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Fluorine in PDB 1m34: Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate

Enzymatic activity of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate

All present enzymatic activity of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate:
1.18.6.1;

Protein crystallography data

The structure of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate, PDB code: 1m34 was solved by B.Schmid, O.Einsle, H.-J.Chiu, A.Willing, M.Yoshida, J.B.Howard, D.C.Rees, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 326.100, 75.800, 312.200, 90.00, 102.60, 90.00
R / Rfree (%) 20 / 23.6

Other elements in 1m34:

The structure of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate also contains other interesting chemical elements:

Molybdenum (Mo) 4 atoms
Magnesium (Mg) 8 atoms
Aluminium (Al) 8 atoms
Iron (Fe) 76 atoms
Calcium (Ca) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Fluorine atom in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate (pdb code 1m34). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 32 binding sites of Fluorine where determined in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate, PDB code: 1m34:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 32 in 1m34

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Fluorine binding site 1 out of 32 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F3093

b:38.9
occ:1.00
 F1 E:ALF3093 0.0 38.9 1.0
AL E:ALF3093 1.8 38.5 1.0
F4 E:ALF3093 2.4 38.2 1.0
F3 E:ALF3093 2.6 40.4 1.0
N E:GLY128 2.7 38.4 1.0
O E:HOH3130 2.7 34.1 1.0
CA E:GLY128 3.0 38.2 1.0
NZ E:LYS15 3.0 32.1 1.0
CA E:GLY11 3.1 25.6 1.0
N E:GLY12 3.4 27.4 1.0
F2 E:ALF3093 3.5 33.4 1.0
C E:LEU127 3.7 39.1 1.0
C E:GLY11 3.8 26.2 1.0
O3B E:ADP3091 3.9 30.9 1.0
OD2 F:ASP129 4.0 40.4 1.0
O1B E:ADP3091 4.1 38.9 1.0
N E:GLY11 4.2 28.1 1.0
CA E:LEU127 4.2 38.2 1.0
O E:LYS10 4.2 25.9 1.0
C E:GLY128 4.3 40.7 1.0
PB E:ADP3091 4.3 33.1 1.0
CE E:LYS15 4.5 36.9 1.0
C E:LYS10 4.6 27.3 1.0
CA E:GLY12 4.6 29.7 1.0
OD1 F:ASP129 4.6 35.3 1.0
N E:ASP129 4.7 40.5 1.0
O E:LEU127 4.7 41.7 1.0
CB E:LEU127 4.7 38.8 1.0
CG F:ASP129 4.7 38.8 1.0
MG E:MG3092 4.8 35.6 1.0
O E:GLY9 4.9 27.9 1.0
CA F:GLY11 5.0 25.3 1.0
O2B E:ADP3091 5.0 31.9 1.0
O E:GLY11 5.0 25.6 1.0

Fluorine binding site 2 out of 32 in 1m34

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Fluorine binding site 2 out of 32 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F3093

b:33.4
occ:1.00
 F2 E:ALF3093 0.0 33.4 1.0
AL E:ALF3093 1.7 38.5 1.0
F3 E:ALF3093 2.5 40.4 1.0
F4 E:ALF3093 2.5 38.2 1.0
O1B E:ADP3091 2.7 38.9 1.0
O E:HOH3130 2.7 34.1 1.0
NZ F:LYS10 2.9 22.9 1.0
O E:HOH3131 3.0 46.2 1.0
MG E:MG3092 3.1 35.6 1.0
NZ E:LYS41 3.4 50.6 1.0
F1 E:ALF3093 3.5 38.9 1.0
PB E:ADP3091 3.8 33.1 1.0
OD2 E:ASP39 3.9 40.0 1.0
O E:HOH3133 3.9 38.6 1.0
CE F:LYS10 3.9 22.9 1.0
CE E:LYS41 4.0 49.6 1.0
O F:HOH954 4.2 37.6 1.0
O2B E:ADP3091 4.2 31.9 1.0
O2A E:ADP3091 4.4 32.7 1.0
CD F:LYS10 4.5 24.2 1.0
OD2 E:ASP43 4.5 54.7 1.0
O3B E:ADP3091 4.6 30.9 1.0
OD1 F:ASP129 4.8 35.3 1.0
N E:GLY12 4.8 27.4 1.0
O E:HOH3132 4.8 31.4 1.0
O3A E:ADP3091 4.9 35.5 1.0
CG E:ASP39 4.9 40.7 1.0

