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

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 16 binding sites of Fluorine where determined in the Cryoem Structure of the 2:1 Adp-Tetrafluoroaluminate Stabilized Nitrogenase Complex From Azotobacter Vinelandii, PDB code: 8dfd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in 8dfd

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Fluorine binding site 1 out of 16 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 Fluorine with other atoms in the F 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:F602

b:32.9
occ:1.00
 F1 E:ALF602 0.0 32.9 1.0
AL E:ALF602 1.8 35.3 1.0
O3B E:ADP601 2.4 42.1 1.0
F4 E:ALF602 2.5 34.8 1.0
F3 E:ALF602 2.5 42.9 1.0
O E:HOH701 2.6 26.1 1.0
MG E:MG603 2.7 38.3 1.0
O2B E:ADP601 2.8 35.3 1.0
PB E:ADP601 3.0 31.7 1.0
O E:HOH736 3.1 32.5 1.0
O E:HOH703 3.3 33.2 1.0
O1B E:ADP601 3.4 34.3 1.0
F2 E:ALF602 3.6 39.0 1.0
OD2 E:ASP39 3.6 28.7 1.0
CE E:LYS15 3.6 19.6 1.0
NZ E:LYS15 3.7 20.8 1.0
CA E:LEU127 3.8 22.9 1.0
N E:GLY128 4.1 11.8 1.0
O E:VAL126 4.1 37.1 1.0
C E:LEU127 4.3 18.6 1.0
OG E:SER16 4.4 34.0 1.0
CB E:LEU127 4.5 18.6 1.0
O3A E:ADP601 4.6 37.8 1.0
N E:LEU127 4.6 27.5 1.0
C E:VAL126 4.7 25.4 1.0
CG E:ASP39 4.7 26.8 1.0
OD2 E:ASP125 4.8 27.2 1.0
CD E:LYS15 4.9 21.2 1.0
CB E:LYS15 4.9 23.5 1.0
N E:GLY12 4.9 23.4 1.0
O2A E:ADP601 5.0 43.8 1.0

Fluorine binding site 2 out of 16 in 8dfd

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Fluorine binding site 2 out of 16 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 Fluorine with other atoms in the F 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
E:F602

b:39.0
occ:1.00
 F2 E:ALF602 0.0 39.0 1.0
AL E:ALF602 1.8 35.3 1.0
F3 E:ALF602 2.5 42.9 1.0
F4 E:ALF602 2.5 34.8 1.0
O3B E:ADP601 2.5 42.1 1.0
NZ F:LYS10 2.6 27.6 1.0
F1 E:ALF602 3.6 32.9 1.0
N E:GLY12 3.7 23.4 1.0
CE F:LYS10 3.8 34.5 1.0
NZ E:LYS41 4.0 36.1 1.0
PB E:ADP601 4.0 31.7 1.0
CD F:LYS10 4.0 29.1 1.0
OD1 F:ASP129 4.1 33.2 1.0
CA E:GLY12 4.1 26.2 1.0
CG F:LYS10 4.1 31.5 1.0
N F:GLY11 4.2 25.4 1.0
O F:HOH703 4.4 33.8 1.0
O E:HOH701 4.5 26.1 1.0
CA F:GLY11 4.6 23.1 1.0
C E:GLY11 4.7 23.6 1.0
CE E:LYS41 4.7 37.8 1.0
O1B E:ADP601 4.7 34.3 1.0
O3A E:ADP601 4.7 37.8 1.0
OD2 F:ASP129 4.8 27.0 1.0
CG F:ASP129 4.8 33.0 1.0
O F:GLY11 4.8 31.4 1.0
O2B E:ADP601 4.9 35.3 1.0
CA E:GLY11 4.9 19.8 1.0

Fluorine binding site 3 out of 16 in 8dfd

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Fluorine binding site 3 out of 16 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 Fluorine with other atoms in the F 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
E:F602

