Fluorine in PDB 7f35: Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin
Protein crystallography data
The structure of Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin, PDB code: 7f35
was solved by
L.T.Wang,
W.Y.Jiao,
X.Shen,
H.T.Lei,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
44.64 /
2.60
|
Space group
|
P 42 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
184.071,
184.071,
100.66,
90,
90,
90
|
R / Rfree (%)
|
20 /
23.5
|
Other elements in 7f35:
The structure of Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin
(pdb code 7f35). 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 Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin, PDB code: 7f35:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 7f35
Go back to
Fluorine Binding Sites List in 7f35
Fluorine binding site 1 out
of 3 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin
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 Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:48.2
occ:1.00
|
F27
|
A:GFN301
|
0.0
|
48.2
|
1.0
|
C09
|
A:GFN301
|
1.4
|
52.2
|
1.0
|
C10
|
A:GFN301
|
2.3
|
48.6
|
1.0
|
C08
|
A:GFN301
|
2.4
|
50.5
|
1.0
|
N04
|
A:GFN301
|
2.7
|
51.5
|
1.0
|
C03
|
A:GFN301
|
2.9
|
46.5
|
1.0
|
CD2
|
A:PHE34
|
3.1
|
52.3
|
1.0
|
CG
|
A:PHE34
|
3.4
|
49.0
|
1.0
|
CZ3
|
B:TRP99
|
3.4
|
51.2
|
1.0
|
C02
|
A:GFN301
|
3.5
|
45.5
|
1.0
|
C11
|
A:GFN301
|
3.6
|
46.9
|
1.0
|
C13
|
A:GFN301
|
3.7
|
46.6
|
1.0
|
CB
|
A:PHE34
|
3.7
|
47.4
|
1.0
|
CE2
|
A:PHE34
|
3.7
|
52.6
|
1.0
|
CH2
|
B:TRP99
|
3.8
|
54.5
|
1.0
|
CE3
|
B:TRP99
|
3.9
|
47.9
|
1.0
|
NE2
|
A:HIS36
|
4.0
|
44.4
|
1.0
|
C05
|
A:GFN301
|
4.1
|
46.2
|
1.0
|
CG2
|
A:THR93
|
4.1
|
44.1
|
1.0
|
C12
|
A:GFN301
|
4.1
|
46.9
|
1.0
|
CD1
|
A:PHE34
|
4.2
|
49.6
|
1.0
|
CD2
|
A:HIS36
|
4.2
|
44.5
|
1.0
|
CB
|
A:THR93
|
4.4
|
47.0
|
1.0
|
C01
|
A:GFN301
|
4.4
|
40.1
|
1.0
|
CZ
|
A:PHE34
|
4.4
|
54.3
|
1.0
|
OG1
|
A:THR93
|
4.5
|
55.6
|
1.0
|
CZ2
|
B:TRP99
|
4.5
|
53.4
|
1.0
|
C06
|
A:GFN301
|
4.6
|
43.0
|
1.0
|
CE1
|
A:PHE34
|
4.6
|
55.0
|
1.0
|
CD2
|
B:TRP99
|
4.6
|
52.0
|
1.0
|
N07
|
A:GFN301
|
4.6
|
47.4
|
1.0
|
O14
|
A:GFN301
|
4.8
|
48.0
|
1.0
|
C19
|
A:GFN301
|
4.8
|
52.7
|
1.0
|
CE2
|
B:TRP99
|
4.9
|
51.5
|
1.0
|
O20
|
A:GFN301
|
5.0
|
49.7
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 7f35
Go back to
Fluorine Binding Sites List in 7f35
Fluorine binding site 2 out
of 3 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin
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 Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F301
b:47.8
occ:1.00
|
F27
|
C:GFN301
|
0.0
|
47.8
|
1.0
|
C09
|
C:GFN301
|
1.3
|
48.9
|
1.0
|
C08
|
C:GFN301
|
2.4
|
46.8
|
1.0
|
C10
|
C:GFN301
|
2.4
|
44.1
|
1.0
|
N04
|
C:GFN301
|
2.7
|
51.7
|
1.0
|
C03
|
C:GFN301
|
2.9
|
48.9
|
1.0
|
CD2
|
C:PHE34
|
3.3
|
46.3
|
1.0
|
C02
|
C:GFN301
|
3.4
|
47.5
|
1.0
|
