Fluorine in PDB 1he1: Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac
Protein crystallography data
The structure of Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac, PDB code: 1he1
was solved by
M.Wurtele,
E.Wolf,
K.J.Pederson,
G.Buchwald,
M.R.Ahmadian,
J.T.Barbieri,
A.Wittinghofer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.92 /
2.0
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.025,
125.087,
136.284,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.5 /
22.4
|
Other elements in 1he1:
The structure of Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac
(pdb code 1he1). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac, PDB code: 1he1:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 1he1
Go back to
Fluorine Binding Sites List in 1he1
Fluorine binding site 1 out
of 6 in the Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac
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 Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F201
b:16.4
occ:1.00
|
F1
|
C:AF3201
|
0.0
|
16.4
|
1.0
|
AL
|
C:AF3201
|
1.9
|
16.0
|
1.0
|
O3B
|
C:GDP200
|
2.7
|
14.6
|
1.0
|
NE2
|
C:GLN61
|
2.7
|
13.7
|
1.0
|
O
|
C:HOH2050
|
2.7
|
14.1
|
1.0
|
NE
|
A:ARG146
|
2.8
|
13.8
|
1.0
|
O
|
C:HOH2026
|
2.8
|
13.4
|
1.0
|
F2
|
C:AF3201
|
3.1
|
13.6
|
1.0
|
F3
|
C:AF3201
|
3.2
|
15.1
|
1.0
|
NH2
|
A:ARG146
|
3.4
|
10.8
|
1.0
|
CZ
|
A:ARG146
|
3.4
|
14.4
|
1.0
|
CA
|
C:GLY12
|
3.5
|
13.6
|
1.0
|
N
|
C:ALA13
|
3.6
|
13.3
|
1.0
|
CD
|
C:GLN61
|
3.6
|
17.7
|
1.0
|
OE1
|
C:GLN61
|
3.7
|
16.5
|
1.0
|
CD
|
A:ARG146
|
3.7
|
14.2
|
1.0
|
C
|
C:GLY12
|
3.9
|
14.7
|
1.0
|
CG
|
A:ARG146
|
4.2
|
12.5
|
1.0
|
PB
|
C:GDP200
|
4.3
|
14.7
|
1.0
|
OG1
|
A:THR150
|
4.5
|
15.7
|
1.0
|
CA
|
C:ALA13
|
4.6
|
13.2
|
1.0
|
NH1
|
A:ARG146
|
4.7
|
13.0
|
1.0
|
OH
|
C:TYR32
|
4.7
|
14.4
|
1.0
|
N
|
C:GLY12
|
4.8
|
15.1
|
1.0
|
O2B
|
C:GDP200
|
4.8
|
13.2
|
1.0
|
O
|
A:GLY141
|
4.9
|
15.1
|
1.0
|
O3A
|
C:GDP200
|
4.9
|
14.4
|
1.0
|
MG
|
C:MG202
|
5.0
|
15.2
|
1.0
|
N
|
C:GLY60
|
5.0
|
16.5
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 1he1
Go back to
Fluorine Binding Sites List in 1he1
Fluorine binding site 2 out
of 6 in the Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac
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 Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F201