b:42.9
occ:1.00
 F3 E:ALF602 0.0 42.9 1.0
AL E:ALF602 1.8 35.3 1.0
F2 E:ALF602 2.5 39.0 1.0
F1 E:ALF602 2.5 32.9 1.0
O E:HOH701 2.6 26.1 1.0
O3B E:ADP601 2.6 42.1 1.0
O E:HOH736 3.2 32.5 1.0
OD2 E:ASP39 3.4 28.7 1.0
NZ E:LYS41 3.5 36.1 1.0
F4 E:ALF602 3.6 34.8 1.0
NZ F:LYS10 3.6 27.6 1.0
OD2 E:ASP43 3.7 42.7 1.0
CE E:LYS41 3.7 37.8 1.0
PB E:ADP601 3.8 31.7 1.0
O2B E:ADP601 3.8 35.3 1.0
MG E:MG603 3.9 38.3 1.0
O2A E:ADP601 4.1 43.8 1.0
OD1 E:ASP43 4.3 47.2 1.0
CG E:ASP39 4.4 26.8 1.0
CG E:ASP43 4.4 41.1 1.0
OD1 F:ASP129 4.6 33.2 1.0
O3A E:ADP601 4.8 37.8 1.0
OG E:SER16 4.8 34.0 1.0
O1B E:ADP601 4.9 34.3 1.0
OD1 E:ASP39 5.0 30.3 1.0

Fluorine binding site 4 out of 16 in 8dfd

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Fluorine binding site 4 out of 16 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 Fluorine with other atoms in the F 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
E:F602

b:34.8
occ:1.00
 F4 E:ALF602 0.0 34.8 1.0
AL E:ALF602 1.8 35.3 1.0
O3B E:ADP601 2.3 42.1 1.0
F1 E:ALF602 2.5 32.9 1.0
F2 E:ALF602 2.5 39.0 1.0
N E:GLY12 2.8 23.4 1.0
NZ E:LYS15 2.9 20.8 1.0
O1B E:ADP601 3.2 34.3 1.0
PB E:ADP601 3.3 31.7 1.0
CA E:GLY11 3.3 19.8 1.0
C E:GLY11 3.5 23.6 1.0
N E:GLY128 3.5 11.8 1.0
F3 E:ALF602 3.6 42.9 1.0
CE E:LYS15 3.8 19.6 1.0
O F:HOH703 3.8 33.8 1.0
CA E:GLY12 3.8 26.2 1.0
CA E:GLY128 4.0 21.9 1.0
O2B E:ADP601 4.2 35.3 1.0
OD2 F:ASP129 4.4 27.0 1.0
N E:GLY11 4.5 26.1 1.0
O E:LYS10 4.5 31.1 1.0
C E:LEU127 4.5 18.6 1.0
O E:HOH701 4.5 26.1 1.0
OD1 F:ASP129 4.5 33.2 1.0
NZ F:LYS10 4.5 27.6 1.0
O3A E:ADP601 4.6 37.8 1.0
CA E:LEU127 4.7 22.9 1.0
O E:GLY11 4.7 28.3 1.0
CG F:ASP129 4.9 33.0 1.0
C E:LYS10 4.9 26.9 1.0
C E:GLY12 4.9 30.8 1.0

Fluorine binding site 5 out of 16 in 8dfd

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Fluorine binding site 5 out of 16 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 Fluorine with other atoms in the F binding site number 5 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:F601

b:51.0
occ:1.00
 F1 F:ALF601 0.0 51.0 1.0
AL F:ALF601 1.8 39.5 1.0
F4 F:ALF601 2.5 52.4 1.0
F3 F:ALF601 2.5 48.0 1.0
O E:HOH757 2.5 31.7 1.0
O1B F:ADP600 2.6 30.8 1.0
N F:GLY12 2.8 34.1 1.0
CE E:LYS10 3.5 28.0 1.0
CA F:GLY11 3.5 23.1 1.0
C F:GLY11 3.6 29.0 1.0
F2 F:ALF601 3.6 47.3 1.0
CA F:GLY12 3.7 32.5 1.0
CA E:GLY11 3.8 19.8 1.0
NZ E:LYS10 3.8 27.0 1.0
N E:GLY11 3.9 26.1 1.0
O F:HOH703 3.9 33.8 1.0
OD2 E:ASP129 4.0 30.7 1.0
PB F:ADP600 4.0 24.5 1.0
O E:GLY11 4.2 28.3 1.0
C E:GLY11 4.4 23.6 1.0
CD E:LYS10 4.4 29.5 1.0
O2B F:ADP600 4.5 26.6 1.0
OD1 E:ASP129 4.6 33.0 1.0
O F:GLY11 4.6 31.4 1.0
NZ F:LYS41 4.6 28.2 1.0
CG E:ASP129 4.7 29.5 1.0
CG E:LYS10 4.7 25.1 1.0
NZ F:LYS15 4.8 24.4 1.0
O3A F:ADP600 4.9 33.5 1.0
N F:GLY128 4.9 25.1 1.0
N F:GLY11 4.9 25.4 1.0
O3B F:ADP600 5.0 35.2 1.0

