Nickel in PDB 9c0q: Carbon Monoxide Dehydrogenase (Codh) From Methanosarcina Thermophila, Specimen Prepared on Blot Plunger

All present enzymatic activity of Carbon Monoxide Dehydrogenase (Codh) From Methanosarcina Thermophila, Specimen Prepared on Blot Plunger:
1.2.7.4;

The structure of Carbon Monoxide Dehydrogenase (Codh) From Methanosarcina Thermophila, Specimen Prepared on Blot Plunger also contains other interesting chemical elements:

Iron

(Fe)

36 atoms

The binding sites of Nickel atom in the Carbon Monoxide Dehydrogenase (Codh) From Methanosarcina Thermophila, Specimen Prepared on Blot Plunger (pdb code 9c0q). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Carbon Monoxide Dehydrogenase (Codh) From Methanosarcina Thermophila, Specimen Prepared on Blot Plunger, PDB code: 9c0q:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Carbon Monoxide Dehydrogenase (Codh) From Methanosarcina Thermophila, Specimen Prepared on Blot Plunger


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 (Codh) From Methanosarcina Thermophila, Specimen Prepared on Blot Plunger within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni901 b:74.2 occ:0.50 NI A:RQM901 0.0 74.2 0.5 SG A:CYS584 2.2 66.5 1.0 S1 A:RQM901 2.3 69.1 1.0 S4 A:RQM901 2.3 54.5 1.0 FE2 A:RQM901 2.4 64.9 1.0 FE3 A:RQM901 2.7 98.5 1.0 FE1 A:RQM901 3.4 73.3 1.0 CB A:CYS584 3.4 43.9 1.0 S3 A:RQM901 3.5 56.5 1.0 FE4 A:RQM901 3.5 75.0 1.0 NE2 A:HIS249 3.7 46.6 1.0 NZ A:LYS634 3.9 33.0 1.0 SG A:CYS277 4.0 52.7 1.0 CE1 A:HIS249 4.4 43.7 1.0 S2 A:RQM901 4.5 83.1 1.0 CA A:CYS584 4.6 37.7 1.0 SG A:CYS520 4.6 36.9 1.0 CE A:LYS634 4.7 27.7 1.0 CD2 A:HIS249 4.8 43.9 1.0 N A:CYS584 4.9 36.8 1.0

Nickel binding site 2 out of 2 in the Carbon Monoxide Dehydrogenase (Codh) From Methanosarcina Thermophila, Specimen Prepared on Blot Plunger


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 (Codh) From Methanosarcina Thermophila, Specimen Prepared on Blot Plunger within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni902 b:118.0 occ:1.00 NI B:RQM902 0.0 118.0 1.0 SG B:CYS584 2.2 70.4 1.0 S1 B:RQM902 2.3 80.3 1.0 S4 B:RQM902 2.3 61.5 1.0 FE2 B:RQM902 2.4 70.7 1.0 FE3 B:RQM902 2.7 103.7 1.0 FE1 B:RQM902 3.3 77.8 1.0 CB B:CYS584 3.4 47.6 1.0 FE4 B:RQM902 3.5 77.3 1.0 S3 B:RQM902 3.5 59.0 1.0 NE2 B:HIS249 3.8 51.9 1.0 NZ B:LYS634 3.9 38.5 1.0 SG B:CYS277 4.0 51.4 1.0 CE1 B:HIS249 4.4 48.1 1.0 S2 B:RQM902 4.5 89.0 1.0 CA B:CYS584 4.6 40.4 1.0 SG B:CYS520 4.6 36.1 1.0 CE B:LYS634 4.8 31.4 1.0 N B:CYS584 4.9 38.6 1.0 CD2 B:HIS249 4.9 47.9 1.0

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