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Nickel in PDB 9g7i: Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum

Enzymatic activity of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum

All present enzymatic activity of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum:
1.2.7.4; 2.3.1.169;

Protein crystallography data

The structure of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum, PDB code: 9g7i was solved by O.N.Lemaire, M.D.Yin, B.J.Murphy, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.68 / 2.93
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 298.077, 298.077, 127.526, 90, 90, 90
R / Rfree (%) 19 / 22

Other elements in 9g7i:

The structure of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum also contains other interesting chemical elements:

Iron (Fe) 28 atoms
Chlorine (Cl) 8 atoms
Calcium (Ca) 10 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum (pdb code 9g7i). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum, PDB code: 9g7i:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 9g7i

Go back to Nickel Binding Sites List in 9g7i
Nickel binding site 1 out of 6 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni802

b:117.1
occ:1.00
 N A:CYS576 1.9 104.3 1.0
N A:GLY575 2.0 115.8 1.0
SG A:CYS574 2.3 139.6 1.0
NI A:NI803 2.6 183.3 1.0
SG A:CYS576 2.7 110.3 1.0
C A:GLY575 2.7 112.2 1.0
CA A:GLY575 2.8 109.1 1.0
CA A:CYS576 3.0 88.1 1.0
CB A:CYS574 3.0 110.5 1.0
C A:CYS574 3.1 121.8 1.0
CB A:CYS576 3.3 115.8 1.0
CA A:CYS574 3.4 115.9 1.0
N A:PHE577 3.6 103.3 1.0
C A:CYS576 3.7 95.6 1.0
N A:CYS574 3.9 115.5 1.0
O A:GLY575 3.9 110.3 1.0
O A:CYS574 4.2 119.0 1.0
CD2 A:PHE577 4.2 100.2 1.0
CZ A:PHE491 4.4 120.3 1.0
CE2 A:PHE491 4.4 116.5 1.0
SG A:CYS488 4.6 122.2 1.0
CE2 A:PHE577 4.7 92.2 1.0
O A:CYS576 4.7 105.1 1.0
CA A:PHE577 4.8 93.3 1.0
CG A:PHE577 4.8 95.0 1.0

Nickel binding site 2 out of 6 in 9g7i

Go back to Nickel Binding Sites List in 9g7i
Nickel binding site 2 out of 6 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni803

b:183.3
occ:1.00
 SG A:CYS576 2.0 110.3 1.0
SG A:CYS574 2.1 139.6 1.0
SG A:CYS488 2.4 122.2 1.0
NI A:NI802 2.6 117.1 1.0
S1 A:SF4801 2.9 181.3 1.0
FE4 A:SF4801 3.2 161.8 1.0
CB A:CYS574 3.2 110.5 1.0
CB A:CYS576 3.6 115.8 1.0
CB A:CYS488 3.7 131.4 1.0
N A:CYS576 4.0 104.3 1.0
CZ A:PHE491 4.2 120.3 1.0
N A:GLY575 4.2 115.8 1.0
CA A:CYS576 4.4 88.1 1.0
CA A:CYS574 4.5 115.9 1.0
CB A:CYS507 4.5 143.3 1.0
N A:CYS507 4.6 125.3 1.0
FE2 A:SF4801 4.7 169.7 1.0
FE3 A:SF4801 4.7 102.4 1.0
NE2 A:HIS495 4.7 121.2 1.0
CA A:CYS507 4.8 126.2 1.0
C A:CYS574 4.8 121.8 1.0
S3 A:SF4801 4.8 99.0 1.0
CB A:LEU506 4.9 116.8 1.0
CE2 A:PHE491 4.9 116.5 1.0
S2 A:SF4801 4.9 172.6 1.0
N A:CYS574 5.0 115.5 1.0
CA A:CYS488 5.0 124.2 1.0
C A:GLY575 5.0 112.2 1.0

Nickel binding site 3 out of 6 in 9g7i

Go back to Nickel Binding Sites List in 9g7i
Nickel binding site 3 out of 6 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni705

b:88.0
occ:1.00
 NI B:XCC705 0.0 88.0 1.0
SG B:CYS523 2.3 111.2 1.0
S1 B:XCC705 2.3 62.3 1.0
FE2 B:XCC705 2.6 75.7 1.0
S4 B:XCC705 2.7 53.0 1.0
CB B:CYS523 3.4 49.5 1.0
FE3 B:XCC705 3.4 69.3 1.0
S3 B:XCC705 3.6 55.5 1.0
SG B:CYS295 3.7 85.0 1.0
FE4 B:XCC705 3.8 60.6 1.0
FE1 B:XCC705 4.1 64.9 1.0
S2 B:XCC705 4.2 45.8 1.0
CA B:GLY480 4.5 57.7 1.0
NE2 B:HIS259 4.5 66.4 1.0
CA B:CYS523 4.6 64.2 1.0
N B:CYS523 4.6 45.6 1.0
N B:CYS481 5.0 47.2 1.0