Fluorine binding site 3 out of 32 in 1m34

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Fluorine binding site 3 out of 32 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F3093

b:40.4
occ:1.00
 F3 E:ALF3093 0.0 40.4 1.0
AL E:ALF3093 1.8 38.5 1.0
F2 E:ALF3093 2.5 33.4 1.0
F1 E:ALF3093 2.6 38.9 1.0
N E:GLY12 3.1 27.4 1.0
O E:HOH3130 3.2 34.1 1.0
CA F:GLY11 3.4 25.3 1.0
O1B E:ADP3091 3.4 38.9 1.0
N F:GLY11 3.4 27.6 1.0
NZ F:LYS10 3.5 22.9 1.0
F4 E:ALF3093 3.5 38.2 1.0
CE F:LYS10 3.6 22.9 1.0
CA E:GLY12 3.7 29.7 1.0
CD F:LYS10 3.8 24.2 1.0
C E:GLY11 3.9 26.2 1.0
CA E:GLY11 4.0 25.6 1.0
O F:GLY11 4.1 24.1 1.0
C F:GLY11 4.1 24.1 1.0
OD1 F:ASP129 4.4 35.3 1.0
PB E:ADP3091 4.4 33.1 1.0
O3B E:ADP3091 4.5 30.9 1.0
CG F:LYS10 4.7 25.0 1.0
C F:LYS10 4.7 27.3 1.0
OD2 F:ASP129 4.7 40.4 1.0
O E:GLY11 4.9 25.6 1.0
CG F:ASP129 4.9 38.8 1.0

Fluorine binding site 4 out of 32 in 1m34

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Fluorine binding site 4 out of 32 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F3093

b:38.2
occ:1.00
 F4 E:ALF3093 0.0 38.2 1.0
AL E:ALF3093 1.8 38.5 1.0
O E:HOH3130 2.2 34.1 1.0
F1 E:ALF3093 2.4 38.9 1.0
F2 E:ALF3093 2.5 33.4 1.0
MG E:MG3092 2.6 35.6 1.0
O E:HOH3132 3.1 31.4 1.0
CA E:LEU127 3.3 38.2 1.0
NZ E:LYS15 3.3 32.1 1.0
N E:GLY128 3.4 38.4 1.0
O1B E:ADP3091 3.5 38.9 1.0
OD2 E:ASP39 3.5 40.0 1.0
F3 E:ALF3093 3.5 40.4 1.0
O E:HOH3133 3.6 38.6 1.0
C E:LEU127 3.7 39.1 1.0
O2B E:ADP3091 3.7 31.9 1.0
PB E:ADP3091 3.7 33.1 1.0
O3B E:ADP3091 4.0 30.9 1.0
O E:HOH3131 4.0 46.2 1.0
O E:VAL126 4.0 36.2 1.0
CB E:LEU127 4.1 38.8 1.0
N E:LEU127 4.4 36.1 1.0
CA E:GLY128 4.4 38.2 1.0
C E:VAL126 4.6 34.8 1.0
CE E:LYS15 4.6 36.9 1.0
CG E:LYS15 4.7 36.4 1.0
O E:LEU127 4.7 41.7 1.0
CG E:ASP39 4.7 40.7 1.0
CD E:LYS15 4.8 36.3 1.0
OG E:SER16 4.8 36.3 1.0
N E:GLY12 4.9 27.4 1.0

Fluorine binding site 5 out of 32 in 1m34

Go back to Fluorine Binding Sites List in 1m34
Fluorine binding site 5 out of 32 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F3193

b:42.5
occ:1.00
 F1 F:ALF3193 0.0 42.5 1.0
AL F:ALF3193 1.8 41.3 1.0
F4 F:ALF3193 2.4 40.1 1.0
F3 F:ALF3193 2.6 46.8 1.0
O E:HOH3134 2.9 39.0 1.0
N F:GLY12 3.0 22.7 1.0
N F:GLY128 3.0 35.4 1.0
NZ F:LYS15 3.1 34.4 1.0
CA F:GLY11 3.1 25.3 1.0
CA F:GLY128 3.2 36.3 1.0
F2 F:ALF3193 3.5 40.5 1.0
C F:GLY11 3.6 24.1 1.0
O1B F:ADP3191 3.8 32.0 1.0
O3B F:ADP3191 3.8 31.3 1.0
OD2 E:ASP129 4.0 50.4 1.0
C F:LEU127 4.1 35.4 1.0
CA F:GLY12 4.1 25.0 1.0
O F:LYS10 4.2 27.5 1.0
PB F:ADP3191 4.2 28.1 1.0
N F:GLY11 4.2 27.6 1.0
C F:GLY128 4.4 37.3 1.0
OD1 E:ASP129 4.6 49.7 1.0
CE F:LYS15 4.6 33.8 1.0
C F:LYS10 4.6 27.3 1.0
CA F:LEU127 4.6 35.8 1.0
CG E:ASP129 4.7 49.2 1.0
O F:GLY11 4.8 24.1 1.0
N F:ASP129 4.8 37.9 1.0
CA E:GLY11 4.8 25.6 1.0
O2B F:ADP3191 4.8 28.9 1.0
MG F:MG3192 4.9 31.0 1.0
O F:GLY9 5.0 30.8 1.0

