Fluorine in PDB 8dfc: Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii

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

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

Other elements in 8dfc:

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

Molybdenum (Mo) 2 atoms
Aluminium (Al) 2 atoms
Magnesium (Mg) 2 atoms
Iron (Fe) 36 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii (pdb code 8dfc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii, PDB code: 8dfc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 8dfc

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Fluorine binding site 1 out of 8 in the Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F302

b:69.7
occ:1.00
 F1 E:ALF302 0.0 69.7 1.0
AL E:ALF302 1.8 69.0 1.0
MG E:MG303 2.1 60.8 1.0
O E:HOH414 2.5 57.2 1.0
F4 E:ALF302 2.5 78.0 1.0
F3 E:ALF302 2.5 70.1 1.0
O3B E:ADP301 2.6 55.9 1.0
O1B E:ADP301 2.9 64.8 1.0
PB E:ADP301 3.3 72.6 1.0
F2 E:ALF302 3.6 72.5 1.0
NZ E:LYS15 3.8 46.2 1.0
O1A E:ADP301 3.8 74.6 1.0
CE E:LYS15 3.8 36.4 1.0
O3A E:ADP301 4.1 70.0 1.0
CB E:SER16 4.3 48.5 1.0
PA E:ADP301 4.4 66.9 1.0
NZ F:LYS10 4.6 34.4 1.0
N E:SER16 4.6 56.6 1.0
OD2 E:ASP39 4.6 69.5 1.0
O2B E:ADP301 4.6 83.3 1.0
O2A E:ADP301 4.8 59.3 1.0
NZ E:LYS41 4.8 63.1 1.0
N E:GLY12 4.9 55.0 1.0
OD2 E:ASP43 4.9 73.4 1.0

Fluorine binding site 2 out of 8 in 8dfc

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Fluorine binding site 2 out of 8 in the Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F302

b:72.5
occ:1.00
 F2 E:ALF302 0.0 72.5 1.0
AL E:ALF302 1.8 69.0 1.0
F4 E:ALF302 2.5 78.0 1.0
F3 E:ALF302 2.5 70.1 1.0
NZ E:LYS41 3.0 63.1 1.0
F1 E:ALF302 3.6 69.7 1.0
OD2 F:ASP129 3.7 37.9 1.0
OD1 F:ASP129 3.7 33.9 1.0
NZ F:LYS10 4.0 34.4 1.0
O3B E:ADP301 4.0 55.9 1.0
CG F:ASP129 4.1 39.2 1.0
N E:GLY12 4.2 55.0 1.0
CE F:LYS10 4.3 36.2 1.0
CD F:LYS10 4.3 43.5 1.0
CE E:LYS41 4.4 64.8 1.0
CA E:GLY11 4.6 49.1 1.0
N F:GLY11 4.6 36.9 1.0
OD2 E:ASP39 4.8 69.5 1.0
C E:GLY11 4.8 51.5 1.0
CA F:GLY11 4.9 32.1 1.0
N E:GLY128 4.9 33.5 1.0

Fluorine binding site 3 out of 8 in 8dfc

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Fluorine binding site 3 out of 8 in the Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F302

b:70.1
occ:1.00
 F3 E:ALF302 0.0 70.1 1.0
AL E:ALF302 1.8 69.0 1.0
O3B E:ADP301 2.4 55.9 1.0
NZ E:LYS15 2.5 46.2 1.0
F2 E:ALF302 2.5 72.5 1.0
F1 E:ALF302 2.5 69.7 1.0
N E:GLY12 3.2 55.0 1.0
CE E:LYS15 3.3 36.4 1.0
CA E:GLY11 3.3 49.1 1.0
N E:GLY128 3.5 33.5 1.0
F4 E:ALF302 3.6 78.0 1.0
C E:GLY11 3.8 51.5 1.0
PB E:ADP301 3.8 72.6 1.0
CA E:GLY128 4.0 41.8 1.0
CA E:GLY12 4.3 55.0 1.0
O1B E:ADP301 4.4 64.8 1.0
O E:LYS10 4.4 50.5 1.0
O E:HOH414 4.4 57.2 1.0
C E:LEU127 4.4 35.4 1.0
N E:GLY11 4.4 60.2 1.0
OD2 F:ASP129 4.4 37.9 1.0
CA E:LEU127 4.6 40.2 1.0
MG E:MG303 4.7 60.8 1.0
CD E:LYS15 4.7 40.1 1.0
O2B E:ADP301 4.7 83.3 1.0
O3A E:ADP301 4.8 70.0 1.0
C E:LYS10 4.8 52.9 1.0
O E:GLY11 5.0 56.7 1.0