Nickel binding site 4 out of 6 in 9g7i

Go back to Nickel Binding Sites List in 9g7i
Nickel binding site 4 out of 6 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni704

b:128.9
occ:1.00
 NI C:XCC704 0.0 128.9 1.0
S1 C:XCC704 2.3 107.0 1.0
S4 C:XCC704 2.5 65.3 1.0
FE2 C:XCC704 2.6 126.5 1.0
SG C:CYS523 2.9 120.5 1.0
S3 C:XCC704 3.2 74.2 1.0
CB C:CYS523 3.4 56.1 1.0
FE3 C:XCC704 3.4 119.2 1.0
SG C:CYS295 3.5 98.3 1.0
FE4 C:XCC704 3.6 81.3 1.0
FE1 C:XCC704 3.6 123.9 1.0
S2 C:XCC704 3.8 55.8 1.0
CA C:GLY480 3.9 76.3 1.0
N C:CYS481 4.2 56.6 1.0
N C:CYS523 4.4 67.7 1.0
CA C:CYS523 4.4 78.2 1.0
NE2 C:HIS259 4.5 93.3 1.0
C C:GLY480 4.6 59.7 1.0
O C:GLY450 4.8 73.3 1.0
SG C:CYS481 4.9 72.5 1.0
N C:GLY480 4.9 63.7 1.0

Nickel binding site 5 out of 6 in 9g7i

Go back to Nickel Binding Sites List in 9g7i
Nickel binding site 5 out of 6 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni802

b:75.4
occ:1.00
 SG D:CYS488 1.9 78.2 1.0
SG D:CYS576 2.2 76.7 1.0
SG D:CYS574 2.3 71.5 1.0
FE4 D:SF4801 2.7 72.2 1.0
S1 D:SF4801 2.8 81.3 1.0
NI D:NI803 2.9 53.5 1.0
CB D:CYS488 3.1 52.8 1.0
CB D:CYS574 3.5 50.3 1.0
CB D:CYS576 3.8 59.0 1.0
S1P D:ACO805 4.1 105.9 1.0
N D:CYS576 4.3 57.3 1.0
CH3 D:ACO805 4.4 53.0 1.0
FE2 D:SF4801 4.4 72.0 1.0
S3 D:SF4801 4.4 85.2 1.0
CA D:CYS488 4.4 66.5 1.0
FE3 D:SF4801 4.5 73.5 1.0
S2 D:SF4801 4.5 94.0 1.0
N D:GLY575 4.6 49.6 1.0
C D:ACO805 4.6 90.7 1.0
CA D:CYS576 4.6 50.8 1.0
NE2 D:HIS495 4.8 76.7 1.0
CB D:CYS507 4.8 72.5 1.0
CA D:CYS574 4.9 60.8 1.0
CD2 D:HIS495 4.9 85.0 1.0
N D:CYS488 5.0 70.5 1.0

Nickel binding site 6 out of 6 in 9g7i

Go back to Nickel Binding Sites List in 9g7i
Nickel binding site 6 out of 6 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) in Complex with Acetyl-Coenyzme A From Clostridium Autoethanogenum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni803

b:53.5
occ:1.00
 N D:CYS576 1.9 57.3 1.0
SG D:CYS574 2.1 71.5 1.0
N D:GLY575 2.2 49.6 1.0
SG D:CYS576 2.4 76.7 1.0
C D:GLY575 2.8 68.0 1.0
NI D:NI802 2.9 75.4 1.0
CA D:CYS576 2.9 50.8 1.0
CA D:GLY575 2.9 61.3 1.0
CB D:CYS576 3.1 59.0 1.0
CB D:CYS574 3.1 50.3 1.0
C D:CYS574 3.3 65.6 1.0
N D:PHE577 3.4 62.6 1.0
CA D:CYS574 3.6 60.8 1.0
C D:CYS576 3.6 66.7 1.0
O D:GLY575 3.9 77.2 1.0
N D:CYS574 4.1 70.2 1.0
CD2 D:PHE577 4.1 72.5 1.0
S1P D:ACO805 4.2 105.9 1.0
O D:CYS574 4.4 80.7 1.0
CE2 D:PHE577 4.5 75.8 1.0
SG D:CYS488 4.6 78.2 1.0
S1 D:SF4801 4.7 81.3 1.0
CA D:PHE577 4.7 60.3 1.0
CG D:PHE577 4.7 66.8 1.0
O D:CYS576 4.8 80.4 1.0
C D:ACO805 5.0 90.7 1.0
C3P D:ACO805 5.0 85.0 1.0

Reference:

M.D.Yin, O.N.Lemaire, J.G.Rosas Jimenez, M.Belhamri, A.Shevchenko, G.Hummer, T.Wagner, B.J.Murphy. Conformational Dynamics of A Multienzyme Complex in Anaerobic Carbon Fixation. Science V. 387 498 2025.
ISSN: ESSN 1095-9203
PubMed: 39883773
DOI: 10.1126/SCIENCE.ADR9672
Page generated: Tue Feb 25 11:46:41 2025

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