Fluorine in PDB 7dzi: Intermediate of Fabp with A Delay Time of 300 Ns
Protein crystallography data
The structure of Intermediate of Fabp with A Delay Time of 300 Ns, PDB code: 7dzi
was solved by
H.Li,
L.-J.Yu,
X.Liu,
J.-R.Shen,
J.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.75 /
1.65
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.44,
66.26,
68.91,
90,
90,
90
|
R / Rfree (%)
|
18.3 /
21.4
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Intermediate of Fabp with A Delay Time of 300 Ns
(pdb code 7dzi). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Intermediate of Fabp with A Delay Time of 300 Ns, PDB code: 7dzi:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 7dzi
Go back to
Fluorine Binding Sites List in 7dzi
Fluorine binding site 1 out
of 4 in the Intermediate of Fabp with A Delay Time of 300 Ns
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Intermediate of Fabp with A Delay Time of 300 Ns within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F63
b:29.2
occ:0.79
|
F14
|
A:HP963
|
0.0
|
29.2
|
0.8
|
F14
|
A:HP963
|
0.1
|
24.8
|
0.2
|
C10
|
A:HP963
|
1.3
|
23.8
|
0.8
|
C10
|
A:HP963
|
1.3
|
23.8
|
0.2
|
C11
|
A:HP963
|
2.3
|
21.4
|
0.8
|
C9
|
A:HP963
|
2.4
|
23.3
|
0.2
|
C9
|
A:HP963
|
2.4
|
23.6
|
0.8
|
C11
|
A:HP963
|
2.4
|
21.1
|
0.2
|
C5
|
A:PLM201
|
3.4
|
41.3
|
1.0
|
C6
|
A:PLM201
|
3.6
|
35.5
|
1.0
|
CD1
|
A:ILE52
|
3.6
|
26.9
|
1.0
|
C6
|
A:HP963
|
3.6
|
18.7
|
0.8
|
C8
|
A:HP963
|
3.6
|
24.0
|
0.8
|
C8
|
A:HP963
|
3.6
|
22.4
|
0.2
|
C6
|
A:HP963
|
3.6
|
19.6
|
0.2
|
CE
|
A:PLM201
|
3.7
|
42.6
|
1.0
|
C8
|
A:PLM201
|
3.7
|
35.9
|
1.0
|
C7
|
A:PLM201
|
3.8
|
35.0
|
1.0
|
CG
|
A:PLM201
|
4.1
|
46.5
|
1.0
|
C7
|
A:HP963
|
4.1
|
18.4
|
0.8
|
C7
|
A:HP963
|
4.1
|
20.0
|
0.2
|
CF
|
A:PLM201
|
4.2
|
43.6
|
1.0
|
C4
|
A:PLM201
|
4.5
|
36.4
|
1.0
|
CD2
|
A:PHE50
|
4.6
|
20.4
|
1.0
|
CE2
|
A:PHE50
|
4.7
|
23.4
|
1.0
|
OD1
|
A:ASN111
|
4.8
|
28.6
|
1.0
|
CG1
|
A:ILE52
|
4.8
|
20.4
|
1.0
|
CD
|
A:PLM201
|
4.8
|
42.4
|
1.0
|
C3
|
A:HP963
|
4.8
|
24.7
|
0.8
|
C3
|
A:HP963
|
4.9
|
22.8
|
0.2
|
OG1
|
A:THR102
|
5.0
|
20.5
|
1.0
|
CC
|
A:PLM201
|
5.0
|
43.0
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 7dzi
Go back to
Fluorine Binding Sites List in 7dzi
Fluorine binding site 2 out
of 4 in the Intermediate of Fabp with A Delay Time of 300 Ns
