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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:

Iron (Fe) 44 atoms

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 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 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 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 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 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 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

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