b:13.6
occ:1.00
|
F2
|
C:AF3201
|
0.0
|
13.6
|
1.0
|
AL
|
C:AF3201
|
1.9
|
16.0
|
1.0
|
NZ
|
C:LYS16
|
2.5
|
11.5
|
1.0
|
N
|
C:GLY60
|
2.7
|
16.5
|
1.0
|
O
|
C:HOH2050
|
2.9
|
14.1
|
1.0
|
O3B
|
C:GDP200
|
2.9
|
14.6
|
1.0
|
F1
|
C:AF3201
|
3.1
|
16.4
|
1.0
|
F3
|
C:AF3201
|
3.2
|
15.1
|
1.0
|
CE
|
C:LYS16
|
3.3
|
12.2
|
1.0
|
CA
|
C:GLY12
|
3.3
|
13.6
|
1.0
|
CA
|
C:GLY60
|
3.4
|
17.0
|
1.0
|
O
|
C:THR58
|
3.6
|
17.5
|
1.0
|
C
|
C:ALA59
|
3.7
|
17.2
|
1.0
|
CA
|
C:ALA59
|
3.8
|
16.7
|
1.0
|
PB
|
C:GDP200
|
3.9
|
14.7
|
1.0
|
N
|
C:GLY12
|
3.9
|
15.1
|
1.0
|
O
|
C:HOH2047
|
4.0
|
13.3
|
1.0
|
O1B
|
C:GDP200
|
4.0
|
15.7
|
1.0
|
O
|
C:ASP11
|
4.1
|
14.4
|
1.0
|
OE1
|
C:GLN61
|
4.2
|
16.5
|
1.0
|
N
|
C:ALA13
|
4.3
|
13.3
|
1.0
|
C
|
C:ASP11
|
4.3
|
14.6
|
1.0
|
O2B
|
C:GDP200
|
4.3
|
13.2
|
1.0
|
O
|
C:GLY10
|
4.3
|
15.8
|
1.0
|
C
|
C:GLY12
|
4.3
|
14.7
|
1.0
|
NE2
|
C:GLN61
|
4.4
|
13.7
|
1.0
|
C
|
C:GLY60
|
4.5
|
16.6
|
1.0
|
C
|
C:THR58
|
4.5
|
16.5
|
1.0
|
MG
|
C:MG202
|
4.5
|
15.2
|
1.0
|
CD
|
C:GLN61
|
4.6
|
17.7
|
1.0
|
N
|
C:GLN61
|
4.6
|
16.3
|
1.0
|
N
|
C:ALA59
|
4.7
|
16.5
|
1.0
|
CD
|
C:LYS16
|
4.7
|
12.3
|
1.0
|
O
|
C:ALA59
|
4.8
|
19.9
|
1.0
|
CB
|
C:ALA59
|
5.0
|
15.1
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 1he1
Go back to
Fluorine Binding Sites List in 1he1
Fluorine binding site 3 out
of 6 in the Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac
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 Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F201
b:15.1
occ:1.00
|
F3
|
C:AF3201
|
0.0
|
15.1
|
1.0
|
AL
|
C:AF3201
|
1.7
|
16.0
|
1.0
|
MG
|
C:MG202
|
2.0
|
15.2
|
1.0
|
O3B
|
C:GDP200
|
2.8
|
14.6
|
1.0
|
O
|
C:HOH2050
|
2.8
|
14.1
|
1.0
|
O
|
C:HOH2047
|
2.9
|
13.3
|
1.0
|
OG1
|
C:THR35
|
2.9
|
14.7
|
1.0
|
O2B
|
C:GDP200
|
2.9
|
13.2
|
1.0
|
CB
|
C:THR35
|
2.9
|
16.4
|
1.0
|
O
|
C:HOH2224
|
3.0
|
16.6
|
1.0
|
F1
|
C:AF3201
|
3.2
|
16.4
|
1.0
|
F2
|
C:AF3201
|
3.2
|
13.6
|
1.0
|
N
|
C:THR35
|
3.3
|
14.9
|
1.0
|
PB
|
C:GDP200
|
3.5
|
14.7
|
1.0
|
O
|
C:HOH2026
|
3.5
|
13.4
|
1.0
|
CA
|
C:THR35
|
3.6
|
15.9
|
1.0
|
O
|
C:THR35
|
3.9
|
16.1
|
1.0
|
OG1
|
C:THR17
|
4.0
|
14.0
|
1.0
|
O
|
C:THR58
|
4.1
|
17.5
|
1.0
|
C
|
C:THR35
|
4.2
|
16.7
|
1.0
|
CG2
|
C:THR35
|
4.3
|
17.6
|
1.0
|
NH2
|
A:ARG146
|
4.4
|
10.8
|
1.0
|
C
|
C:PRO34
|
4.4
|
15.0
|
1.0
|