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Intermediate of Fabp with A Delay Time of 300 Ns within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F63
b:24.8
occ:0.21
|
F14
|
A:HP963
|
0.0
|
24.8
|
0.2
|
F14
|
A:HP963
|
0.1
|
29.2
|
0.8
|
C10
|
A:HP963
|
1.3
|
23.8
|
0.2
|
C10
|
A:HP963
|
1.3
|
23.8
|
0.8
|
C11
|
A:HP963
|
2.3
|
21.4
|
0.8
|
C9
|
A:HP963
|
2.4
|
23.3
|
0.2
|
C11
|
A:HP963
|
2.4
|
21.1
|
0.2
|
C9
|
A:HP963
|
2.4
|
23.6
|
0.8
|
C5
|
A:PLM201
|
3.5
|
41.3
|
1.0
|
C6
|
A:HP963
|
3.6
|
18.7
|
0.8
|
C8
|
A:HP963
|
3.6
|
24.0
|
0.8
|
C6
|
A:HP963
|
3.6
|
19.6
|
0.2
|
C8
|
A:HP963
|
3.6
|
22.4
|
0.2
|
CE
|
A:PLM201
|
3.6
|
42.6
|
1.0
|
CD1
|
A:ILE52
|
3.7
|
26.9
|
1.0
|
C6
|
A:PLM201
|
3.7
|
35.5
|
1.0
|
C8
|
A:PLM201
|
3.7
|
35.9
|
1.0
|
C7
|
A:PLM201
|
3.9
|
35.0
|
1.0
|
CG
|
A:PLM201
|
4.0
|
46.5
|
1.0
|
C7
|
A:HP963
|
4.1
|
18.4
|
0.8
|
C7
|
A:HP963
|
4.1
|
20.0
|
0.2
|
CF
|
A:PLM201
|
4.1
|
43.6
|
1.0
|
C4
|
A:PLM201
|
4.6
|
36.4
|
1.0
|
CD
|
A:PLM201
|
4.7
|
42.4
|
1.0
|
CD2
|
A:PHE50
|
4.7
|
20.4
|
1.0
|
CE2
|
A:PHE50
|
4.8
|
23.4
|
1.0
|
OD1
|
A:ASN111
|
4.8
|
28.6
|
1.0
|
C3
|
A:HP963
|
4.8
|
24.7
|
0.8
|
C3
|
A:HP963
|
4.9
|
22.8
|
0.2
|
CG1
|
A:ILE52
|
4.9
|
20.4
|
1.0
|
CC
|
A:PLM201
|
4.9
|
43.0
|
1.0
|
OG1
|
A:THR102
|
5.0
|
20.5
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 7dzi
Go back to
Fluorine Binding Sites List in 7dzi
Fluorine binding site 3 out
of 4 in the Intermediate of Fabp with A Delay Time of 300 Ns
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Intermediate of Fabp with A Delay Time of 300 Ns within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F63
b:28.6
occ:0.35
|
F14
|
B:HP963
|
0.0
|
28.6
|
0.3
|
F14
|
B:HP963
|
0.3
|
31.8
|
0.7
|
C10
|
B:HP963
|
1.3
|
31.6
|
0.3
|
C10
|
B:HP963
|
1.4
|
32.4
|
0.7
|
C11
|
B:HP963
|
2.3
|
29.3
|
0.3
|
C9
|
B:HP963
|
2.4
|
30.4
|
0.3
|
C9
|
B:HP963
|
2.4
|
30.7
|
0.7
|
C11
|
B:HP963
|
2.5
|
27.3
|
0.7
|
CE
|
B:PLM201
|
3.4
|
50.4
|
1.0
|
C5
|
B:PLM201
|
3.5
|
47.3
|
1.0
|
C6
|
B:HP963
|
3.6
|
28.7
|
0.3
|
C8
|
B:HP963
|
3.6
|
28.2
|
0.3
|
C8
|
B:HP963
|
3.7
|
27.8
|
0.7
|
C6
|
B:PLM201
|
3.7
|
43.9
|
1.0
|
CG
|
B:PLM201
|
3.7
|
60.3
|
1.0
|
C6
|
B:HP963
|
3.7
|
27.9
|
0.7
|
C8
|
B:PLM201
|
3.9
|
42.2
|
1.0
|
CD1
|
B:ILE52
|
3.9
|
29.6
|
1.0
|
C7
|
B:PLM201
|
3.9
|
39.7
|
1.0
|
C7
|
B:HP963
|
4.1
|
28.2
|
0.3
|
CF
|
B:PLM201
|
4.1
|
53.0
|
1.0
|
C7
|
B:HP963
|
4.2
|
27.4
|
0.7
|
C4
|
B:PLM201
|
