Fluorine in PDB 8gu1: Crystal Structure of Putative Amino Acid Binding Periplasmic Abc Transporter Protein From Candidatus Liberibacter Asiaticus in Complex with Pimozide
Protein crystallography data
The structure of Crystal Structure of Putative Amino Acid Binding Periplasmic Abc Transporter Protein From Candidatus Liberibacter Asiaticus in Complex with Pimozide, PDB code: 8gu1
was solved by
S.Lonare,
M.Sharma,
A.K.Sharma,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.80 /
2.65
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
90.014,
45.795,
115.675,
90,
91.99,
90
|
R / Rfree (%)
|
23.7 /
28.3
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Putative Amino Acid Binding Periplasmic Abc Transporter Protein From Candidatus Liberibacter Asiaticus in Complex with Pimozide
(pdb code 8gu1). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Crystal Structure of Putative Amino Acid Binding Periplasmic Abc Transporter Protein From Candidatus Liberibacter Asiaticus in Complex with Pimozide, PDB code: 8gu1:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 8gu1
Go back to
Fluorine Binding Sites List in 8gu1
Fluorine binding site 1 out
of 4 in the Crystal Structure of Putative Amino Acid Binding Periplasmic Abc Transporter Protein From Candidatus Liberibacter Asiaticus in Complex with Pimozide
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 Putative Amino Acid Binding Periplasmic Abc Transporter Protein From Candidatus Liberibacter Asiaticus in Complex with Pimozide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:109.7
occ:1.00
|
F01
|
A:1II301
|
0.0
|
109.7
|
1.0
|
C33
|
A:1II301
|
1.4
|
111.0
|
1.0
|
C29
|
A:1II301
|
2.4
|
104.5
|
1.0
|
C31
|
A:1II301
|
2.6
|
107.8
|
1.0
|
CG
|
A:PRO162
|
3.0
|
15.2
|
1.0
|
CZ
|
A:PHE144
|
3.1
|
10.2
|
1.0
|
CE2
|
A:PHE144
|
3.4
|
10.9
|
1.0
|
CD
|
A:PRO162
|
3.5
|
14.8
|
1.0
|
C25
|
A:1II301
|
3.8
|
101.9
|
1.0
|
CB
|
A:PRO162
|
3.9
|
16.3
|
1.0
|
C24
|
A:1II301
|
3.9
|
99.4
|
1.0
|
C27
|
A:1II301
|
4.0
|
91.9
|
1.0
|
C22
|
A:1II301
|
4.1
|
100.9
|
1.0
|
C23
|
A:1II301
|
4.1
|
103.0
|
1.0
|
CE1
|
A:PHE144
|
4.2
|
9.7
|
1.0
|
O
|
A:HOH422
|
4.3
|
19.0
|
1.0
|
ND2
|
A:ASN75
|
4.3
|
14.4
|
1.0
|
CD2
|
A:HIS95
|
4.3
|
8.8
|
1.0
|
C20
|
A:1II301
|
4.4
|
92.8
|
1.0
|
CG
|
A:PRO165
|
4.4
|
13.5
|
1.0
|
C18
|
A:1II301
|
4.4
|
98.5
|
1.0
|
C19
|
A:1II301
|
4.5
|
99.4
|
1.0
|
NE2
|
A:HIS95
|
4.5
|
8.4
|
1.0
|
C14
|
A:1II301
