.9 1.0
OE1 F:GLU15 4.3 28.9 1.0
O F:HOH414 4.3 31.5 1.0
O F:HOH419 4.5 38.8 1.0
O F:HOH406 4.6 22.8 1.0
O F:ALA11 4.6 16.7 1.0
O D:ALA373 4.6 14.4 1.0
CD F:GLU14 4.6 20.8 1.0
CB F:ALA11 4.8 21.7 1.0
CG F:GLU14 4.8 18.6 1.0
CA F:ALA11 4.8 16.3 1.0
O D:HOH882 4.8 27.4 1.0
CB F:GLU14 4.9 18.9 1.0
O D:HOH913 5.0 31.4 1.0

Reference:

D.Sippel, O.Einsle. The Structure of Vanadium Nitrogenase Reveals An Unusual Bridging Ligand. Nat. Chem. Biol. V. 13 956 2017.
ISSN: ESSN 1552-4469
PubMed: 28692069
DOI: 10.1038/NCHEMBIO.2428
Page generated: Mon Dec 14 20:55:08 2020

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