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Aluminium 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:

Magnesium (Mg) 4 atoms
Fluorine (F) 16 atoms
Iron (Fe) 40 atoms
Molybdenum (Mo) 2 atoms

Aluminium Binding Sites:

The binding sites of Aluminium 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 Aluminium atom.
In total 4 binding sites of Aluminium where determined in the Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii, PDB code: 8dfd:
Jump to Aluminium binding site number: 1; 2; 3; 4;

Aluminium binding site 1 out of 4 in 8dfd

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Aluminium 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 Aluminium with other atoms in the Al 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:Al602

b:35.3
occ:1.00
 AL E:ALF602 0.0 35.3 1.0
O3B E:ADP601 1.7 42.1 1.0
F1 E:ALF602 1.8 32.9 1.0
F4 E:ALF602 1.8 34.8 1.0
F3 E:ALF602 1.8 42.9 1.0
F2 E:ALF602 1.8 39.0 1.0
PB E:ADP601 3.1 31.7 1.0
O E:HOH701 3.2 26.1 1.0
O2B E:ADP601 3.6 35.3 1.0
NZ F:LYS10 3.7 27.6 1.0
O1B E:ADP601 3.7 34.3 1.0
OD2 E:ASP39 4.0 28.7 1.0
N E:GLY12 4.0 23.4 1.0
O E:HOH736 4.2 32.5 1.0
MG E:MG603 4.2 38.3 1.0
OD1 F:ASP129 4.2 33.2 1.0
NZ E:LYS15 4.2 20.8 1.0
O3A E:ADP601 4.3 37.8 1.0
NZ E:LYS41 4.5 36.1 1.0
N E:GLY128 4.5 11.8 1.0
CA E:GLY12 4.5 26.2 1.0
CE E:LYS15 4.7 19.6 1.0
O2A E:ADP601 4.7 43.8 1.0
CA E:LEU127 4.8 22.9 1.0
O F:HOH703 4.9 33.8 1.0
OD2 F:ASP129 4.9 27.0 1.0
C E:GLY11 5.0 23.6 1.0

Aluminium binding site 2 out of 4 in 8dfd

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Aluminium 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 Aluminium with other atoms in the Al 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:Al601

b:39.5
occ:1.00
 AL F:ALF601 0.0 39.5 1.0
O1B F:ADP600 1.7 30.8 1.0
F4 F:ALF601 1.8 52.4 1.0
F3 F:ALF601 1.8 48.0 1.0
F2 F:ALF601 1.8 47.3 1.0
F1 F:ALF601 1.8 51.0 1.0
PB F:ADP600 3.1 24.5 1.0
O E:HOH757 3.5 31.7 1.0
O3B F:ADP600 3.6 35.2 1.0
O F:HOH701 3.6 32.1 1.0
O2B F:ADP600 3.7 26.6 1.0
N F:GLY12 3.8 34.1 1.0
NZ E:LYS10 3.9 27.0 1.0
NZ F:LYS41 4.0 28.2 1.0
CE E:LYS10 4.2 28.0 1.0
OD2 E:ASP129 4.3 30.7 1.0
OD2 F:ASP39 4.3 28.8 1.0
NZ F:LYS15 4.3 24.4 1.0
O3A F:ADP600 4.3 33.5 1.0
N F:GLY128 4.5 25.1 1.0
CA F:GLY11 4.5 23.1 1.0
CA F:GLY12 4.6 32.5 1.0
OD1 E:ASP129 4.6 33.0 1.0
MG F:MG602 4.6 40.1 1.0
O F:HOH716 4.7 29.9 1.0
C F:GLY11 4.7 29.0 1.0
O1A F:ADP600 4.7 31.4 1.0
CE F:LYS15 4.7 19.3 1.0
O F:HOH702 4.8 35.8 1.0
CA F:LEU127 4.8 18.1 1.0
CG E:ASP129 4.9 29.5 1.0