|
4.6
|
96.6
|
1.0
|
OD1
|
A:ASN75
|
4.7
|
17.9
|
1.0
|
CD2
|
A:PHE144
|
4.7
|
10.8
|
1.0
|
N
|
A:PRO162
|
4.9
|
17.6
|
1.0
|
CD
|
A:PRO165
|
4.9
|
13.5
|
1.0
|
CG
|
A:ASN75
|
4.9
|
15.3
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 8gu1
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Fluorine Binding Sites List in 8gu1
Fluorine binding site 2 out
of 4 in the Crystal Structure of Putative Amino Acid Binding Periplasmic Abc Transporter Protein From Candidatus Liberibacter Asiaticus in Complex with Pimozide
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 Putative Amino Acid Binding Periplasmic Abc Transporter Protein From Candidatus Liberibacter Asiaticus in Complex with Pimozide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:83.1
occ:1.00
|
F02
|
A:1II301
|
0.0
|
83.1
|
1.0
|
C34
|
A:1II301
|
1.3
|
74.8
|
1.0
|
OG1
|
A:THR14
|
2.2
|
12.4
|
1.0
|
C30
|
A:1II301
|
2.4
|
74.4
|
1.0
|
C32
|
A:1II301
|
2.5
|
76.0
|
1.0
|
CB
|
A:SER22
|
3.0
|
9.5
|
1.0
|
OG
|
A:SER22
|
3.1
|
9.8
|
1.0
|
O
|
A:ASP15
|
3.1
|
11.6
|
1.0
|
CB
|
A:THR14
|
3.4
|
12.6
|
1.0
|
N
|
A:ASP15
|
3.4
|
13.7
|
1.0
|
C26
|
A:1II301
|
3.8
|
86.5
|
1.0
|
C28
|
A:1II301
|
3.8
|
83.0
|
1.0
|
CA
|
A:THR14
|
3.9
|
13.2
|
1.0
|
C
|
A:ASP15
|
4.0
|
13.1
|
1.0
|
C
|
A:THR14
|
4.2
|
13.1
|
1.0
|
CG2
|
A:VAL74
|
4.2
|
19.0
|
1.0
|
CA
|
A:ASP15
|
4.3
|
13.9
|
1.0
|
C21
|
A:1II301
|
4.3
|
89.2
|
1.0
|
CA
|
A:SER22
|
4.5
|
9.8
|
1.0
|
CG2
|
A:THR14
|
4.5
|
13.8
|
1.0
|
CD2
|
A:TYR18
|
4.8
|
14.5
|
1.0
|
CB
|
A:ASP15
|
4.8
|
16.0
|
1.0
|
O
|
A:SER22
|
4.8
|
9.8
|
1.0
|
CB
|
A:TYR18
|
4.8
|
13.2
|
1.0
|
N
|
A:SER22
|
4.9
|
10.3
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 8gu1
Go back to
Fluorine Binding Sites List in 8gu1
Fluorine binding site 3 out
of 4 in the Crystal Structure of Putative Amino Acid Binding Periplasmic Abc Transporter Protein From Candidatus Liberibacter Asiaticus in Complex with Pimozide
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 Putative Amino Acid Binding Periplasmic Abc Transporter Protein From Candidatus Liberibacter Asiaticus in Complex with Pimozide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F301
b:110.3
occ:1.00
|
F01
|
B:1II301
|
0.0
|
110.3
|
1.0
|
C33
|
B:1II301
|
1.4
|
98.1
|
1.0
|
CZ
|
B:PHE144
|
2.3
|
8.7
|
1.0
|
C31
|
B:1II301
|
2.4
|
83.6
|
1.0
|
C29
|
B:1II301
|
2.5
|
102.0
|
1.0
|
C23
|
B:1II301
|
2.9
|
86.5
|
1.0
|
CE1
|
B:PHE144
|
