Chlorine in PDB 6et9: Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A
Enzymatic activity of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A
All present enzymatic activity of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A:
2.3.1.9;
2.3.3.10;
Protein crystallography data
The structure of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A, PDB code: 6et9
was solved by
S.Engilberge,
B.Voegeli,
E.Girard,
F.Riobe,
O.Maury,
T.J.Erb,
S.Shima,
T.Wagner,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.39 /
2.75
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
106.617,
144.014,
230.585,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19 /
22.5
|
Other elements in 6et9:
The structure of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A
(pdb code 6et9). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A, PDB code: 6et9:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 6et9
Go back to
Chlorine Binding Sites List in 6et9
Chlorine binding site 1 out
of 6 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A
![](/pictures/CL/pdb/et/6et9-CL-sphere_01.jpg) Mono view
![](/pictures/CL/pdb/et/6et9-CL-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl403
b:53.5
occ:1.00
|
O
|
F:HOH319
|
3.2
|
41.5
|
1.0
|
NE
|
F:ARG39
|
3.4
|
0.5
|
1.0
|
N
|
C:GLY41
|
3.4
|
57.2
|
1.0
|
NH2
|
F:ARG39
|
3.7
|
0.0
|
1.0
|
CB
|
F:ARG38
|
3.9
|
95.2
|
1.0
|
CA
|
C:GLY41
|
3.9
|
54.6
|
1.0
|
CZ
|
F:ARG39
|
4.0
|
0.5
|
1.0
|
CD
|
F:ARG38
|
4.1
|
99.5
|
1.0
|
N
|
F:ARG39
|
4.3
|
99.7
|
1.0
|
CB
|
F:ARG39
|
4.3
|
0.9
|
1.0
|
CG
|
F:ARG39
|
4.3
|
0.9
|
1.0
|
CD
|
F:ARG39
|
4.4
|
0.3
|
1.0
|
C
|
C:ASP40
|
4.5
|
67.1
|
1.0
|
CG
|
F:ARG38
|
4.5
|
94.6
|
1.0
|
NE
|
F:ARG38
|
4.6
|
0.7
|
1.0
|
CA
|
C:ASP40
|
4.8
|
72.7
|
1.0
|
CA
|
F:ARG39
|
4.9
|
0.9
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 6et9
Go back to
Chlorine Binding Sites List in 6et9
Chlorine binding site 2 out
of 6 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A
![](/pictures/CL/pdb/et/6et9-CL-sphere_02.jpg) Mono view
![](/pictures/CL/pdb/et/6et9-CL-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl202
b:73.0
occ:1.00
|
NZ
|
L:LYS212
|
4.0
|
74.1
|
1.0
|
NZ
|
E:LYS10
|
4.2
|
0.5
|
1.0
|
CE
|
E:LYS10
|
4.7
|
95.1
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 6et9
Go back to
Chlorine Binding Sites List in 6et9
Chlorine binding site 3 out
of 6 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A