Fluorine binding site 6 out of 32 in 1m34

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Fluorine binding site 6 out of 32 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F3193

b:40.5
occ:1.00
 F2 F:ALF3193 0.0 40.5 1.0
AL F:ALF3193 1.8 41.3 1.0
F3 F:ALF3193 2.5 46.8 1.0
F4 F:ALF3193 2.5 40.1 1.0
O E:HOH3134 2.6 39.0 1.0
MG F:MG3192 2.8 31.0 1.0
O1B F:ADP3191 3.0 32.0 1.0
O F:HOH3196 3.0 25.9 1.0
NZ F:LYS41 3.1 46.6 1.0
NZ E:LYS10 3.2 33.5 1.0
F1 F:ALF3193 3.5 42.5 1.0
O F:HOH3198 3.6 41.2 1.0
OD2 F:ASP39 3.7 38.1 1.0
CE F:LYS41 3.9 46.3 1.0
PB F:ADP3191 3.9 28.1 1.0
O2B F:ADP3191 4.0 28.9 1.0
CE E:LYS10 4.3 31.1 1.0
O E:HOH3105 4.3 33.4 1.0
OD2 F:ASP43 4.4 46.6 1.0
O F:HOH3197 4.5 27.0 1.0
O2A F:ADP3191 4.6 31.6 1.0
OD1 E:ASP129 4.6 49.7 1.0
CG F:ASP39 4.7 38.4 1.0
O3B F:ADP3191 4.8 31.3 1.0
CD E:LYS10 4.9 31.4 1.0

Fluorine binding site 7 out of 32 in 1m34

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Fluorine binding site 7 out of 32 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F3193

b:46.8
occ:1.00
 F3 F:ALF3193 0.0 46.8 1.0
AL F:ALF3193 1.8 41.3 1.0
F2 F:ALF3193 2.5 40.5 1.0
F1 F:ALF3193 2.6 42.5 1.0
O E:HOH3134 2.8 39.0 1.0
F4 F:ALF3193 3.6 40.1 1.0
N E:GLY11 3.6 28.1 1.0
NZ E:LYS10 3.6 33.5 1.0
O1B F:ADP3191 3.6 32.0 1.0
N F:GLY12 3.6 22.7 1.0
CA E:GLY11 3.8 25.6 1.0
OD1 E:ASP129 3.8 49.7 1.0
CE E:LYS10 3.8 31.1 1.0
CD E:LYS10 3.9 31.4 1.0
CA F:GLY12 4.2 25.0 1.0
OD2 E:ASP129 4.4 50.4 1.0
CG E:ASP129 4.5 49.2 1.0
C F:GLY11 4.5 24.1 1.0
O E:GLY11 4.5 25.6 1.0
CA F:GLY11 4.6 25.3 1.0
C E:GLY11 4.6 26.2 1.0
NZ F:LYS41 4.6 46.6 1.0
CE F:LYS41 4.7 46.3 1.0
CG E:LYS10 4.7 31.4 1.0
PB F:ADP3191 4.8 28.1 1.0
C E:LYS10 4.8 27.3 1.0
O E:HOH3098 4.9 27.4 1.0

Fluorine binding site 8 out of 32 in 1m34

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Fluorine binding site 8 out of 32 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F3193

b:40.1
occ:1.00
 F4 F:ALF3193 0.0 40.1 1.0
AL F:ALF3193 1.8 41.3 1.0
F1 F:ALF3193 2.4 42.5 1.0
F2 F:ALF3193 2.5 40.5 1.0
MG F:MG3192 2.7 31.0 1.0
O E:HOH3134 2.9 39.0 1.0
O F:HOH3197 3.0 27.0 1.0
O2B F:ADP3191 3.1 28.9 1.0
NZ F:LYS15 3.2 34.4 1.0
O1B F:ADP3191 3.2 32.0 1.0
PB F:ADP3191 3.3 28.1 1.0
O3B F:ADP3191 3.5 31.3 1.0
N F:GLY128 3.5 35.4 1.0
F3 F:ALF3193 3.6 46.8 1.0
CA F:LEU127 3.7 35.8 1.0
C F:LEU127 3.9 35.4 1.0
O F:HOH3198 4.0 41.2 1.0
OD2 F:ASP39 4.0 38.1 1.0
CG F:LYS15 4.1 33.9 1.0
CD F:LYS15 4.1 34.3 1.0
O F:HOH3196 4.2 25.9 1.0
CE F:LYS15 4.3 33.8 1.0
O F:VAL126 4.3 39.4 1.0
CA F:GLY128 4.3 36.3 1.0
CB F:LEU127 4.4 35.3 1.0
N F:GLY12 4.6 22.7 1.0
OG F:SER16 4.7 28.8 1.0
N F:LEU127 4.7 37.3 1.0
O3A F:ADP3191 4.8 32.0 1.0
O F:LEU127 4.9 37.2 1.0
C F:VAL126 4.9 36.5 1.0