3.0
|
8.8
|
1.0
|
CE2
|
B:PHE144
|
3.2
|
9.7
|
1.0
|
C19
|
B:1II301
|
3.2
|
92.8
|
1.0
|
CD1
|
B:ILE122
|
3.7
|
9.8
|
1.0
|
C27
|
B:1II301
|
3.8
|
86.7
|
1.0
|
C25
|
B:1II301
|
3.9
|
98.0
|
1.0
|
CD1
|
B:PHE144
|
4.2
|
9.7
|
1.0
|
C24
|
B:1II301
|
4.3
|
92.5
|
1.0
|
C20
|
B:1II301
|
4.3
|
92.0
|
1.0
|
CD2
|
B:PHE144
|
4.4
|
9.6
|
1.0
|
CG2
|
B:THR125
|
4.7
|
10.6
|
1.0
|
CE1
|
B:TYR18
|
4.7
|
10.9
|
1.0
|
O
|
B:HOH406
|
4.7
|
5.8
|
1.0
|
C14
|
B:1II301
|
4.8
|
80.3
|
1.0
|
CG
|
B:PHE144
|
4.8
|
10.1
|
1.0
|
CD
|
B:PRO162
|
4.8
|
12.1
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 8gu1
Go back to
Fluorine Binding Sites List in 8gu1
Fluorine binding site 4 out
of 4 in the Crystal Structure of Putative Amino Acid Binding Periplasmic Abc Transporter Protein From Candidatus Liberibacter Asiaticus in Complex with Pimozide
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of Putative Amino Acid Binding Periplasmic Abc Transporter Protein From Candidatus Liberibacter Asiaticus in Complex with Pimozide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F301
b:100.8
occ:1.00
|
F02
|
B:1II301
|
0.0
|
100.8
|
1.0
|
C34
|
B:1II301
|
1.3
|
76.2
|
1.0
|
C32
|
B:1II301
|
2.4
|
80.5
|
1.0
|
C30
|
B:1II301
|
2.5
|
74.3
|
1.0
|
O
|
B:ASP15
|
3.0
|
13.3
|
1.0
|
CB
|
B:SER22
|
3.0
|
8.7
|
1.0
|
OG
|
B:SER22
|
3.1
|
8.0
|
1.0
|
CG2
|
B:THR14
|
3.1
|
19.7
|
1.0
|
CB
|
B:THR14
|
3.2
|
14.6
|
1.0
|
N
|
B:ASP15
|
3.5
|
15.0
|
1.0
|
C26
|
B:1II301
|
3.8
|
82.4
|
1.0
|
C28
|
B:1II301
|
3.8
|
87.6
|
1.0
|
C
|
B:ASP15
|
3.9
|
14.9
|
1.0
|
CA
|
B:THR14
|
4.0
|
15.5
|
1.0
|
CA
|
B:ASP15
|
4.2
|
15.1
|
1.0
|
C
|
B:THR14
|
4.3
|
14.8
|
1.0
|
C21
|
B:1II301
|
4.3
|
88.9
|
1.0
|
CG2
|
B:VAL74
|
4.3
|
16.4
|
1.0
|
OG1
|
B:THR14
|
4.4
|
16.8
|
1.0
|
CA
|
B:SER22
|
4.4
|
8.8
|
1.0
|
CD2
|
B:TYR18
|
4.6
|
11.2
|
1.0
|
O
|
B:SER22
|
4.7
|
9.5
|
1.0
|
CB
|
B:TYR18
|
4.7
|
11.8
|
1.0
|
CB
|
B:ASP15
|
4.7
|
17.4
|
1.0
|
N
|
B:SER22
|
4.9
|
9.1
|
1.0
|
CG
|
B:TYR18
|
5.0
|
11.4
|
1.0
|
N
|
B:GLY16
|
5.0
|
15.9
|
1.0
|
|
Reference:
S.Lonare,
M.Sharma,
V.Dalal,
M.Gubyad,
P.Kumar,
D.Nath Gupta,
A.Pareek,
S.Tomar,
D.Kumar Ghosh,
P.Kumar,
A.Kumar Sharma.
Identification and Evaluation of Potential Inhibitor Molecules Against Tcya From Candidatus Liberibacter Asiaticus. J.Struct.Biol. V. 215 07992 2023.
ISSN: ESSN 1095-8657
PubMed: 37394197
DOI: 10.1016/J.JSB.2023.107992
Page generated: Fri Aug 2 19:56:41 2024
|