![](/pictures/CL/pdb/et/6et9-CL-sphere_03.jpg) Mono view
![](/pictures/CL/pdb/et/6et9-CL-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl203
b:30.7
occ:1.00
|
O
|
E:HOH318
|
2.2
|
25.5
|
1.0
|
NE
|
E:ARG38
|
3.3
|
82.2
|
1.0
|
N
|
B:GLY41
|
3.6
|
49.6
|
1.0
|
CB
|
E:ARG38
|
3.8
|
82.0
|
1.0
|
NE
|
E:ARG39
|
3.8
|
91.5
|
1.0
|
CA
|
B:GLY41
|
3.8
|
48.0
|
1.0
|
CD
|
E:ARG38
|
3.9
|
81.1
|
1.0
|
NH2
|
E:ARG39
|
4.1
|
93.3
|
1.0
|
CB
|
E:ARG39
|
4.1
|
89.5
|
1.0
|
N
|
E:ARG39
|
4.2
|
85.5
|
1.0
|
CZ
|
E:ARG38
|
4.4
|
81.8
|
1.0
|
CZ
|
E:ARG39
|
4.4
|
93.5
|
1.0
|
CG
|
E:ARG38
|
4.4
|
80.3
|
1.0
|
NH1
|
E:ARG38
|
4.5
|
83.1
|
1.0
|
O
|
B:HOH556
|
4.5
|
48.7
|
1.0
|
CA
|
E:ARG39
|
4.8
|
87.7
|
1.0
|
C
|
B:ASP40
|
4.8
|
59.8
|
1.0
|
CD
|
E:ARG39
|
4.8
|
91.6
|
1.0
|
O
|
E:HOH324
|
4.8
|
35.4
|
1.0
|
C
|
B:GLY41
|
5.0
|
45.2
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 6et9
Go back to
Chlorine Binding Sites List in 6et9
Chlorine binding site 4 out
of 6 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A
![](/pictures/CL/pdb/et/6et9-CL-sphere_04.jpg) Mono view
![](/pictures/CL/pdb/et/6et9-CL-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl203
b:33.5
occ:1.00
|
O
|
G:HOH328
|
3.1
|
33.6
|
1.0
|
NE
|
G:ARG38
|
3.2
|
63.8
|
1.0
|
NE
|
G:ARG39
|
3.5
|
72.8
|
1.0
|
N
|
D:GLY41
|
3.5
|
36.1
|
1.0
|
NH2
|
G:ARG39
|
3.7
|
73.9
|
1.0
|
O
|
G:HOH308
|
3.8
|
34.4
|
1.0
|
CD
|
G:ARG38
|
3.9
|
62.5
|
1.0
|
CB
|
G:ARG38
|
3.9
|
63.7
|
1.0
|
CA
|
D:GLY41
|
3.9
|
35.5
|
1.0
|
CZ
|
G:ARG39
|
4.0
|
74.2
|
1.0
|
NH2
|
G:ARG38
|
4.0
|
64.7
|
1.0
|
CZ
|
G:ARG38
|
4.1
|
63.3
|
1.0
|
N
|
G:ARG39
|
4.4
|
67.2
|
1.0
|
CB
|
G:ARG39
|
4.4
|
71.3
|
1.0
|
CG
|
G:ARG39
|
4.4
|
71.3
|
1.0
|
CG
|
G:ARG38
|
4.5
|
61.9
|
1.0
|
CD
|
G:ARG39
|
4.5
|
73.2
|
1.0
|
C
|
D:ASP40
|
4.7
|
35.7
|
1.0
|
CA
|
D:ASP40
|
4.9
|
36.6
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 6et9
Go back to
Chlorine Binding Sites List in 6et9
Chlorine binding site 5 out
of 6 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A
![](/pictures/CL/pdb/et/6et9-CL-sphere_05.jpg) Mono view
![](/pictures/CL/pdb/et/6et9-CL-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Cl203
b:87.0
occ:1.00
|
NH1
|
H:ARG39
|
2.9
|
0.7
|
1.0
|
NE
|
H:ARG39
|
3.0
|
0.8
|
1.0
|
NE
|
H:ARG38
|
3.1
|
0.7
|
1.0
|
CZ
|
H:ARG39
|
3.3
|
0.7
|
1.0
|
CB
|
H:ARG38
|
3.7
|
0.4
|
1.0
|
CD
|
H:ARG38
|
3.8
|
0.9
