Fluorine in PDB 1w0j: Beryllium Fluoride Inhibited Bovine F1-Atpase
Enzymatic activity of Beryllium Fluoride Inhibited Bovine F1-Atpase
All present enzymatic activity of Beryllium Fluoride Inhibited Bovine F1-Atpase:
3.6.3.14;
Protein crystallography data
The structure of Beryllium Fluoride Inhibited Bovine F1-Atpase, PDB code: 1w0j
was solved by
R.Kagawa,
M.G.Montgomery,
K.Braig,
J.E.Walker,
A.G.W.Leslie,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.2
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
283.520,
107.374,
137.936,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.4 /
23.6
|
Other elements in 1w0j:
The structure of Beryllium Fluoride Inhibited Bovine F1-Atpase also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Beryllium Fluoride Inhibited Bovine F1-Atpase
(pdb code 1w0j). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Beryllium Fluoride Inhibited Bovine F1-Atpase, PDB code: 1w0j:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 1w0j
Go back to
Fluorine Binding Sites List in 1w0j
Fluorine binding site 1 out
of 6 in the Beryllium Fluoride Inhibited Bovine F1-Atpase
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Beryllium Fluoride Inhibited Bovine F1-Atpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F1478
b:25.9
occ:1.00
|
F1
|
D:BEF1478
|
0.0
|
25.9
|
1.0
|
BE
|
D:BEF1478
|
1.6
|
17.3
|
1.0
|
F3
|
D:BEF1478
|
2.5
|
23.6
|
1.0
|
O1B
|
D:ADP1476
|
2.6
|
23.2
|
1.0
|
F2
|
D:BEF1478
|
2.6
|
20.4
|
1.0
|
O
|
D:HOH2064
|
2.7
|
36.3
|
1.0
|
NH2
|
D:ARG189
|
3.1
|
19.6
|
1.0
|
NH2
|
C:ARG373
|
3.1
|
26.8
|
1.0
|
NH1
|
C:ARG373
|
3.1
|
22.6
|
1.0
|
CA
|
C:SER344
|
3.2
|
22.8
|
1.0
|
N
|
D:GLY159
|
3.4
|
23.6
|
1.0
|
CZ
|
C:ARG373
|
3.5
|
23.5
|
1.0
|
CB
|
C:SER344
|
3.7
|
24.9
|
1.0
|
O
|
C:SER344
|
3.8
|
26.0
|
1.0
|
NH1
|
D:ARG189
|
3.8
|
19.2
|
1.0
|
CA
|
D:ALA158
|
3.8
|
26.1
|
1.0
|
C
|
C:SER344
|
3.8
|
24.6
|
1.0
|
CZ
|
D:ARG189
|
3.9
|
28.7
|
1.0
|
O
|
C:ILE343
|
3.9
|
27.2
|
1.0
|
CB
|
D:ALA158
|
4.0
|
24.6
|
1.0
|
PB
|
D:ADP1476
|
4.0
|
19.5
|
1.0
|
C
|
D:ALA158
|
4.0
|
23.8
|
1.0
|
N
|
C:SER344
|
4.2
|
24.7
|
1.0
|
CA
|
D:GLY159
|
4.3
|
21.3
|
1.0
|
C
|
C:ILE343
|
4.4
|
25.7
|
1.0
|
O2B
|
D:ADP1476
|
4.5
|
19.0
|
1.0
|
MG
|
D:MG1477
|
4.5
|
30.0
|
1.0
|
O
|
D:HOH2065
|
4.6
|
28.7
|
1.0
|
O3A
|
D:ADP1476
|
4.7
|
24.3
|
1.0
|
O
|
D:HOH2068
|
4.7
|
31.4
|
1.0
|
NE
|
C:ARG373
|
4.8
|
26.6
|
1.0
|
N
|
C:ILE345
|
4.9
|
25.7
|
1.0
|
NZ
|
D:LYS162
|
4.9
|
18.9
|
1.0
|
OG
|
C:SER344
|
5.0
|
21.6
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 1w0j
Go back to
Fluorine Binding Sites List in 1w0j