O1B
|
C:GDP200
|
4.5
|
15.7
|
1.0
|
O3A
|
C:GDP200
|
4.6
|
14.4
|
1.0
|
NZ
|
C:LYS16
|
4.7
|
11.5
|
1.0
|
O2A
|
C:GDP200
|
4.8
|
13.2
|
1.0
|
CA
|
C:PRO34
|
4.9
|
13.8
|
1.0
|
O
|
C:ILE33
|
4.9
|
13.2
|
1.0
|
CA
|
C:ALA59
|
5.0
|
16.7
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 1he1
Go back to
Fluorine Binding Sites List in 1he1
Fluorine binding site 4 out
of 6 in the Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac
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 the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F201
b:15.1
occ:1.00
|
F1
|
D:AF3201
|
0.0
|
15.1
|
1.0
|
AL
|
D:AF3201
|
1.8
|
13.6
|
1.0
|
MG
|
D:MG202
|
1.9
|
13.8
|
1.0
|
O3B
|
D:GDP200
|
2.8
|
9.6
|
1.0
|
O
|
D:HOH2046
|
2.8
|
12.4
|
1.0
|
O
|
D:HOH2224
|
2.8
|
10.3
|
1.0
|
OG1
|
D:THR35
|
2.9
|
12.3
|
1.0
|
O
|
D:HOH2049
|
2.9
|
15.2
|
1.0
|
O2B
|
D:GDP200
|
2.9
|
14.0
|
1.0
|
CB
|
D:THR35
|
2.9
|
14.8
|
1.0
|
F2
|
D:AF3201
|
3.2
|
15.1
|
1.0
|
N
|
D:THR35
|
3.3
|
14.7
|
1.0
|
F3
|
D:AF3201
|
3.3
|
14.5
|
1.0
|
PB
|
D:GDP200
|
3.5
|
14.3
|
1.0
|
O
|
D:HOH2025
|
3.5
|
15.0
|
1.0
|
CA
|
D:THR35
|
3.6
|
13.6
|
1.0
|
O
|
D:THR35
|
3.9
|
13.7
|
1.0
|
OG1
|
D:THR17
|
4.0
|
14.5
|
1.0
|
O
|
D:THR58
|
4.2
|
16.1
|
1.0
|
C
|
D:THR35
|
4.3
|
15.6
|
1.0
|
CG2
|
D:THR35
|
4.3
|
15.0
|
1.0
|
NH2
|
B:ARG146
|
4.3
|
11.8
|
1.0
|
C
|
D:PRO34
|
4.4
|
15.2
|
1.0
|
O1B
|
D:GDP200
|
4.5
|
13.4
|
1.0
|
O3A
|
D:GDP200
|
4.6
|
13.2
|
1.0
|
O2A
|
D:GDP200
|
4.7
|
14.2
|
1.0
|
NZ
|
D:LYS16
|
4.8
|
11.9
|
1.0
|
O
|
D:ILE33
|
4.8
|
14.7
|
1.0
|
CA
|
D:PRO34
|
4.8
|
15.4
|
1.0
|
CB
|
D:THR17
|
5.0
|
13.8
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 1he1
Go back to
Fluorine Binding Sites List in 1he1
Fluorine binding site 5 out
of 6 in the Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F201
b:15.1
occ:1.00
|
F2
|
D:AF3201
|
0.0
|
15.1
|
1.0
|
AL
|
D:AF3201
|
1.9
|
13.6
|
1.0
|
O
|
D:HOH2025
|
2.6
|
15.0
|
1.0
|
O
|
D:HOH2049
|
2.7
|
15.2
|
1.0
|
NE
|
B:ARG146
|
2.7
|
13.6
|
1.0
|
O3B
|
D:GDP200
|
2.8
|
9.6
|
1.0
|
NE2
|
D:GLN61
|
2.8
|
13.8
|
1.0
|
F3
|
D:AF3201
|
3.1
|
14.5
|
1.0
|
F1
|
D:AF3201
|
3.2
|
15.1
|
1.0
|
NH2
|
B:ARG146
|
3.3
|
11.8
|
1.0
|
CZ
|
B:ARG146
|
3.4
|
13.7
|
1.0
|
CA
|
D:GLY12
|
3.6
|
13.9
|
1.0
|
CD
|
B:ARG146
|
3.7
|
12.7
|
1.0
|
N
|
D:ALA13
|
3.7
|
12.4
|
1.0
|
CD
|
D:GLN61
|
3.7
|