Fluorine binding site 6 out of 16 in 8dfd

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Fluorine binding site 6 out of 16 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 Fluorine with other atoms in the F binding site number 6 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:F601

b:47.3
occ:1.00
 F2 F:ALF601 0.0 47.3 1.0
AL F:ALF601 1.8 39.5 1.0
O F:HOH701 2.3 32.1 1.0
O1B F:ADP600 2.3 30.8 1.0
F3 F:ALF601 2.5 48.0 1.0
F4 F:ALF601 2.5 52.4 1.0
O3B F:ADP600 2.6 35.2 1.0
MG F:MG602 2.9 40.1 1.0
PB F:ADP600 3.0 24.5 1.0
O F:HOH716 3.0 29.9 1.0
OD2 F:ASP39 3.2 28.8 1.0
O F:HOH702 3.4 35.8 1.0
F1 F:ALF601 3.6 51.0 1.0
O2B F:ADP600 3.7 26.6 1.0
OG F:SER16 4.0 29.4 1.0
NZ F:LYS41 4.1 28.2 1.0
CA F:LEU127 4.2 18.1 1.0
CG F:ASP39 4.4 30.1 1.0
O1A F:ADP600 4.4 31.4 1.0
CE F:LYS15 4.4 19.3 1.0
O3A F:ADP600 4.5 33.5 1.0
NZ F:LYS15 4.5 24.4 1.0
O F:VAL126 4.6 28.1 1.0
OD2 F:ASP43 4.6 35.5 1.0
NZ E:LYS10 4.6 27.0 1.0
CB F:LEU127 4.7 21.2 1.0
N F:GLY128 4.7 25.1 1.0
O E:HOH757 4.9 31.7 1.0
C F:LEU127 4.9 23.8 1.0
OD1 F:ASP43 5.0 34.9 1.0

Fluorine binding site 7 out of 16 in 8dfd

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Fluorine binding site 7 out of 16 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 Fluorine with other atoms in the F binding site number 7 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:F601

b:48.0
occ:1.00
 F3 F:ALF601 0.0 48.0 1.0
AL F:ALF601 1.8 39.5 1.0
F2 F:ALF601 2.5 47.3 1.0
F1 F:ALF601 2.5 51.0 1.0
O1B F:ADP600 2.5 30.8 1.0
NZ E:LYS10 2.7 27.0 1.0
NZ F:LYS41 2.7 28.2 1.0
O E:HOH757 3.0 31.7 1.0
CE E:LYS10 3.4 28.0 1.0
F4 F:ALF601 3.6 52.4 1.0
O F:HOH701 3.6 32.1 1.0
CE F:LYS41 3.7 28.3 1.0
O E:HOH724 3.8 39.1 1.0
PB F:ADP600 3.9 24.5 1.0
OD2 F:ASP43 4.1 35.5 1.0
O3B F:ADP600 4.1 35.2 1.0
O1A F:ADP600 4.2 31.4 1.0
CD E:LYS10 4.3 29.5 1.0
OD2 F:ASP39 4.4 28.8 1.0
O F:HOH716 4.5 29.9 1.0
OD1 E:ASP129 4.6 33.0 1.0
O3A F:ADP600 4.7 33.5 1.0
N F:GLY12 4.8 34.1 1.0
CD F:LYS41 4.9 28.3 1.0
O2B F:ADP600 5.0 26.6 1.0

Fluorine binding site 8 out of 16 in 8dfd

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Fluorine binding site 8 out of 16 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 Fluorine with other atoms in the F binding site number 8 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:F601

b:52.4
occ:1.00
 F4 F:ALF601 0.0 52.4 1.0
AL F:ALF601 1.8 39.5 1.0
O1B F:ADP600 2.4 30.8 1.0
F1 F:ALF601 2.5 51.0 1.0
F2 F:ALF601 2.5 47.3 1.0
NZ F:LYS15 2.7 24.4 1.0
O2B F:ADP600 3.1 26.6 1.0
N F:GLY128 3.1 25.1 1.0
CE F:LYS15 3.2 19.3 1.0
PB F:ADP600 3.2 24.5 1.0
N F:GLY12 3.5 34.1 1.0
CA F:GLY11 3.5 23.1 1.0
F3 F:ALF601 3.6 48.0 1.0
CA F:GLY128 3.7 15.2 1.0
O3B F:ADP600 3.9 35.2 1.0
C F:LEU127 3.9 23.8 1.0
CA F:LEU127 4.0 18.1 1.0
C F:GLY11 4.0 29.0 1.0
OD2 E:ASP129 4.1 30.7 1.0
O F:LYS10 4.2 33.1 1.0
O F:HOH702 4.2 35.8 1.0
N F:GLY11 4.5 25.4 1.0
O F:HOH701 4.5 32.1 1.0
CA F:GLY12 4.6 32.5 1.0
CB F:LEU127 4.6 21.2 1.0
O E:HOH757 4.6 31.7 1.0
CD F:LYS15 4.6 19.2 1.0
O3A F:ADP600 4.7 33.5 1.0
C F:LYS10 4.7 30.6 1.0
O F:HOH703 4.7 33.8 1.0
O F:VAL126 4.8 28.1 1.0
MG F:MG602 4.8 40.1 1.0
O F:LEU127 4.8 28.8 1.0
OD2 F:ASP39 4.9 28.8 1.0

