Nickel in PDB 9c0t: Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila
Enzymatic activity of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila
All present enzymatic activity of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila:
1.2.7.4;
2.3.1.169;
Other elements in 9c0t:
The structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila also contains other interesting chemical elements:
Nickel Binding Sites:
The binding sites of Nickel atom in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila
(pdb code 9c0t). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the
Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila, PDB code: 9c0t:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
Nickel binding site 1 out
of 6 in 9c0t
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Nickel Binding Sites List in 9c0t
Nickel binding site 1 out
of 6 in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni901
b:105.2
occ:1.00
|
NI
|
A:RQM901
|
0.0
|
105.2
|
1.0
|
SG
|
A:CYS584
|
2.2
|
87.0
|
1.0
|
S1
|
A:RQM901
|
2.3
|
84.3
|
1.0
|
S4
|
A:RQM901
|
2.3
|
79.3
|
1.0
|
FE3
|
A:RQM901
|
2.6
|
139.7
|
1.0
|
FE2
|
A:RQM901
|
3.2
|
80.7
|
1.0
|
FE1
|
A:RQM901
|
3.5
|
91.6
|
1.0
|
CB
|
A:CYS584
|
3.6
|
51.7
|
1.0
|
FE4
|
A:RQM901
|
3.6
|
100.2
|
1.0
|
S3
|
A:RQM901
|
3.9
|
76.9
|
1.0
|
NE2
|
A:HIS249
|
4.3
|
56.6
|
1.0
|
NZ
|
A:LYS634
|
4.4
|
44.0
|
1.0
|
SG
|
A:CYS277
|
4.4
|
55.4
|
1.0
|
SG
|
A:CYS520
|
4.4
|
47.5
|
1.0
|
S2
|
A:RQM901
|
4.5
|
90.9
|
1.0
|
CA
|
A:CYS584
|
4.8
|
43.6
|
1.0
|
O
|
A:GLY519
|
4.9
|
45.1
|
1.0
|
CD
|
A:LYS634
|
4.9
|
32.1
|
1.0
|
|
Nickel binding site 2 out
of 6 in 9c0t
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Nickel Binding Sites List in 9c0t
Nickel binding site 2 out
of 6 in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni902
b:99.5
occ:1.00
|
NI
|
B:RQM902
|
0.0
|
99.5
|
1.0
|
S1
|
B:RQM902
|
2.3
|
75.4
|
1.0
|
S4
|
B:RQM902
|
2.3
|
74.6
|
1.0
|
SG
|
B:CYS584
|
2.4
|
84.2
|
1.0
|
FE2
|
B:RQM902
|
2.5
|
79.5
|
1.0
|
FE3
|
B:RQM902
|
2.8
|
116.7
|
1.0
|
FE1
|
B:RQM902
|
3.4
|
84.0
|
1.0
|
CB
|
B:CYS584
|
3.4
|
50.2
|
1.0
|
FE4
|
B:RQM902
|
3.5
|
96.4
|
1.0
|
S3
|
B:RQM902
|
3.6
|
67.5
|
1.0
|
SG
|
B:CYS277
|
3.8
|
49.6
|
1.0
|
NE2
|
B:HIS249
|
3.8
|
54.6
|
1.0
|
NZ
|
B:LYS634
|
4.3
|
42.0
|
1.0
|
S2
|
B:RQM902
|
4.5
|
79.8
|
1.0
|
CE1
|
B:HIS249
|
4.7
