Fluorine in PDB 7efn: Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State
Protein crystallography data
The structure of Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State, PDB code: 7efn
was solved by
K.Abe,
K.Yamamoto,
K.Irie,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.71 /
3.20
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.94,
105.94,
372.01,
90,
90,
120
|
R / Rfree (%)
|
26.8 /
30.8
|
Other elements in 7efn:
The structure of Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State
(pdb code 7efn). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State, PDB code: 7efn:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 7efn
Go back to
Fluorine Binding Sites List in 7efn
Fluorine binding site 1 out
of 3 in the Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F385
b:64.6
occ:1.00
|
F1
|
A:BFD385
|
0.0
|
64.6
|
1.0
|
BE
|
A:BFD385
|
1.7
|
50.6
|
1.0
|
ND2
|
A:ASN729
|
2.4
|
48.6
|
1.0
|
F3
|
A:BFD385
|
2.7
|
46.9
|
1.0
|
OD1
|
A:BFD385
|
3.0
|
45.3
|
1.0
|
CA
|
A:GLY229
|
3.0
|
47.8
|
1.0
|
F2
|
A:BFD385
|
3.1
|
57.7
|
1.0
|
N
|
A:GLY229
|
3.1
|
54.4
|
1.0
|
N
|
A:GLY627
|
3.2
|
52.8
|
1.0
|
NZ
|
A:LYS707
|
3.6
|
47.3
|
1.0
|
CG
|
A:ASN729
|
3.7
|
53.3
|
1.0
|
C
|
A:THR228
|
3.8
|
57.8
|
1.0
|
CA
|
A:GLY627
|
3.8
|
47.9
|
1.0
|
CG
|
A:BFD385
|
4.0
|
44.7
|
1.0
|
C
|
A:THR626
|
4.1
|
55.8
|
1.0
|
O
|
A:THR228
|
4.2
|
62.0
|
1.0
|
CA
|
A:THR626
|
4.2
|
52.8
|
1.0
|
OG1
|
A:THR626
|
4.3
|
61.4
|
1.0
|
OD2
|
A:BFD385
|
4.3
|
39.5
|
1.0
|
C
|
A:GLY229
|
4.4
|
49.6
|
1.0
|
CB
|
A:ASN729
|
4.4
|
49.0
|
1.0
|
CE
|
A:LYS707
|
4.5
|
39.3
|
1.0
|
OD1
|
A:ASN729
|
4.5
|
61.9
|
1.0
|
CA
|
A:THR228
|
4.7
|
49.9
|
1.0
|
C
|
A:GLY627
|
4.7
|
48.7
|
1.0
|
N
|
A:ASP628
|
4.8
|
53.8
|
1.0
|
O
|
A:GLY229
|
4.9
|
51.1
|
1.0
|
CB
|
A:THR626
|
4.9
|
57.3
|
1.0
|
O
|
A:VAL625
|
4.9
|
47.8
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 7efn
Go back to
Fluorine Binding Sites List in 7efn
Fluorine binding site 2 out
of 3 in the Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F385
b:57.7
occ:1.00
|
F2
|
A:BFD385
|
0.0
|
57.7
|
1.0
|
BE
|
A:BFD385
|
1.8
|
50.6
|
1.0
|
F3
|
A:BFD385
|
2.6
|
46.9
|
1.0
|
OD2
|
A:BFD385
|
2.8
|
39.5
|
1.0
|
MG
|
A:MG1101
|
3.0
|
41.7
|
1.0
|
OD1
|
A:BFD385
|
3.0
|
45.3
|
1.0
|
F1
|
A:BFD385
|
3.1
|
64.6
|
1.0
|
CA
|
A:GLY229
|
3.1
|
47.8
|
1.0
|
CB
|
A:THR387
|
3.2
|
48.6
|
1.0
|
CG
|
A:BFD385