Fluorine binding site 4 out of 8 in 8dfc

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Fluorine binding site 4 out of 8 in the Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F302

b:78.0
occ:1.00
 F4 E:ALF302 0.0 78.0 1.0
AL E:ALF302 1.8 69.0 1.0
NZ E:LYS41 2.4 63.1 1.0
F2 E:ALF302 2.5 72.5 1.0
F1 E:ALF302 2.5 69.7 1.0
CE E:LYS41 3.2 64.8 1.0
NZ F:LYS10 3.3 34.4 1.0
MG E:MG303 3.3 60.8 1.0
F3 E:ALF302 3.6 70.1 1.0
OD2 E:ASP43 3.6 73.4 1.0
O1A E:ADP301 3.9 74.6 1.0
OD2 E:ASP39 4.0 69.5 1.0
O3B E:ADP301 4.2 55.9 1.0
CE F:LYS10 4.3 36.2 1.0
OD1 E:ASP43 4.3 66.9 1.0
O E:HOH414 4.4 57.2 1.0
CG E:ASP43 4.4 67.3 1.0
CD E:LYS41 4.6 63.1 1.0
CG E:ASP39 4.8 64.7 1.0
CD F:LYS10 4.8 43.5 1.0
O1B E:ADP301 5.0 64.8 1.0
OD1 E:ASP39 5.0 61.4 1.0

Fluorine binding site 5 out of 8 in 8dfc

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Fluorine binding site 5 out of 8 in the Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F303

b:54.2
occ:1.00
 F1 F:ALF303 0.0 54.2 1.0
AL F:ALF303 1.8 67.2 1.0
O1B F:ADP302 2.3 39.4 1.0
F3 F:ALF303 2.5 64.5 1.0
F4 F:ALF303 2.5 64.5 1.0
N F:GLY128 3.3 20.3 1.0
PB F:ADP302 3.4 36.2 1.0
NZ F:LYS15 3.4 35.7 1.0
F2 F:ALF303 3.6 77.7 1.0
O E:HOH404 3.6 39.3 1.0
CE F:LYS15 3.7 31.8 1.0
N F:GLY12 3.8 37.1 1.0
O2B F:ADP302 3.8 47.6 1.0
CA F:GLY128 3.9 20.5 1.0
CA F:GLY11 4.0 32.1 1.0
MG F:MG301 4.0 36.9 1.0
OD2 E:ASP129 4.1 47.6 1.0
O3B F:ADP302 4.1 45.8 1.0
OD2 F:ASP39 4.2 37.7 1.0
C F:LEU127 4.2 22.6 1.0
CA F:LEU127 4.3 22.4 1.0
C F:GLY11 4.4 38.0 1.0
O3A F:ADP302 4.7 45.0 1.0
NZ E:LYS10 4.8 45.8 1.0
CA F:GLY12 4.8 31.2 1.0
CB F:LEU127 4.8 23.6 1.0

Fluorine binding site 6 out of 8 in 8dfc

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Fluorine binding site 6 out of 8 in the Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F303

