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Magnesium in PDB 8dfd: Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii

Enzymatic activity of Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii

All present enzymatic activity of Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii:
1.18.6.1;

Other elements in 8dfd:

The structure of Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii also contains other interesting chemical elements:

Fluorine (F) 16 atoms
Iron (Fe) 40 atoms
Molybdenum (Mo) 2 atoms
Aluminium (Al) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii (pdb code 8dfd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii, PDB code: 8dfd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8dfd

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Magnesium binding site 1 out of 4 in the Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg603

b:38.3
occ:1.00
 OG E:SER16 2.0 34.0 1.0
O E:HOH703 2.1 33.2 1.0
O E:HOH701 2.1 26.1 1.0
O E:HOH736 2.1 32.5 1.0
OD2 E:ASP125 2.2 27.2 1.0
O2B E:ADP601 2.5 35.3 1.0
F1 E:ALF602 2.7 32.9 1.0
CG E:ASP125 3.1 33.0 1.0
OD1 E:ASP125 3.2 33.0 1.0
CB E:SER16 3.3 28.7 1.0
N E:SER16 3.6 24.3 1.0
CA E:SER16 3.8 26.0 1.0
PB E:ADP601 3.8 31.7 1.0
F3 E:ALF602 3.9 42.9 1.0
O E:VAL126 4.0 37.1 1.0
O3B E:ADP601 4.1 42.1 1.0
AL E:ALF602 4.2 35.3 1.0
CB E:LYS15 4.3 23.5 1.0
OD2 E:ASP39 4.5 28.7 1.0
C E:LYS15 4.5 28.4 1.0
CB E:ASP125 4.5 31.4 1.0
O1B E:ADP601 4.5 34.3 1.0
CE E:LYS15 4.6 19.6 1.0
C E:VAL126 4.6 25.4 1.0
OD1 E:ASP43 4.7 47.2 1.0
CB E:SER44 4.8 36.9 1.0
O2A E:ADP601 4.8 43.8 1.0
CA E:LYS15 4.9 26.5 1.0
C E:ASP125 4.9 28.1 1.0
O E:ASP125 5.0 26.1 1.0
CA E:LEU127 5.0 22.9 1.0

Magnesium binding site 2 out of 4 in 8dfd

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Magnesium binding site 2 out of 4 in the Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg602

b:40.1
occ:1.00
 OG F:SER16 1.9 29.4 1.0
O F:HOH702 2.0 35.8 1.0
O F:HOH701 2.1 32.1 1.0
O F:HOH716 2.1 29.9 1.0
OD2 F:ASP125 2.2 32.4 1.0
O3B F:ADP600 2.6 35.2 1.0
F2 F:ALF601 2.9 47.3 1.0
CG F:ASP125 3.0 29.8 1.0
CB F:SER16 3.2 28.2 1.0
OD1 F:ASP125 3.3 30.8 1.0
N F:SER16 3.6 21.1 1.0
OG F:SER44 3.7 35.4 1.0
CA F:SER16 3.7 23.4 1.0
O F:VAL126 3.9 28.1 1.0
PB F:ADP600 4.0 24.5 1.0
OD2 F:ASP39 4.1 28.8 1.0
CB F:ASP125 4.4 27.0 1.0
CB F:LYS15 4.4 25.6 1.0
O1B F:ADP600 4.4 30.8 1.0
C F:LYS15 4.5 24.1 1.0
O2B F:ADP600 4.5 26.6 1.0
AL F:ALF601 4.6 39.5 1.0
C F:VAL126 4.6 19.9 1.0
OD1 F:ASP43 4.7 34.9 1.0
CB F:SER44 4.8 27.3 1.0
F4 F:ALF601 4.8 52.4 1.0
O F:ASP125 4.8 29.3 1.0
C F:ASP125 4.9 28.4 1.0
O1A F:ADP600 4.9 31.4 1.0
CE F:LYS15 4.9 19.3 1.0
CG F:ASP39 5.0 30.1 1.0
CA F:LYS15 5.0 20.6 1.0