Fluorine binding site 9 out of 32 in 1m34

Go back to Fluorine Binding Sites List in 1m34
Fluorine binding site 9 out of 32 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F3293

b:47.3
occ:1.00
 F1 G:ALF3293 0.0 47.3 1.0
AL G:ALF3293 1.7 45.0 1.0
F4 G:ALF3293 2.3 44.3 1.0
F3 G:ALF3293 2.6 47.1 1.0
N G:GLY12 2.8 33.8 1.0
CA G:GLY11 3.0 34.3 1.0
NZ G:LYS15 3.0 29.4 1.0
N G:GLY128 3.1 37.5 1.0
O G:HOH3345 3.2 43.7 1.0
CA G:GLY128 3.3 39.1 1.0
C G:GLY11 3.3 34.0 1.0
O3B G:ADP3291 3.5 33.6 1.0
F2 G:ALF3293 3.5 44.9 1.0
O1B G:ADP3291 3.9 39.4 1.0
CA G:GLY12 3.9 33.1 1.0
O G:LYS10 4.1 34.3 1.0
N G:GLY11 4.1 35.5 1.0
PB G:ADP3291 4.1 31.6 1.0
OD2 H:ASP129 4.2 48.9 1.0
C G:LEU127 4.3 38.1 1.0
CE G:LYS15 4.5 32.6 1.0
C G:GLY128 4.5 40.9 1.0
C G:LYS10 4.5 35.4 1.0
O G:GLY11 4.6 34.1 1.0
CA G:LEU127 4.7 39.4 1.0
OD1 H:ASP129 4.8 49.1 1.0
MG G:MG3292 4.8 48.6 1.0
CA H:GLY11 4.8 31.1 1.0
CG H:ASP129 4.9 48.8 1.0
O2B G:ADP3291 5.0 37.2 1.0
N G:ASP129 5.0 41.2 1.0

Fluorine binding site 10 out of 32 in 1m34

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Fluorine binding site 10 out of 32 in the Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Nitrogenase Complex From Azotobacter Vinelandii Stabilized By Adp- Tetrafluoroaluminate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F3293

b:44.9
occ:1.00
 F2 G:ALF3293 0.0 44.9 1.0
AL G:ALF3293 1.8 45.0 1.0
O G:HOH3345 2.3 43.7 1.0
F3 G:ALF3293 2.5 47.1 1.0
F4 G:ALF3293 2.5 44.3 1.0
O1B G:ADP3291 2.8 39.4 1.0
NZ G:LYS41 3.0 44.8 1.0
MG G:MG3292 3.1 48.6 1.0
NZ H:LYS10 3.2 33.1 1.0
O G:HOH3346 3.3 27.1 1.0
F1 G:ALF3293 3.5 47.3 1.0
OD2 G:ASP39 3.6 35.4 1.0
CE G:LYS41 3.7 45.1 1.0
O G:HOH3348 4.0 42.7 1.0
PB G:ADP3291 4.1 31.6 1.0
CE H:LYS10 4.1 33.0 1.0
O H:HOH3394 4.1 24.5 1.0
OD1 H:ASP129 4.4 49.1 1.0
CD H:LYS10 4.6 33.2 1.0
O2B G:ADP3291 4.6 37.2 1.0
OD2 G:ASP43 4.7 56.7 1.0
O3B G:ADP3291 4.7 33.6 1.0
O G:HOH3347 4.7 26.4 1.0
CG G:ASP39 4.7 39.9 1.0
O2A G:ADP3291 4.8 35.2 1.0
N G:GLY12 4.9 33.8 1.0

Reference:

B.Schmid, O.Einsle, H.-J.Chiu, A.Willing, M.Yoshida, J.B.Howard, D.C.Rees. Biochemical and Structural Characterization of the Crosslinked Complex of Nitrogenase: Comparison to the Adp-ALF4 Stabilized Structure Biochemistry V. 41 15557 2002.
ISSN: ISSN 0006-2960
PubMed: 12501184
DOI: 10.1021/BI026642B
Page generated: Wed Jul 31 11:49:57 2024

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