Fluorine binding site 2 out
of 6 in the Beryllium Fluoride Inhibited Bovine F1-Atpase
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Beryllium Fluoride Inhibited Bovine F1-Atpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F1478
b:20.4
occ:1.00
|
F2
|
D:BEF1478
|
0.0
|
20.4
|
1.0
|
BE
|
D:BEF1478
|
1.6
|
17.3
|
1.0
|
O
|
D:HOH2065
|
2.5
|
28.7
|
1.0
|
F3
|
D:BEF1478
|
2.6
|
23.6
|
1.0
|
F1
|
D:BEF1478
|
2.6
|
25.9
|
1.0
|
O
|
D:HOH2064
|
2.6
|
36.3
|
1.0
|
O1B
|
D:ADP1476
|
2.7
|
23.2
|
1.0
|
NZ
|
D:LYS162
|
2.9
|
18.9
|
1.0
|
CE
|
D:LYS162
|
3.3
|
21.8
|
1.0
|
CD1
|
D:TYR311
|
3.4
|
21.3
|
1.0
|
PB
|
D:ADP1476
|
3.7
|
19.5
|
1.0
|
CA
|
D:ALA158
|
3.7
|
26.1
|
1.0
|
CE1
|
D:TYR311
|
3.8
|
24.1
|
1.0
|
O
|
D:HOH2090
|
3.8
|
24.1
|
1.0
|
O2B
|
D:ADP1476
|
4.0
|
19.0
|
1.0
|
N
|
D:GLY159
|
4.1
|
23.6
|
1.0
|
MG
|
D:MG1477
|
4.2
|
30.0
|
1.0
|
O3B
|
D:ADP1476
|
4.3
|
20.5
|
1.0
|
CB
|
C:SER344
|
4.3
|
24.9
|
1.0
|
O
|
D:GLY157
|
4.3
|
23.1
|
1.0
|
CB
|
D:ALA158
|
4.4
|
24.6
|
1.0
|
C
|
D:ALA158
|
4.5
|
23.8
|
1.0
|
CG
|
D:TYR311
|
4.5
|
24.1
|
1.0
|
N
|
D:ALA158
|
4.5
|
28.2
|
1.0
|
C
|
D:GLY157
|
4.7
|
25.6
|
1.0
|
CA
|
C:SER344
|
4.7
|
22.8
|
1.0
|
NH2
|
D:ARG260
|
4.7
|
31.8
|
1.0
|
CD
|
D:LYS162
|
4.8
|
23.4
|
1.0
|
OE1
|
D:GLU188
|
4.8
|
36.5
|
1.0
|
CB
|
D:TYR311
|
4.8
|
20.2
|
1.0
|
ND2
|
D:ASN257
|
4.9
|
23.8
|
1.0
|
O
|
D:GLY156
|
5.0
|
20.6
|
1.0
|
OE2
|
D:GLU188
|
5.0
|
41.8
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 1w0j
Go back to
Fluorine Binding Sites List in 1w0j
Fluorine binding site 3 out
of 6 in the Beryllium Fluoride Inhibited Bovine F1-Atpase
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Beryllium Fluoride Inhibited Bovine F1-Atpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F1478
b:23.6
occ:1.00
|
F3
|
D:BEF1478
|
0.0
|
23.6
|
1.0
|
BE
|
D:BEF1478
|
1.5
|
17.3
|
1.0
|
MG
|
D:MG1477
|
2.1
|
30.0
|
1.0
|
O
|
D:HOH2064
|
2.5
|
36.3
|
1.0
|
F1
|
D:BEF1478
|
2.5
|
25.9
|
1.0
|
F2
|
D:BEF1478
|
2.6
|
20.4
|
1.0
|
O1B
|
D:ADP1476
|
2.6
|
23.2
|
1.0
|
O2B
|
D:ADP1476
|
2.8
|
19.0
|
1.0
|
O
|
D:HOH2068
|
3.0
|
31.4
|
1.0
|
O
|
D:HOH2090
|
3.0
|
24.1
|
1.0
|
NH1
|
D:ARG189
|
3.1
|
19.2
|
1.0
|
O
|
D:HOH2063
|
3.2
|
37.5
|
1.0
|
PB
|
D:ADP1476
|
3.2
|
19.5
|
1.0
|
O
|
D:HOH2065
|
3.3
|
28.7
|
1.0
|
OE1
|
D:GLU188
|
3.5
|
36.5
|
1.0
|
NH1
|
C:ARG373
|
3.6
|
22.6
|
1.0
|
CZ
|
D:ARG189
|
4.0
|
28.7
|
1.0
|
NH2
|
D:ARG189
|
4.0
|
19.6
|
1.0
|
OG1
|
D:THR163
|
4.1
|
29.8
|
1.0
|
CD
|
D:GLU188
|
4.3
|
34.6
|
1.0
|
O3A
|
D:ADP1476
|
4.3
|
24.3
|
1.0
|
O3B
|
D:ADP1476
|
4.5
|
20.5
|
1.0
|
NZ
|