16.6
|
1.0
|
OE1
|
D:GLN61
|
3.8
|
13.9
|
1.0
|
CG
|
B:ARG146
|
4.1
|
14.1
|
1.0
|
C
|
D:GLY12
|
4.1
|
13.0
|
1.0
|
PB
|
D:GDP200
|
4.3
|
14.3
|
1.0
|
OG1
|
B:THR150
|
4.4
|
16.2
|
1.0
|
OH
|
D:TYR32
|
4.6
|
16.3
|
1.0
|
NH1
|
B:ARG146
|
4.7
|
10.8
|
1.0
|
CA
|
D:ALA13
|
4.7
|
12.2
|
1.0
|
O2B
|
D:GDP200
|
4.8
|
14.0
|
1.0
|
O
|
B:GLY141
|
4.9
|
17.0
|
1.0
|
N
|
D:GLY12
|
4.9
|
13.6
|
1.0
|
MG
|
D:MG202
|
4.9
|
13.8
|
1.0
|
O
|
D:HOH2224
|
5.0
|
10.3
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 1he1
Go back to
Fluorine Binding Sites List in 1he1
Fluorine binding site 6 out
of 6 in the Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of the Complex Between the Gap Domain of the Pseudomonas Aeruginosa Exos Toxin and Human Rac within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F201
b:14.5
occ:1.00
|
F3
|
D:AF3201
|
0.0
|
14.5
|
1.0
|
AL
|
D:AF3201
|
1.9
|
13.6
|
1.0
|
NZ
|
D:LYS16
|
2.6
|
11.9
|
1.0
|
N
|
D:GLY60
|
2.7
|
15.9
|
1.0
|
O
|
D:HOH2049
|
2.8
|
15.2
|
1.0
|
O3B
|
D:GDP200
|
2.9
|
9.6
|
1.0
|
F2
|
D:AF3201
|
3.1
|
15.1
|
1.0
|
CA
|
D:GLY12
|
3.3
|
13.9
|
1.0
|
F1
|
D:AF3201
|
3.3
|
15.1
|
1.0
|
CA
|
D:GLY60
|
3.4
|
15.0
|
1.0
|
CE
|
D:LYS16
|
3.4
|
12.9
|
1.0
|
O
|
D:THR58
|
3.7
|
16.1
|
1.0
|
C
|
D:ALA59
|
3.7
|
16.1
|
1.0
|
N
|
D:GLY12
|
3.9
|
13.6
|
1.0
|
PB
|
D:GDP200
|
3.9
|
14.3
|
1.0
|
CA
|
D:ALA59
|
4.0
|
15.8
|
1.0
|
O
|
D:ASP11
|
4.0
|
12.4
|
1.0
|
O1B
|
D:GDP200
|
4.0
|
13.4
|
1.0
|
O
|
D:HOH2046
|
4.0
|
12.4
|
1.0
|
OE1
|
D:GLN61
|
4.2
|
13.9
|
1.0
|
C
|
D:ASP11
|
4.2
|
12.8
|
1.0
|
N
|
D:ALA13
|
4.2
|
12.4
|
1.0
|
O
|
D:GLY10
|
4.3
|
15.0
|
1.0
|
C
|
D:GLY12
|
4.3
|
13.0
|
1.0
|
O2B
|
D:GDP200
|
4.3
|
14.0
|
1.0
|
NE2
|
D:GLN61
|
4.4
|
13.8
|
1.0
|
C
|
D:GLY60
|
4.5
|
16.2
|
1.0
|
CD
|
D:GLN61
|
4.6
|
16.6
|
1.0
|
MG
|
D:MG202
|
4.6
|
13.8
|
1.0
|
N
|
D:GLN61
|
4.6
|
13.8
|
1.0
|
C
|
D:THR58
|
4.7
|
16.5
|
1.0
|
N
|
D:ALA59
|
4.8
|
14.0
|
1.0
|
O
|
D:ALA59
|
4.9
|
18.1
|
1.0
|
CD
|
D:LYS16
|
4.9
|
13.9
|
1.0
|
|
Reference:
M.Wurtele,
E.Wolf,
K.J.Pederson,
G.Buchwald,
M.R.Ahmadian,
J.T.Barbieri,
A.Wittinghofer.
How the Pseudomonas Aeruginosa Exos Toxin Downregulates Rac Nat.Struct.Biol. V. 8 23 2001.
ISSN: ISSN 1072-8368
PubMed: 11135665
DOI: 10.1038/83007
Page generated: Wed Jul 31 11:30:37 2024
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