|
47.7
|
1.0
|
CA
|
B:CYS584
|
4.7
|
42.5
|
1.0
|
SG
|
B:CYS520
|
4.7
|
47.7
|
1.0
|
CD2
|
B:HIS249
|
4.8
|
49.8
|
1.0
|
N
|
B:CYS584
|
4.8
|
39.1
|
1.0
|
CD
|
B:LYS634
|
4.8
|
32.8
|
1.0
|
|
Nickel binding site 3 out
of 6 in 9c0t
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Nickel Binding Sites List in 9c0t
Nickel binding site 3 out
of 6 in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ni501
b:75.0
occ:1.00
|
C
|
E:CMO503
|
2.0
|
16.9
|
1.0
|
SG
|
E:CYS278
|
2.2
|
20.8
|
1.0
|
SG
|
E:CYS280
|
2.2
|
19.6
|
1.0
|
SG
|
E:CYS192
|
2.2
|
17.6
|
1.0
|
NI
|
E:NI502
|
2.8
|
36.8
|
1.0
|
O
|
E:CMO503
|
3.2
|
16.8
|
1.0
|
CB
|
E:CYS192
|
3.3
|
10.2
|
1.0
|
CB
|
E:CYS280
|
3.5
|
9.6
|
1.0
|
CB
|
E:CYS278
|
3.5
|
13.4
|
1.0
|
FE4
|
E:SF4500
|
3.7
|
19.4
|
1.0
|
S3
|
E:SF4500
|
4.0
|
17.6
|
1.0
|
N
|
E:GLY279
|
4.2
|
15.4
|
1.0
|
N
|
E:CYS280
|
4.3
|
11.1
|
1.0
|
CA
|
E:CYS192
|
4.5
|
8.8
|
1.0
|
CA
|
E:CYS280
|
4.6
|
10.8
|
1.0
|
CA
|
E:CYS278
|
4.7
|
18.4
|
1.0
|
C
|
E:CYS278
|
5.0
|
21.5
|
1.0
|
|
Nickel binding site 4 out
of 6 in 9c0t
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Nickel Binding Sites List in 9c0t
Nickel binding site 4 out
of 6 in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ni502
b:36.8
occ:1.00
|
N
|
E:GLY279
|
1.9
|
15.4
|
1.0
|
N
|
E:CYS280
|
1.9
|
11.1
|
1.0
|
SG
|
E:CYS280
|
2.2
|
19.6
|
1.0
|
SG
|
E:CYS278
|
2.2
|
20.8
|
1.0
|
C
|
E:GLY279
|
2.7
|
9.4
|
1.0
|
CA
|
E:GLY279
|
2.7
|
11.4
|
1.0
|
NI
|
E:NI501
|
2.8
|
75.0
|
1.0
|
CA
|
E:CYS280
|
2.9
|
10.8
|
1.0
|
CB
|
E:CYS280
|
3.0
|
9.6
|
1.0
|
C
|
E:CYS278
|
3.0
|
21.5
|
1.0
|
CB
|
E:CYS278
|
3.1
|
13.4
|
1.0
|
CA
|
E:CYS278
|
3.3
|
18.4
|
1.0
|
N
|
E:CYS278
|
3.5
|
17.4
|
1.0
|
C
|
E:CMO503
|
3.8
|
16.9
|
1.0
|
O
|
E:GLY279
|
3.8
|
9.7
|
1.0
|
CD1
|
E:LEU210
|
3.9
|
16.0
|
1.0
|
C
|
E:CYS280
|
3.9
|
15.0
|
1.0
|
O
|
E:CYS278
|
4.1
|
27.4
|
1.0
|
N
|
E:PHE281
|
4.4
|
15.1
|
1.0
|
CE1
|
E:PHE281
|
4.5
|
17.2
|
1.0
|
CE1
|
A:PHE601
|
4.5
|
43.7
|
1.0
|
O
|
E:CYS280
|
4.6
|
17.3
|
1.0
|
C
|
E:SER277
|
4.6
|
16.7
|
1.0
|
CD1
|
E:PHE281
|
4.7
|
12.4
|
1.0
|
CD1
|
A:PHE601
|
4.7
|
30.5
|
1.0
|
O
|
E:CMO503
|
4.8
|
16.8
|
1.0
|
SG
|
E:CYS192
|
4.9
|
17.6
|
1.0
|
|
Nickel binding site 5 out
of 6 in 9c0t
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Nickel Binding Sites List in 9c0t
Nickel binding site 5 out