D:LYS162
|
4.6
|
18.9
|
1.0
|
CE
|
D:LYS162
|
4.6
|
21.8
|
1.0
|
CZ
|
C:ARG373
|
4.7
|
23.5
|
1.0
|
OE2
|
D:GLU188
|
4.7
|
41.8
|
1.0
|
O
|
C:SER344
|
4.7
|
26.0
|
1.0
|
O2A
|
D:ADP1476
|
4.8
|
18.3
|
1.0
|
NH2
|
C:ARG373
|
4.9
|
26.8
|
1.0
|
OE2
|
D:GLU192
|
4.9
|
28.7
|
1.0
|
N
|
D:GLY159
|
4.9
|
23.6
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 1w0j
Go back to
Fluorine Binding Sites List in 1w0j
Fluorine binding site 4 out
of 6 in the Beryllium Fluoride Inhibited Bovine F1-Atpase
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Beryllium Fluoride Inhibited Bovine F1-Atpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F1477
b:28.8
occ:1.00
|
F1
|
F:BEF1477
|
0.0
|
28.8
|
1.0
|
BE
|
F:BEF1477
|
1.6
|
31.6
|
1.0
|
F2
|
F:BEF1477
|
2.5
|
23.4
|
1.0
|
F3
|
F:BEF1477
|
2.6
|
27.6
|
1.0
|
O1B
|
F:ADP1475
|
2.6
|
26.8
|
1.0
|
NH2
|
F:ARG189
|
2.7
|
26.6
|
1.0
|
NH2
|
B:ARG373
|
2.8
|
24.5
|
1.0
|
CA
|
B:SER344
|
3.1
|
27.4
|
1.0
|
NH1
|
F:ARG189
|
3.3
|
25.3
|
1.0
|
NH1
|
B:ARG373
|
3.4
|
29.8
|
1.0
|
CZ
|
F:ARG189
|
3.5
|
25.6
|
1.0
|
CZ
|
B:ARG373
|
3.5
|
31.1
|
1.0
|
N
|
F:GLY159
|
3.7
|
25.9
|
1.0
|
O
|
B:ILE343
|
3.7
|
25.6
|
1.0
|
C
|
B:SER344
|
3.7
|
26.8
|
1.0
|
O
|
B:SER344
|
3.8
|
26.1
|
1.0
|
CB
|
B:SER344
|
3.8
|
23.0
|
1.0
|
N
|
B:SER344
|
4.0
|
23.7
|
1.0
|
O
|
F:HOH2075
|
4.0
|
34.6
|
1.0
|
PB
|
F:ADP1475
|
4.0
|
25.8
|
1.0
|
C
|
B:ILE343
|
4.1
|
24.5
|
1.0
|
O
|
F:HOH2189
|
4.2
|
19.4
|
1.0
|
CA
|
F:GLY159
|
4.2
|
26.2
|
1.0
|
MG
|
F:MG1476
|
4.4
|
25.1
|
1.0
|
C
|
F:ALA158
|
4.5
|
26.8
|
1.0
|
CA
|
F:ALA158
|
4.5
|
25.2
|
1.0
|
O2B
|
F:ADP1475
|
4.5
|
24.9
|
1.0
|
CB
|
F:ALA158
|
4.6
|
24.7
|
1.0
|
O3A
|
F:ADP1475
|
4.6
|
23.4
|
1.0
|
N
|
B:ILE345
|
4.7
|
28.5
|
1.0
|
NE
|
F:ARG189
|
4.8
|
19.7
|
1.0
|
NE
|
B:ARG373
|
4.8
|
24.5
|
1.0
|
O
|
F:HOH2074
|
5.0
|
22.9
|
1.0
|
NZ
|
F:LYS162
|
5.0
|
28.7
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 1w0j
Go back to
Fluorine Binding Sites List in 1w0j
Fluorine binding site 5 out
of 6 in the Beryllium Fluoride Inhibited Bovine F1-Atpase
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Beryllium Fluoride Inhibited Bovine F1-Atpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F1477
b:23.4
occ:1.00
|
F2
|
F:BEF1477
|
0.0
|
23.4
|
1.0
|
BE
|
F:BEF1477
|
1.5
|
31.6
|
1.0
|
F1
|
F:BEF1477
|
2.5
|
28.8
|
1.0
|
O1B
|
F:ADP1475
|
2.5
|
26.8
|
1.0
|
F3
|
F:BEF1477
|
2.6
|
27.6
|
1.0
|
NZ
|
F:LYS162
|
2.8
|
28.7
|
1.0
|
O
|
F:HOH2074
|
3.3
|
22.9
|
1.0
|
N
|
F:GLY159
|
3.4
|
25.9
|
1.0
|
CA
|
F:ALA158
|
3.4
|
25.2
|
1.0
|
PB
|
F:ADP1475
|
3.5
|
25.8
|
1.0
|
O
|
F:HOH2075
