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Nickel in PDB 9g01: Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State)

Enzymatic activity of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State)

All present enzymatic activity of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State):
1.2.7.4; 2.3.1.169;

Other elements in 9g01:

The structure of Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State) also contains other interesting chemical elements:

Iron (Fe) 24 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State) (pdb code 9g01). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State), PDB code: 9g01:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 9g01

Go back to Nickel Binding Sites List in 9g01
Nickel binding site 1 out of 4 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State)


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) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni703

b:30.8
occ:0.52
 NI B:RQM703 0.0 30.8 0.5
SG B:CYS523 2.1 41.6 1.0
S1 B:RQM703 2.3 27.4 1.0
S4 B:RQM703 2.4 27.3 0.8
FE2 B:RQM703 2.5 31.7 0.6
FE3 B:RQM703 3.0 25.9 0.9
FE1 B:RQM703 3.2 25.8 1.0
S3 B:RQM703 3.3 28.5 0.9
CB B:CYS523 3.4 37.5 1.0
FE4 B:RQM703 3.5 25.4 1.0
SG B:CYS295 4.0 35.7 1.0
NE2 B:HIS259 4.2 38.8 1.0
NZ B:LYS560 4.4 30.0 1.0
S2 B:RQM703 4.5 25.5 1.0
CA B:CYS523 4.7 33.5 1.0
CE B:LYS560 4.8 30.4 1.0
CD2 B:HIS259 4.9 35.9 1.0
SG B:CYS451 5.0 25.4 1.0

Nickel binding site 2 out of 4 in 9g01

Go back to Nickel Binding Sites List in 9g01
Nickel binding site 2 out of 4 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State)


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) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni702

b:31.1
occ:0.53
 NI C:RQM702 0.0 31.1 0.5
SG C:CYS523 2.1 41.4 1.0
S1 C:RQM702 2.3 27.5 1.0
S4 C:RQM702 2.4 27.2 0.8
FE2 C:RQM702 2.5 31.6 0.6
FE3 C:RQM702 3.0 25.9 1.0
FE1 C:RQM702 3.2 25.7 1.0
CB C:CYS523 3.3 37.1 1.0
S3 C:RQM702 3.3 28.4 0.9
FE4 C:RQM702 3.5 25.5 1.0
SG C:CYS295 4.0 35.8 1.0
NE2 C:HIS259 4.2 38.8 1.0
NZ C:LYS560 4.4 29.9 1.0
S2 C:RQM702 4.5 25.5 1.0
CA C:CYS523 4.7 33.1 1.0
CE C:LYS560 4.9 30.3 1.0
CD2 C:HIS259 5.0 35.9 1.0
SG C:CYS451 5.0 25.4 1.0

Nickel binding site 3 out of 4 in 9g01

Go back to Nickel Binding Sites List in 9g01
Nickel binding site 3 out of 4 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State)


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) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni802

b:154.4
occ:1.00
 C D:CMO804 1.6 132.4 1.0
SG D:CYS488 2.3 120.4 1.0
SG D:CYS574 2.4 115.2 1.0
SG D:CYS576 2.5 121.8 1.0
NI D:NI803 2.8 135.1 1.0
O D:CMO804 2.9 131.0 1.0
CB D:CYS488 3.2 122.5 1.0
CB D:CYS576 3.5 120.3 1.0
CB D:CYS574 3.6 116.3 1.0
FE4 D:SF4801 3.8 110.2 1.0
S1 D:SF4801 4.2 106.0 1.0
N D:GLY575 4.3 116.8 1.0
N D:CYS576 4.3 119.4 1.0
CA D:CYS488 4.4 124.0 1.0
CA D:CYS576 4.6 119.6 1.0
CA D:CYS574 4.8 116.8 1.0
CG2 D:VAL125 4.9 114.0 1.0
CG2 D:VAL128 5.0 118.2 1.0
C D:CYS574 5.0 117.2 1.0
O D:CYS488 5.0 128.0 1.0

Nickel binding site 4 out of 4 in 9g01

Go back to Nickel Binding Sites List in 9g01
Nickel binding site 4 out of 4 in the Structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State)


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) From Clostridium Autoethanogenum (Composite Structure, Closed and Co-Bound State) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni803

b:135.1
occ:1.00
 N D:CYS576 2.0 119.4 1.0
N D:GLY575 2.0 116.8 1.0
SG D:CYS576 2.3 121.8 1.0
SG D:CYS574 2.3 115.2 1.0
C D:GLY575 2.7 117.4 1.0
CA D:GLY575 2.8 116.4 1.0
NI D:NI802 2.8 154.4 1.0
CB D:CYS576 2.9 120.3 1.0
CA D:CYS576 2.9 119.6 1.0
C D:CYS574 3.1 117.2 1.0
CB D:CYS574 3.2 116.3 1.0
CA D:CYS574 3.4 116.8 1.0
N D:CYS574 3.5 117.4 1.0
C D:CMO804 3.6 132.4 1.0
CD1 D:LEU506 3.7 104.4 1.0
C D:CYS576 3.9 118.5 1.0
O D:GLY575 3.9 116.3 1.0
N D:PHE577 4.0 116.8 1.0
O D:CYS574 4.2 118.3 1.0
O D:CMO804 4.5 131.0 1.0
CE1 D:PHE209 4.7 81.9 1.0
CD2 D:PHE577 4.7 113.5 1.0
CD1 D:PHE209 4.7 80.9 1.0
C D:SER573 4.8 118.4 1.0
O D:CYS576 4.9 118.7 1.0
SG D:CYS488 4.9 120.4 1.0

Reference:

M.D.Yin, O.N.Lemaire, M.Belhamri, J.G.Rosas-Jimenez, G.Hummer, T.Wagner, B.J.Murphy. Snapshots of Acetyl-Coa Synthesis, the Last Step of CO2 Fixation in the Wood-Ljungdahl Pathway Science 2025.
ISSN: ESSN 1095-9203
DOI: 10.1126/SCIENCE.ADR9672
Page generated: Sun Feb 9 08:46:01 2025

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