Aluminium binding site 3 out of 4 in 8dfd

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Aluminium 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 Aluminium with other atoms in the Al 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:Al602

b:35.2
occ:1.00
 AL G:ALF602 0.0 35.2 1.0
O3B G:ADP601 1.7 43.2 1.0
F3 G:ALF602 1.8 37.2 1.0
F1 G:ALF602 1.8 34.2 1.0
F4 G:ALF602 1.8 45.2 1.0
F2 G:ALF602 1.8 41.0 1.0
PB G:ADP601 3.1 25.8 1.0
MG G:MG603 3.4 33.0 1.0
O2B G:ADP601 3.7 32.7 1.0
O1B G:ADP601 3.8 35.3 1.0
NZ H:LYS10 3.8 24.8 1.0
O G:HOH746 3.9 32.2 1.0
O G:HOH725 3.9 30.6 1.0
N G:GLY12 4.0 24.8 1.0
OD2 G:ASP39 4.0 27.5 1.0
NZ G:LYS41 4.1 30.6 1.0
O G:HOH744 4.2 27.0 1.0
NZ G:LYS15 4.3 20.6 1.0
OD1 H:ASP129 4.3 35.5 1.0
O3A G:ADP601 4.3 41.0 1.0
N G:GLY128 4.4 12.1 1.0
CE G:LYS15 4.6 20.3 1.0
CA G:GLY12 4.6 24.5 1.0
CE G:LYS41 4.8 34.3 1.0
O H:HOH401 4.9 37.1 1.0
O2A G:ADP601 4.9 42.2 1.0
OD2 H:ASP129 4.9 30.4 1.0
CA G:LEU127 4.9 25.1 1.0
CA G:GLY11 4.9 24.0 1.0
CE H:LYS10 4.9 30.5 1.0
C G:GLY11 4.9 25.1 1.0

Aluminium binding site 4 out of 4 in 8dfd

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Aluminium 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 Aluminium with other atoms in the Al 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:Al303

b:36.9
occ:1.00
 AL H:ALF303 0.0 36.9 1.0
O1B H:ADP302 1.7 28.4 1.0
F3 H:ALF303 1.8 42.5 1.0
F2 H:ALF303 1.8 47.8 1.0
F1 H:ALF303 1.8 51.7 1.0
F4 H:ALF303 1.8 48.0 1.0
PB H:ADP302 3.1 18.5 1.0
MG H:MG304 3.5 26.8 1.0
O G:HOH761 3.5 29.5 1.0
O H:HOH405 3.6 27.5 1.0
O2B H:ADP302 3.6 31.7 1.0
NZ H:LYS41 3.7 29.5 1.0
N H:GLY12 3.7 27.4 1.0
O3B H:ADP302 3.8 22.6 1.0
NZ G:LYS10 4.0 27.8 1.0
CE G:LYS10 4.1 27.1 1.0
NZ H:LYS15 4.2 21.7 1.0
OD2 H:ASP39 4.3 28.2 1.0
O3A H:ADP302 4.3 31.0 1.0
OD2 G:ASP129 4.4 28.3 1.0
CA H:GLY12 4.5 29.2 1.0
N H:GLY128 4.5 23.2 1.0
O H:HOH411 4.5 30.5 1.0
OD1 G:ASP129 4.5 30.9 1.0
CA H:GLY11 4.6 19.5 1.0
CE H:LYS15 4.6 17.6 1.0
C H:GLY11 4.6 27.8 1.0
O1A H:ADP302 4.7 31.5 1.0
O H:HOH407 4.7 31.1 1.0
CE H:LYS41 4.7 29.9 1.0
CA H:LEU127 4.9 17.6 1.0
CG G:ASP129 4.9 30.1 1.0

Reference:

R.A.Warmack, D.C.Rees. Anaerobic Single Particle Cryoem of Nitrogenase To Be Published.
Page generated: Sun Jul 6 22:18:40 2025

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