|
3.6
|
34.6
|
1.0
|
CE
|
F:LYS162
|
3.6
|
21.8
|
1.0
|
CB
|
B:SER344
|
3.7
|
23.0
|
1.0
|
CD1
|
F:TYR311
|
3.8
|
22.9
|
1.0
|
C
|
F:ALA158
|
3.9
|
26.8
|
1.0
|
O3B
|
F:ADP1475
|
3.9
|
27.7
|
1.0
|
CE1
|
F:TYR311
|
3.9
|
21.3
|
1.0
|
CA
|
B:SER344
|
4.0
|
27.4
|
1.0
|
CB
|
F:ALA158
|
4.0
|
24.7
|
1.0
|
O2B
|
F:ADP1475
|
4.1
|
24.9
|
1.0
|
MG
|
F:MG1476
|
4.1
|
25.1
|
1.0
|
O
|
F:GLY157
|
4.2
|
26.4
|
1.0
|
O
|
F:HOH2104
|
4.2
|
20.0
|
1.0
|
N
|
F:ALA158
|
4.4
|
22.9
|
1.0
|
CA
|
F:GLY159
|
4.5
|
26.2
|
1.0
|
C
|
F:GLY157
|
4.6
|
22.6
|
1.0
|
O
|
B:SER344
|
4.8
|
26.1
|
1.0
|
O3A
|
F:ADP1475
|
4.8
|
23.4
|
1.0
|
NH2
|
B:ARG373
|
4.9
|
24.5
|
1.0
|
C
|
B:SER344
|
4.9
|
26.8
|
1.0
|
NH1
|
F:ARG189
|
5.0
|
25.3
|
1.0
|
N
|
B:SER344
|
5.0
|
23.7
|
1.0
|
NH2
|
F:ARG189
|
5.0
|
26.6
|
1.0
|
OG
|
B:SER344
|
5.0
|
29.6
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 1w0j
Go back to
Fluorine Binding Sites List in 1w0j
Fluorine binding site 6 out
of 6 in the Beryllium Fluoride Inhibited Bovine F1-Atpase
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Beryllium Fluoride Inhibited Bovine F1-Atpase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F1477
b:27.6
occ:1.00
|
F3
|
F:BEF1477
|
0.0
|
27.6
|
1.0
|
BE
|
F:BEF1477
|
1.6
|
31.6
|
1.0
|
MG
|
F:MG1476
|
1.9
|
25.1
|
1.0
|
F1
|
F:BEF1477
|
2.6
|
28.8
|
1.0
|
F2
|
F:BEF1477
|
2.6
|
23.4
|
1.0
|
O1B
|
F:ADP1475
|
2.7
|
26.8
|
1.0
|
O
|
F:HOH2073
|
2.8
|
21.1
|
1.0
|
O
|
F:HOH2189
|
2.8
|
19.4
|
1.0
|
O
|
F:HOH2104
|
2.9
|
20.0
|
1.0
|
O2B
|
F:ADP1475
|
2.9
|
24.9
|
1.0
|
NH1
|
F:ARG189
|
3.0
|
25.3
|
1.0
|
O
|
F:HOH2075
|
3.3
|
34.6
|
1.0
|
PB
|
F:ADP1475
|
3.3
|
25.8
|
1.0
|
O
|
F:HOH2074
|
3.4
|
22.9
|
1.0
|
OE1
|
F:GLU188
|
3.6
|
46.7
|
1.0
|
OG1
|
F:THR163
|
4.0
|
28.1
|
1.0
|
CZ
|
F:ARG189
|
4.0
|
25.6
|
1.0
|
NH1
|
B:ARG373
|
4.1
|
29.8
|
1.0
|
NH2
|
F:ARG189
|
4.1
|
26.6
|
1.0
|
NZ
|
F:LYS162
|
4.3
|
28.7
|
1.0
|
O3B
|
F:ADP1475
|
4.4
|
27.7
|
1.0
|
O3A
|
F:ADP1475
|
4.5
|
23.4
|
1.0
|
CD
|
F:GLU188
|
4.5
|
44.7
|
1.0
|
CE
|
F:LYS162
|
4.5
|
21.8
|
1.0
|
O
|
B:SER344
|
4.6
|
26.1
|
1.0
|
O2A
|
F:ADP1475
|
4.7
|
26.8
|
1.0
|
NH2
|
B:ARG373
|
4.8
|
24.5
|
1.0
|
OE2
|
F:GLU192
|
4.8
|
34.4
|
1.0
|
CZ
|
B:ARG373
|
4.9
|
31.1
|
1.0
|
CA
|
B:SER344
|
5.0
|
27.4
|
1.0
|
OE2
|
F:GLU188
|
5.0
|
44.4
|
1.0
|
|
Reference:
R.Kagawa,
M.G.Montgomery,
K.Braig,
A.G.W.Leslie,
J.E.Walker.
The Structure of Bovine F1-Atpase Inhibited By Adp and Beryllium Fluoride Embo J. V. 23 2734 2004.
ISSN: ISSN 0261-4189
PubMed: 15229653
DOI: 10.1038/SJ.EMBOJ.7600293
Page generated: Wed Jul 31 13:09:42 2024
|