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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:

Magnesium (Mg) 5 atoms

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: Sun Dec 13 11:33:33 2020

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