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:
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
Go back to
Fluorine Binding Sites List in 8dfc
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 Sites List in 8dfc
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 Sites List in 8dfc
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 Sites List in 8dfc
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 Sites List in 8dfc
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
Go back to
Fluorine Binding Sites List in 8dfc
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
Go back to
Fluorine Binding Sites List in 8dfc
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
Go back to
Fluorine Binding Sites List in 8dfc
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: Fri Aug 2 17:28:30 2024
|