Fluorine binding site 9 out of 16 in 8dfd

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Fluorine binding site 9 out of 16 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 Fluorine with other atoms in the F binding site number 9 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:F602

b:34.2
occ:1.00
 F1 G:ALF602 0.0 34.2 1.0
AL G:ALF602 1.8 35.2 1.0
O G:HOH725 2.2 30.6 1.0
O3B G:ADP601 2.4 43.2 1.0
MG G:MG603 2.4 33.0 1.0
F3 G:ALF602 2.5 37.2 1.0
F4 G:ALF602 2.5 45.2 1.0
O2B G:ADP601 3.0 32.7 1.0
PB G:ADP601 3.1 25.8 1.0
O G:HOH744 3.2 27.0 1.0
CE G:LYS15 3.5 20.3 1.0
O1B G:ADP601 3.5 35.3 1.0
F2 G:ALF602 3.6 41.0 1.0
OD2 G:ASP39 3.6 27.5 1.0
NZ G:LYS15 3.7 20.6 1.0
O G:HOH746 3.8 32.2 1.0
CA G:LEU127 3.9 25.1 1.0
N G:GLY128 3.9 12.1 1.0
O G:VAL126 4.0 39.2 1.0
C G:LEU127 4.3 17.8 1.0
OG G:SER16 4.3 35.5 1.0
O3A G:ADP601 4.6 41.0 1.0
CB G:LEU127 4.7 17.7 1.0
N G:LEU127 4.7 27.1 1.0
C G:VAL126 4.7 27.8 1.0
CD G:LYS15 4.7 20.2 1.0
CG G:ASP39 4.7 29.3 1.0
NZ G:LYS41 4.9 30.6 1.0
CA G:GLY128 4.9 22.0 1.0
N G:GLY12 4.9 24.8 1.0

Fluorine binding site 10 out of 16 in 8dfd

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Fluorine binding site 10 out of 16 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 Fluorine with other atoms in the F binding site number 10 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:F602

b:41.0
occ:1.00
 F2 G:ALF602 0.0 41.0 1.0
AL G:ALF602 1.8 35.2 1.0
F4 G:ALF602 2.5 45.2 1.0
F3 G:ALF602 2.5 37.2 1.0
O3B G:ADP601 2.6 43.2 1.0
NZ H:LYS10 2.7 24.8 1.0
F1 G:ALF602 3.6 34.2 1.0
N G:GLY12 3.7 24.8 1.0
CE H:LYS10 3.7 30.5 1.0
CD H:LYS10 3.9 22.6 1.0
NZ G:LYS41 4.0 30.6 1.0
PB G:ADP601 4.0 25.8 1.0
CA G:GLY12 4.1 24.5 1.0
OD1 H:ASP129 4.1 35.5 1.0
CG H:LYS10 4.2 25.0 1.0
N H:GLY11 4.2 19.4 1.0
CE G:LYS41 4.4 34.3 1.0
O H:HOH401 4.4 37.1 1.0
CA H:GLY11 4.5 19.5 1.0
C G:GLY11 4.6 25.1 1.0
O G:HOH746 4.7 32.2 1.0
O3A G:ADP601 4.7 41.0 1.0
O1B G:ADP601 4.7 35.3 1.0
OD2 H:ASP129 4.8 30.4 1.0
CA G:GLY11 4.8 24.0 1.0
O H:GLY11 4.8 30.7 1.0
MG G:MG603 4.8 33.0 1.0
CG H:ASP129 4.9 33.8 1.0
O2B G:ADP601 5.0 32.7 1.0

Reference:

R.A.Warmack, D.C.Rees. Anaerobic Single Particle Cryoem of Nitrogenase To Be Published.
Page generated: Fri Aug 2 17:29:00 2024

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