Nickel in PDB 9c0r: Carbon Monoxide Dehydrogenase (Codh) From Methanosarcina Thermophila, Specimen Prepared on Chameleon Plunger

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

The structure of Carbon Monoxide Dehydrogenase (Codh) From Methanosarcina Thermophila, Specimen Prepared on Chameleon 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 Chameleon Plunger (pdb code 9c0r). 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 Chameleon Plunger, PDB code: 9c0r:
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 Chameleon 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 Chameleon Plunger within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni901 b:76.8 occ:1.00 NI A:RQM901 0.0 76.8 1.0 SG A:CYS584 2.3 59.7 1.0 S1 A:RQM901 2.3 40.5 1.0 S4 A:RQM901 2.3 47.0 1.0 FE2 A:RQM901 2.6 63.2 1.0 FE3 A:RQM901 2.8 73.6 1.0 CB A:CYS584 3.3 37.2 1.0 FE1 A:RQM901 3.4 63.0 1.0 FE4 A:RQM901 3.6 63.7 1.0 S3 A:RQM901 3.6 43.1 1.0 NE2 A:HIS249 4.0 38.9 1.0 SG A:CYS277 4.1 38.5 1.0 O A:HOH1093 4.3 24.8 1.0 NZ A:LYS634 4.3 29.8 1.0 CA A:CYS584 4.5 33.0 1.0 S2 A:RQM901 4.5 49.4 1.0 SG A:CYS520 4.7 24.6 1.0 CE A:LYS634 4.7 28.5 1.0 CE1 A:HIS249 4.9 32.7 1.0 CD2 A:HIS249 5.0 37.9 1.0

Nickel binding site 2 out of 2 in the Carbon Monoxide Dehydrogenase (Codh) From Methanosarcina Thermophila, Specimen Prepared on Chameleon 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 Chameleon Plunger within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni902 b:76.3 occ:1.00 NI B:RQM902 0.0 76.3 1.0 SG B:CYS584 2.3 60.0 1.0 S1 B:RQM902 2.3 40.9 1.0 S4 B:RQM902 2.3 45.7 1.0 FE2 B:RQM902 2.6 63.8 1.0 FE3 B:RQM902 2.8 74.9 1.0 CB B:CYS584 3.3 38.0 1.0 FE1 B:RQM902 3.4 62.6 1.0 FE4 B:RQM902 3.6 64.8 1.0 S3 B:RQM902 3.6 43.6 1.0 NE2 B:HIS249 4.0 39.4 1.0 SG B:CYS277 4.1 38.4 1.0 O B:HOH1093 4.3 25.1 1.0 NZ B:LYS634 4.4 30.9 1.0 S2 B:RQM902 4.5 51.0 1.0 CA B:CYS584 4.5 32.9 1.0 SG B:CYS520 4.7 23.4 1.0 CE B:LYS634 4.7 29.2 1.0 CD2 B:HIS249 4.9 38.4 1.0 CE1 B:HIS249 5.0 33.5 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