|
3.3
|
44.7
|
1.0
|
O
|
A:THR387
|
3.4
|
48.4
|
1.0
|
ND2
|
A:ASN729
|
3.6
|
48.6
|
1.0
|
N
|
A:THR387
|
3.8
|
41.8
|
1.0
|
CA
|
A:THR387
|
3.8
|
44.4
|
1.0
|
O
|
A:SER225
|
3.9
|
58.4
|
1.0
|
OG1
|
A:THR387
|
3.9
|
50.1
|
1.0
|
C
|
A:THR387
|
3.9
|
45.4
|
1.0
|
CG2
|
A:THR387
|
4.0
|
44.8
|
1.0
|
C
|
A:GLY229
|
4.1
|
49.6
|
1.0
|
N
|
A:GLY229
|
4.2
|
54.4
|
1.0
|
O
|
A:THR228
|
4.2
|
62.0
|
1.0
|
O
|
A:GLY229
|
4.2
|
51.1
|
1.0
|
OD1
|
A:ASP726
|
4.3
|
44.8
|
1.0
|
CG
|
A:ASN729
|
4.5
|
53.3
|
1.0
|
OD1
|
A:ASN729
|
4.5
|
61.9
|
1.0
|
C
|
A:THR228
|
4.6
|
57.8
|
1.0
|
CB
|
A:BFD385
|
4.8
|
39.4
|
1.0
|
C
|
A:SER225
|
5.0
|
58.9
|
1.0
|
C
|
A:LYS386
|
5.0
|
43.7
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 7efn
Go back to
Fluorine Binding Sites List in 7efn
Fluorine binding site 3 out
of 3 in the Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of the Gastric Proton Pump K791S/E820D/Y340N/E936V in (Byk)E2BEF State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F385
b:46.9
occ:1.00
|
F3
|
A:BFD385
|
0.0
|
46.9
|
1.0
|
BE
|
A:BFD385
|
1.8
|
50.6
|
1.0
|
OG1
|
A:THR626
|
2.4
|
61.4
|
1.0
|
OD1
|
A:BFD385
|
2.5
|
45.3
|
1.0
|
F2
|
A:BFD385
|
2.6
|
57.7
|
1.0
|
F1
|
A:BFD385
|
2.7
|
64.6
|
1.0
|
CA
|
A:GLY229
|
3.0
|
47.8
|
1.0
|
N
|
A:THR387
|
3.4
|
41.8
|
1.0
|
O
|
A:GLY229
|
3.5
|
51.1
|
1.0
|
CB
|
A:THR626
|
3.6
|
57.3
|
1.0
|
OG1
|
A:THR387
|
3.6
|
50.1
|
1.0
|
N
|
A:GLY627
|
3.6
|
52.8
|
1.0
|
CA
|
A:THR626
|
3.7
|
52.8
|
1.0
|
C
|
A:GLY229
|
3.7
|
49.6
|
1.0
|
CG
|
A:BFD385
|
3.7
|
44.7
|
1.0
|
CB
|
A:THR387
|
3.8
|
48.6
|
1.0
|
N
|
A:LYS386
|
3.9
|
48.6
|
1.0
|
OD2
|
A:BFD385
|
4.1
|
39.5
|
1.0
|
N
|
A:GLY229
|
4.1
|
54.4
|
1.0
|
CB
|
A:LYS386
|
4.1
|
50.4
|
1.0
|
CA
|
A:THR387
|
4.2
|
44.4
|
1.0
|
C
|
A:THR626
|
4.2
|
55.8
|
1.0
|
N
|
A:ASP628
|
4.3
|
53.8
|
1.0
|
CA
|
A:LYS386
|
4.3
|
48.9
|
1.0
|
C
|
A:LYS386
|
4.4
|
43.7
|
1.0
|
ND2
|
A:ASN729
|
4.6
|
48.6
|
1.0
|
CA
|
A:GLY627
|
4.6
|
47.9
|
1.0
|
C
|
A:BFD385
|
4.7
|
45.3
|
1.0
|
CB
|
A:ASP628
|
4.8
|
44.4
|
1.0
|
CG2
|
A:THR626
|
4.8
|
55.8
|
1.0
|
O
|
A:THR387
|
4.8
|
48.4
|
1.0
|
CE
|
A:LYS386
|
4.8
|
57.0
|
1.0
|
O
|
A:VAL625
|
4.9
|
47.8
|
1.0
|
C
|
A:GLY627
|
5.0
|
48.7
|
1.0
|
CB
|
A:BFD385
|
5.0
|
39.4
|
1.0
|
|
Reference:
K.Abe,
K.Yamamoto,
K.Irie.
Crystal Structure of the Gastric Proton Pump Mutants To Be Published.
Page generated: Fri Aug 2 06:42:03 2024
|