of 6 in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ni501
b:87.2
occ:1.00
|
C
|
F:CMO503
|
2.0
|
20.7
|
1.0
|
SG
|
F:CYS280
|
2.1
|
23.6
|
1.0
|
SG
|
F:CYS192
|
2.1
|
17.6
|
1.0
|
SG
|
F:CYS278
|
2.2
|
28.1
|
1.0
|
NI
|
F:NI502
|
2.9
|
44.0
|
1.0
|
O
|
F:CMO503
|
3.2
|
19.3
|
1.0
|
CB
|
F:CYS192
|
3.2
|
14.2
|
1.0
|
CB
|
F:CYS280
|
3.4
|
14.2
|
1.0
|
CB
|
F:CYS278
|
3.5
|
19.0
|
1.0
|
FE4
|
F:SF4500
|
3.7
|
26.3
|
1.0
|
S3
|
F:SF4500
|
3.9
|
19.4
|
1.0
|
N
|
F:CYS280
|
4.3
|
16.7
|
1.0
|
N
|
F:GLY279
|
4.3
|
26.4
|
1.0
|
CA
|
F:CYS192
|
4.5
|
11.6
|
1.0
|
CA
|
F:CYS280
|
4.5
|
14.5
|
1.0
|
CA
|
F:CYS278
|
4.7
|
25.0
|
1.0
|
CG2
|
B:VAL507
|
4.9
|
44.8
|
1.0
|
|
Nickel binding site 6 out
of 6 in 9c0t
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Nickel Binding Sites List in 9c0t
Nickel binding site 6 out
of 6 in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila
Mono view
Stereo pair view
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Hexamer From Methanosarcina Thermophila within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ni502
b:44.0
occ:1.00
|
N
|
F:CYS280
|
1.9
|
16.7
|
1.0
|
N
|
F:GLY279
|
1.9
|
26.4
|
1.0
|
SG
|
F:CYS278
|
2.2
|
28.1
|
1.0
|
SG
|
F:CYS280
|
2.2
|
23.6
|
1.0
|
C
|
F:GLY279
|
2.7
|
14.5
|
1.0
|
CA
|
F:GLY279
|
2.7
|
17.5
|
1.0
|
NI
|
F:NI501
|
2.9
|
87.2
|
1.0
|
CA
|
F:CYS280
|
2.9
|
14.5
|
1.0
|
CB
|
F:CYS280
|
2.9
|
14.2
|
1.0
|
C
|
F:CYS278
|
2.9
|
31.1
|
1.0
|
CB
|
F:CYS278
|
3.0
|
19.0
|
1.0
|
CA
|
F:CYS278
|
3.3
|
25.0
|
1.0
|
N
|
F:CYS278
|
3.5
|
24.8
|
1.0
|
C
|
F:CMO503
|
3.7
|
20.7
|
1.0
|
O
|
F:GLY279
|
3.9
|
14.0
|
1.0
|
C
|
F:CYS280
|
3.9
|
18.8
|
1.0
|
O
|
F:CYS278
|
4.1
|
36.2
|
1.0
|
CD1
|
F:LEU210
|
4.1
|
21.5
|
1.0
|
N
|
F:PHE281
|
4.2
|
17.5
|
1.0
|
C
|
F:SER277
|
4.5
|
25.4
|
1.0
|
CD1
|
B:PHE601
|
4.5
|
32.4
|
1.0
|
CE1
|
B:PHE601
|
4.5
|
39.5
|
1.0
|
O
|
F:CMO503
|
4.6
|
19.3
|
1.0
|
CD1
|
F:PHE281
|
4.7
|
18.0
|
1.0
|
O
|
F:CYS280
|
4.8
|
23.0
|
1.0
|
SG
|
F:CYS192
|
4.9
|
17.6
|
1.0
|
CE1
|
F:PHE281
|
4.9
|
21.5
|
1.0
|
|
Reference:
A.Biester,
D.A.Grahame,
C.L.Drennan.
Capturing A Methanogenic Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase Complex Via Cryogenic Electron Microscopy. Proc.Natl.Acad.Sci.Usa V. 121 95121 2024.
ISSN: ESSN 1091-6490
PubMed: 39361653
DOI: 10.1073/PNAS.2410995121
Page generated: Thu Oct 31 23:12:06 2024
|