|
1.0
|
NH1
|
H:ARG38
|
3.9
|
0.7
|
1.0
|
CZ
|
H:ARG38
|
3.9
|
0.6
|
1.0
|
N
|
H:ARG39
|
4.2
|
0.2
|
1.0
|
N
|
A:GLY41
|
4.2
|
72.3
|
1.0
|
CD
|
H:ARG39
|
4.3
|
0.6
|
1.0
|
CG
|
H:ARG38
|
4.3
|
0.2
|
1.0
|
CB
|
H:ARG39
|
4.4
|
0.7
|
1.0
|
CG
|
H:ARG39
|
4.4
|
0.5
|
1.0
|
CA
|
A:GLY41
|
4.6
|
70.1
|
1.0
|
NH2
|
H:ARG39
|
4.6
|
0.6
|
1.0
|
O
|
H:CYS37
|
4.9
|
0.4
|
1.0
|
CA
|
H:ARG38
|
4.9
|
0.5
|
1.0
|
CA
|
H:ARG39
|
5.0
|
0.5
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 6et9
Go back to
Chlorine Binding Sites List in 6et9
Chlorine binding site 6 out
of 6 in the Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A
![](/pictures/CL/pdb/et/6et9-CL-sphere_06.jpg) Mono view
![](/pictures/CL/pdb/et/6et9-CL-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Structure of the Acetoacetyl-Coa-Thiolase/Hmg-Coa-Synthase Complex From Methanothermococcus Thermolithotrophicus at 2.75 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Cl403
b:47.1
occ:1.00
|
O
|
I:HOH521
|
2.9
|
16.9
|
1.0
|
N
|
K:ALA113
|
3.3
|
26.9
|
1.0
|
N
|
I:LYS89
|
3.4
|
40.4
|
1.0
|
N
|
K:PHE112
|
3.6
|
34.3
|
1.0
|
CA
|
K:PHE112
|
3.7
|
27.7
|
1.0
|
CA
|
I:VAL88
|
3.8
|
33.5
|
1.0
|
C
|
K:GLU111
|
3.8
|
32.1
|
1.0
|
C
|
I:VAL88
|
3.9
|
33.3
|
1.0
|
N
|
I:PRO90
|
3.9
|
30.5
|
1.0
|
CB
|
K:GLU111
|
3.9
|
40.8
|
1.0
|
C
|
I:LYS89
|
3.9
|
39.0
|
1.0
|
CA
|
I:LYS89
|
3.9
|
41.8
|
1.0
|
C
|
K:PHE112
|
4.0
|
26.8
|
1.0
|
O
|
K:HOH505
|
4.0
|
16.1
|
1.0
|
CD
|
I:PRO90
|
4.1
|
31.2
|
1.0
|
CG1
|
I:VAL88
|
4.1
|
35.1
|
1.0
|
O
|
K:GLU111
|
4.3
|
32.5
|
1.0
|
CA
|
I:PRO90
|
4.3
|
29.4
|
1.0
|
CA
|
K:GLU111
|
4.4
|
36.0
|
1.0
|
CA
|
K:ALA113
|
4.4
|
26.7
|
1.0
|
O
|
I:ALA87
|
4.5
|
35.0
|
1.0
|
CB
|
I:VAL88
|
4.5
|
35.0
|
1.0
|
O
|
I:LYS89
|
4.6
|
39.4
|
1.0
|
CB
|
I:PRO90
|
4.6
|
29.5
|
1.0
|
OE1
|
K:GLU111
|
4.7
|
50.4
|
1.0
|
CG
|
K:GLU111
|
4.7
|
43.5
|
1.0
|
N
|
I:VAL88
|
4.8
|
33.5
|
1.0
|
CG
|
I:PRO90
|
4.8
|
30.6
|
1.0
|
CD
|
K:GLU111
|
4.9
|
49.3
|
1.0
|
CB
|
K:ALA113
|
4.9
|
27.3
|
1.0
|
O
|
I:VAL88
|
4.9
|
34.4
|
1.0
|
|
Reference:
B.Vogeli,
S.Engilberge,
E.Girard,
F.Riobe,
O.Maury,
T.J.Erb,
S.Shima,
T.Wagner.
Archaeal Acetoacetyl-Coa Thiolase/Hmg-Coa Synthase Complex Channels the Intermediate Via A Fused Coa-Binding Site. Proc. Natl. Acad. Sci. V. 115 3380 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29531083
DOI: 10.1073/PNAS.1718649115
Page generated: Sat Dec 12 12:56:24 2020
|