Magnesium binding site 3 out of 4 in 8dfd

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Magnesium binding site 3 out of 4 in the Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg603

b:33.0
occ:1.00
 O G:HOH725 2.1 30.6 1.0
O G:HOH746 2.1 32.2 1.0
O G:HOH744 2.1 27.0 1.0
OG G:SER16 2.1 35.5 1.0
O2B G:ADP601 2.1 32.7 1.0
F1 G:ALF602 2.4 34.2 1.0
F4 G:ALF602 2.9 45.2 1.0
CB G:SER16 3.0 32.0 1.0
O3B G:ADP601 3.1 43.2 1.0
PB G:ADP601 3.2 25.8 1.0
AL G:ALF602 3.4 35.2 1.0
OD2 G:ASP125 3.7 31.3 1.0
N G:SER16 3.8 29.4 1.0
CA G:SER16 4.0 30.0 1.0
OD1 G:ASP43 4.1 43.8 1.0
O1B G:ADP601 4.2 35.3 1.0
O2A G:ADP601 4.3 42.2 1.0
O3A G:ADP601 4.3 41.0 1.0
O1A G:ADP601 4.4 38.1 1.0
OD1 G:ASP125 4.4 33.8 1.0
OD2 G:ASP39 4.4 27.5 1.0
CG G:ASP125 4.4 34.5 1.0
F3 G:ALF602 4.6 37.2 1.0
PA G:ADP601 4.6 38.1 1.0
OG G:SER44 4.7 43.1 1.0
CG G:ASP43 4.7 39.2 1.0
OD2 G:ASP43 4.7 38.3 1.0
F2 G:ALF602 4.8 41.0 1.0
NZ G:LYS41 4.8 30.6 1.0
C G:LYS15 4.9 28.4 1.0
O G:VAL126 5.0 39.2 1.0
CE G:LYS15 5.0 20.3 1.0
CB G:LYS15 5.0 22.8 1.0

Magnesium binding site 4 out of 4 in 8dfd

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Magnesium binding site 4 out of 4 in the Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg304

b:26.8
occ:1.00
 F2 H:ALF303 1.9 47.8 1.0
OG H:SER16 2.0 28.9 1.0
O H:HOH411 2.1 30.5 1.0
O H:HOH405 2.1 27.5 1.0
O H:HOH407 2.1 31.1 1.0
O2B H:ADP302 2.1 31.7 1.0
PB H:ADP302 3.2 18.5 1.0
O1B H:ADP302 3.2 28.4 1.0
CB H:SER16 3.4 25.7 1.0
AL H:ALF303 3.5 36.9 1.0
OD2 H:ASP39 3.7 28.2 1.0
F3 H:ALF303 3.7 42.5 1.0
OD2 H:ASP125 3.8 33.2 1.0
O1A H:ADP302 3.9 31.5 1.0
N H:SER16 4.0 15.8 1.0
F4 H:ALF303 4.1 48.0 1.0
O3B H:ADP302 4.1 22.6 1.0
OD2 H:ASP43 4.2 29.3 1.0
CA H:SER16 4.2 20.3 1.0
OD1 H:ASP43 4.3 32.1 1.0
OD1 H:ASP125 4.4 30.9 1.0
O3A H:ADP302 4.5 31.0 1.0
O H:VAL126 4.5 28.2 1.0
CG H:ASP125 4.5 24.9 1.0
CG H:ASP43 4.6 33.1 1.0
NZ H:LYS41 4.6 29.5 1.0
CG H:ASP39 4.7 28.2 1.0
OG H:SER44 4.8 34.8 1.0
PA H:ADP302 4.8 29.6 1.0
CE H:LYS15 4.8 17.6 1.0
CB H:LYS15 4.8 24.2 1.0
C H:LYS15 5.0 22.0 1.0

Reference:

R.A.Warmack, D.C.Rees. Anaerobic Single Particle Cryoem of Nitrogenase To Be Published.
Page generated: Fri Oct 4 00:38:47 2024

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