4.5
|
48.0
|
1.0
|
CD
|
B:PLM201
|
4.5
|
53.7
|
1.0
|
CE
|
B:MET113
|
4.6
|
30.9
|
0.6
|
OD1
|
B:ASN111
|
4.6
|
26.9
|
1.0
|
C3
|
B:HP963
|
4.8
|
32.4
|
0.3
|
OG1
|
B:THR102
|
4.9
|
23.4
|
1.0
|
OG
|
B:SER100
|
4.9
|
26.5
|
1.0
|
CG1
|
B:ILE52
|
4.9
|
25.2
|
1.0
|
CD2
|
B:PHE50
|
4.9
|
27.8
|
1.0
|
C3
|
B:HP963
|
4.9
|
32.9
|
0.7
|
CE2
|
B:PHE50
|
4.9
|
30.0
|
1.0
|
O13
|
B:HP963
|
5.0
|
34.8
|
0.3
|
|
Fluorine binding site 4 out
of 4 in 7dzi
Go back to
Fluorine Binding Sites List in 7dzi
Fluorine binding site 4 out
of 4 in the Intermediate of Fabp with A Delay Time of 300 Ns
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Intermediate of Fabp with A Delay Time of 300 Ns within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F63
b:31.8
occ:0.65
|
F14
|
B:HP963
|
0.0
|
31.8
|
0.7
|
F14
|
B:HP963
|
0.3
|
28.6
|
0.3
|
C10
|
B:HP963
|
1.3
|
31.6
|
0.3
|
C10
|
B:HP963
|
1.3
|
32.4
|
0.7
|
C11
|
B:HP963
|
2.2
|
29.3
|
0.3
|
C11
|
B:HP963
|
2.3
|
27.3
|
0.7
|
C9
|
B:HP963
|
2.4
|
30.7
|
0.7
|
C9
|
B:HP963
|
2.4
|
30.4
|
0.3
|
CE
|
B:PLM201
|
3.4
|
50.4
|
1.0
|
C5
|
B:PLM201
|
3.4
|
47.3
|
1.0
|
C6
|
B:HP963
|
3.5
|
28.7
|
0.3
|
CD1
|
B:ILE52
|
3.6
|
29.6
|
1.0
|
C6
|
B:HP963
|
3.6
|
27.9
|
0.7
|
C8
|
B:HP963
|
3.6
|
27.8
|
0.7
|
C6
|
B:PLM201
|
3.6
|
43.9
|
1.0
|
C8
|
B:HP963
|
3.6
|
28.2
|
0.3
|
CG
|
B:PLM201
|
3.9
|
60.3
|
1.0
|
C8
|
B:PLM201
|
3.9
|
42.2
|
1.0
|
C7
|
B:PLM201
|
4.0
|
39.7
|
1.0
|
C7
|
B:HP963
|
4.1
|
28.2
|
0.3
|
C7
|
B:HP963
|
4.1
|
27.4
|
0.7
|
CF
|
B:PLM201
|
4.2
|
53.0
|
1.0
|
C4
|
B:PLM201
|
4.4
|
48.0
|
1.0
|
CD
|
B:PLM201
|
4.5
|
53.7
|
1.0
|
CG1
|
B:ILE52
|
4.6
|
25.2
|
1.0
|
CD2
|
B:PHE50
|
4.6
|
27.8
|
1.0
|
C3
|
B:HP963
|
4.7
|
32.4
|
0.3
|
CE2
|
B:PHE50
|
4.7
|
30.0
|
1.0
|
C3
|
B:HP963
|
4.8
|
32.9
|
0.7
|
O13
|
B:HP963
|
4.8
|
34.8
|
0.3
|
OD1
|
B:ASN111
|
4.8
|
26.9
|
1.0
|
CE
|
B:MET113
|
4.9
|
30.9
|
0.6
|
O13
|
B:HP963
|
4.9
|
34.8
|
0.7
|
|
Reference:
X.Liu,
P.Liu,
H.Li,
Z.Xu,
L.Jia,
Y.Xia,
M.Yu,
W.Tang,
X.Zhu,
C.Chen,
Y.Zhang,
E.Nango,
R.Tanaka,
F.Luo,
K.Kato,
Y.Nakajima,
S.Kishi,
H.Yu,
N.Matsubara,
S.Owada,
K.Tono,
S.Iwata,
L.J.Yu,
J.R.Shen,
J.Wang.
Excited-State Intermediates in A Designer Protein Encoding A Phototrigger Caught By An X-Ray Free-Electron Laser. Nat.Chem. V. 14 1054 2022.
ISSN: ESSN 1755-4349
PubMed: 35851837
DOI: 10.1038/S41557-022-00992-3
Page generated: Fri Aug 2 06:33:01 2024
|