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Nickel in PDB 9c0s: Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Pentamer From Methanosarcina Thermophila

Enzymatic activity of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Pentamer From Methanosarcina Thermophila

All present enzymatic activity of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Pentamer From Methanosarcina Thermophila:
1.2.7.4; 2.3.1.169;

Other elements in 9c0s:

The structure of Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Pentamer From Methanosarcina Thermophila also contains other interesting chemical elements:

Iron (Fe) 43 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Pentamer From Methanosarcina Thermophila (pdb code 9c0s). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Pentamer From Methanosarcina Thermophila, PDB code: 9c0s:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 9c0s

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Nickel binding site 1 out of 4 in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Pentamer 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) Pentamer From Methanosarcina Thermophila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni902

b:83.8
occ:1.00
 NI A:RQM902 0.0 83.8 1.0
S4 A:RQM902 2.3 65.3 1.0
S1 A:RQM902 2.3 61.5 1.0
SG A:CYS584 2.4 46.2 1.0
FE2 A:RQM902 2.5 73.6 1.0
FE3 A:RQM902 2.7 93.4 1.0
CB A:CYS584 3.2 40.0 1.0
FE1 A:RQM902 3.3 75.1 1.0
S3 A:RQM902 3.5 56.6 1.0
FE4 A:RQM902 3.5 70.0 1.0
NE2 A:HIS249 3.8 46.8 1.0
NZ A:LYS634 3.9 36.3 1.0
SG A:CYS277 4.2 42.6 1.0
CA A:CYS584 4.4 31.9 1.0
S2 A:RQM902 4.5 66.9 1.0
CE1 A:HIS249 4.6 42.5 1.0
SG A:CYS520 4.6 25.2 1.0
CD2 A:HIS249 4.8 43.7 1.0
CE A:LYS634 4.9 31.1 1.0

Nickel binding site 2 out of 4 in 9c0s

Go back to Nickel Binding Sites List in 9c0s
Nickel binding site 2 out of 4 in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Pentamer 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) Pentamer From Methanosarcina Thermophila within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni903

b:92.7
occ:1.00
 NI B:RQM903 0.0 92.7 1.0
S4 B:RQM903 2.3 66.0 1.0
S1 B:RQM903 2.3 65.1 1.0
SG B:CYS584 2.4 71.1 1.0
FE2 B:RQM903 2.5 80.4 1.0
FE3 B:RQM903 2.7 99.0 1.0
FE1 B:RQM903 3.4 57.8 1.0
CB B:CYS584 3.4 49.8 1.0
FE4 B:RQM903 3.5 78.5 1.0
S3 B:RQM903 3.6 61.6 1.0
NE2 B:HIS249 3.9 45.6 1.0
NZ B:LYS634 3.9 36.4 1.0
SG B:CYS277 4.0 50.7 1.0
S2 B:RQM903 4.5 72.1 1.0
CE1 B:HIS249 4.6 41.6 1.0
CA B:CYS584 4.8 47.8 1.0
SG B:CYS520 4.8 38.3 1.0
N B:CYS584 4.9 45.0 1.0
CD2 B:HIS249 5.0 45.2 1.0

Nickel binding site 3 out of 4 in 9c0s

Go back to Nickel Binding Sites List in 9c0s
Nickel binding site 3 out of 4 in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Pentamer 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) Pentamer From Methanosarcina Thermophila within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni501

b:74.3
occ:1.00
 C A:CMO906 2.0 47.2 1.0
SG E:CYS192 2.2 32.9 1.0
SG E:CYS280 2.2 39.8 1.0
SG E:CYS278 2.2 35.8 1.0
NI E:NI502 3.0 42.8 1.0
O A:CMO906 3.2 45.2 1.0
CB E:CYS192 3.2 16.5 1.0
CB E:CYS280 3.5 17.3 1.0
CB E:CYS278 3.5 26.1 1.0
FE4 E:SF4500 3.6 37.0 1.0
S3 E:SF4500 3.8 31.7 1.0
N E:CYS280 4.5 23.6 1.0
CA E:CYS192 4.5 13.2 1.0
N E:GLY279 4.6 25.6 1.0
CA E:CYS280 4.6 17.6 1.0
ND2 E:ASN199 4.7 31.7 1.0
CA E:CYS278 4.8 29.0 1.0
CD1 A:PHE601 4.9 22.9 1.0

Nickel binding site 4 out of 4 in 9c0s

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Nickel binding site 4 out of 4 in the Carbon Monoxide Dehydrogenase/Acetyl-Coa Synthase (Codh/Acs) Pentamer 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) Pentamer From Methanosarcina Thermophila within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni502

b:42.8
occ:1.00
 N E:CYS280 1.9 23.6 1.0
N E:GLY279 1.9 25.6 1.0
SG E:CYS278 2.2 35.8 1.0
SG E:CYS280 2.2 39.8 1.0
C E:GLY279 2.7 20.4 1.0
CA E:GLY279 2.7 22.4 1.0
CB E:CYS280 2.9 17.3 1.0
CA E:CYS280 2.9 17.6 1.0
CB E:CYS278 2.9 26.1 1.0
C E:CYS278 2.9 29.0 1.0
NI E:NI501 3.0 74.3 1.0
CA E:CYS278 3.2 29.0 1.0
N E:CYS278 3.4 28.9 1.0
O E:GLY279 3.9 18.0 1.0
C E:CYS280 3.9 23.1 1.0
C A:CMO906 3.9 47.2 1.0
O E:CYS278 4.1 33.9 1.0
CD1 A:PHE601 4.1 22.9 1.0
N E:PHE281 4.2 22.7 1.0
CE1 A:PHE601 4.4 28.4 1.0
C E:SER277 4.6 28.1 1.0
O A:CMO906 4.8 45.2 1.0
O E:CYS280 4.9 27.1 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 23:12:05 2024

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