CG
|
C:PHE34
|
3.6
|
46.4
|
1.0
|
C11
|
C:GFN301
|
3.6
|
48.2
|
1.0
|
C13
|
C:GFN301
|
3.6
|
43.9
|
1.0
|
CZ3
|
D:TRP99
|
3.6
|
52.5
|
1.0
|
CE1
|
C:HIS36
|
3.7
|
39.4
|
1.0
|
CE2
|
C:PHE34
|
3.8
|
48.3
|
1.0
|
CH2
|
D:TRP99
|
3.9
|
54.4
|
1.0
|
CB
|
C:PHE34
|
3.9
|
42.9
|
1.0
|
CG2
|
C:THR93
|
4.0
|
48.1
|
1.0
|
C05
|
C:GFN301
|
4.0
|
43.4
|
1.0
|
CE3
|
D:TRP99
|
4.1
|
51.7
|
1.0
|
C12
|
C:GFN301
|
4.1
|
46.9
|
1.0
|
CB
|
C:THR93
|
4.2
|
46.5
|
1.0
|
ND1
|
C:HIS36
|
4.2
|
48.1
|
1.0
|
CD1
|
C:PHE34
|
4.3
|
44.1
|
1.0
|
OG1
|
C:THR93
|
4.4
|
54.2
|
1.0
|
C01
|
C:GFN301
|
4.4
|
41.0
|
1.0
|
C06
|
C:GFN301
|
4.4
|
45.2
|
1.0
|
CZ
|
C:PHE34
|
4.5
|
48.9
|
1.0
|
CZ2
|
D:TRP99
|
4.5
|
50.2
|
1.0
|
N07
|
C:GFN301
|
4.5
|
43.6
|
1.0
|
NE2
|
C:HIS36
|
4.6
|
41.6
|
1.0
|
CE1
|
C:PHE34
|
4.7
|
52.5
|
1.0
|
CD2
|
D:TRP99
|
4.7
|
50.4
|
1.0
|
O14
|
C:GFN301
|
4.7
|
46.0
|
1.0
|
C19
|
C:GFN301
|
4.9
|
50.9
|
1.0
|
CE2
|
D:TRP99
|
4.9
|
49.5
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 7f35
Go back to
Fluorine Binding Sites List in 7f35
Fluorine binding site 3 out
of 3 in the Crystal Structure of Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin
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 Anti S-Gatifloxacin Antibody Fab Fragment in Complex with S-Gatifloxacin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F301
b:66.6
occ:1.00
|
F27
|
E:GFN301
|
0.0
|
66.6
|
1.0
|
C09
|
E:GFN301
|
1.3
|
68.4
|
1.0
|
C10
|
E:GFN301
|
2.3
|
69.2
|
1.0
|
C08
|
E:GFN301
|
2.3
|
69.1
|
1.0
|
N04
|
E:GFN301
|
2.7
|
66.0
|
1.0
|
CD2
|
E:PHE34
|
3.0
|
75.2
|
1.0
|
C03
|
E:GFN301
|
3.1
|
65.6
|
1.0
|
CG
|
E:PHE34
|
3.3
|
82.7
|
1.0
|
C11
|
E:GFN301
|
3.6
|
68.9
|
1.0
|
CE2
|
E:PHE34
|
3.6
|
75.4
|
1.0
|
OG1
|
E:THR93
|
3.6
|
76.1
|
1.0
|
C13
|
E:GFN301
|
3.6
|
68.8
|
1.0
|
CB
|
E:PHE34
|
3.7
|
80.4
|
1.0
|
CH2
|
F:TRP99
|
3.9
|
64.7
|
1.0
|
C02
|
E:GFN301
|
3.9
|
66.6
|
1.0
|
CZ3
|
F:TRP99
|
3.9
|
63.6
|
1.0
|
C05
|
E:GFN301
|
4.0
|
65.8
|
1.0
|
C12
|
E:GFN301
|
4.1
|
69.7
|
1.0
|
CD1
|
E:PHE34
|
4.1
|
74.2
|
1.0
|
CE1
|
E:HIS36
|
4.2
|
76.9
|
1.0
|
CZ
|
E:PHE34
|
4.3
|
79.5
|
1.0
|
CZ2
|
F:TRP99
|
4.5
|
60.5
|
1.0
|
ND1
|
E:HIS36
|
4.6
|
74.3
|
1.0
|
CE1
|
E:PHE34
|
4.6
|
76.6
|
1.0
|
CE3
|
F:TRP99
|
4.6
|
61.2
|
1.0
|
C06
|
E:GFN301
|
4.7
|
69.9
|
1.0
|
O14
|
E:GFN301
|
4.7
|
69.1
|
1.0
|
C19
|
E:GFN301
|
4.7
|
73.6
|
1.0
|
O20
|
E:GFN301
|
4.9
|
71.5
|
1.0
|
CB
|
E:THR93
|
4.9
|
74.2
|
1.0
|
C01
|
E:GFN301
|
4.9
|
62.1
|
1.0
|
N07
|
E:GFN301
|
4.9
|
64.7
|
1.0
|
|
Reference:
L.T.Wang,
W.Xie,
W.Y.Jiao,
C.Zhang,
X.Li,
Z.Xu,
X.Huang,
H.T.Lei,
X.Shen.
Conformational Adaptability Determining Antibody Recognition to Distomer: Structure Analysis of Enantioselective Antibody Against Chiral Drug Gatifloxacin Rsc Adv V. 11 39534 2021.
ISSN: ESSN 2046-2069
DOI: 10.1039/D1RA07143B
Page generated: Fri Aug 2 06:49:34 2024
|