b:77.7
occ:1.00
 F2 F:ALF303 0.0 77.7 1.0
AL F:ALF303 1.8 67.2 1.0
F3 F:ALF303 2.5 64.5 1.0
F4 F:ALF303 2.5 64.5 1.0
MG F:MG301 2.7 36.9 1.0
OD2 F:ASP43 3.2 49.9 1.0
O1A F:ADP302 3.2 49.5 1.0
NZ E:LYS10 3.3 45.8 1.0
OD1 F:ASP43 3.5 43.0 1.0
F1 F:ALF303 3.6 54.2 1.0
O1B F:ADP302 3.6 39.4 1.0
CG F:ASP43 3.7 45.9 1.0
O2B F:ADP302 3.7 47.6 1.0
OD2 F:ASP39 4.0 37.7 1.0
PB F:ADP302 4.2 36.2 1.0
PA F:ADP302 4.5 44.1 1.0
CE E:MET156 4.6 67.4 1.0
CD F:LYS41 4.6 44.8 1.0
O3A F:ADP302 4.6 45.0 1.0
CE F:LYS41 4.6 46.5 1.0
CE E:LYS10 4.6 42.7 1.0
CG F:ASP39 4.7 36.3 1.0
OG F:SER16 4.9 39.5 1.0

Fluorine binding site 7 out of 8 in 8dfc

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Fluorine binding site 7 out of 8 in the Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F303

b:64.5
occ:1.00
 F3 F:ALF303 0.0 64.5 1.0
AL F:ALF303 1.8 67.2 1.0
NZ E:LYS10 2.3 45.8 1.0
F1 F:ALF303 2.5 54.2 1.0
F2 F:ALF303 2.5 77.7 1.0
O1B F:ADP302 2.5 39.4 1.0
CE E:LYS10 3.3 42.7 1.0
F4 F:ALF303 3.6 64.5 1.0
O E:HOH404 3.8 39.3 1.0
PB F:ADP302 3.9 36.2 1.0
N F:GLY12 4.0 37.1 1.0
O1A F:ADP302 4.2 49.5 1.0
O3A F:ADP302 4.3 45.0 1.0
MG F:MG301 4.4 36.9 1.0
O2B F:ADP302 4.4 47.6 1.0
CA F:GLY12 4.4 31.2 1.0
CD E:LYS10 4.4 46.6 1.0
CG E:LYS10 4.6 45.8 1.0
N E:GLY11 4.8 60.2 1.0
OD2 E:ASP129 4.9 47.6 1.0
C F:GLY11 4.9 38.0 1.0
O E:GLY11 4.9 56.7 1.0
PA F:ADP302 4.9 44.1 1.0

Fluorine binding site 8 out of 8 in 8dfc

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Fluorine binding site 8 out of 8 in the Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Cryoem Structure of the 1:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F303

b:64.5
occ:1.00
 F4 F:ALF303 0.0 64.5 1.0
AL F:ALF303 1.8 67.2 1.0
MG F:MG301 1.9 36.9 1.0
F2 F:ALF303 2.5 77.7 1.0
F1 F:ALF303 2.5 54.2 1.0
OD2 F:ASP39 2.7 37.7 1.0
O2B F:ADP302 3.1 47.6 1.0
O1B F:ADP302 3.4 39.4 1.0
F3 F:ALF303 3.6 64.5 1.0
PB F:ADP302 3.7 36.2 1.0
CG F:ASP39 3.9 36.3 1.0
CA F:LEU127 4.1 22.4 1.0
OG F:SER16 4.2 39.5 1.0
CE F:LYS15 4.3 31.8 1.0
OD2 F:ASP43 4.4 49.9 1.0
O1A F:ADP302 4.5 49.5 1.0
N F:GLY128 4.5 20.3 1.0
OD1 F:ASP43 4.6 43.0 1.0
CB F:ASP39 4.6 36.5 1.0
O F:VAL126 4.6 43.8 1.0
OD1 F:ASP39 4.7 39.3 1.0
CB F:LEU127 4.7 23.6 1.0
O3B F:ADP302 4.7 45.8 1.0
C F:LEU127 4.8 22.6 1.0
NZ F:LYS15 4.9 35.7 1.0
O3A F:ADP302 4.9 45.0 1.0
N F:LEU127 4.9 30.7 1.0
CB F:SER16 5.0 36.8 1.0
CG F:ASP43 5.0 45.9 1.0

Reference:

R.A.Warmack, D.C.Rees. Anaerobic Single Particle Cryoem of Nitrogenase To Be Published.
Page generated: Thu Jul 27 13:52:25 2023

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