Nickel in PDB 6elq: Carbon Monoxide Dehydrogenase IV From Carboxydothermus Hydrogenoformans

All present enzymatic activity of Carbon Monoxide Dehydrogenase IV From Carboxydothermus Hydrogenoformans:
1.2.7.4;

The structure of Carbon Monoxide Dehydrogenase IV From Carboxydothermus Hydrogenoformans, PDB code: 6elq was solved by L.Domnik, S.Goetzl, J.H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.63 / 2.52
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	209.150, 209.150, 93.410, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 27.5

The structure of Carbon Monoxide Dehydrogenase IV From Carboxydothermus Hydrogenoformans also contains other interesting chemical elements:

Iron

(Fe)

32 atoms

The binding sites of Nickel atom in the Carbon Monoxide Dehydrogenase IV From Carboxydothermus Hydrogenoformans (pdb code 6elq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Carbon Monoxide Dehydrogenase IV From Carboxydothermus Hydrogenoformans, PDB code: 6elq:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Carbon Monoxide Dehydrogenase IV From Carboxydothermus Hydrogenoformans


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 IV From Carboxydothermus Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ X:Ni702 b:55.6 occ:0.32 NI X:BF8702 0.0 55.6 0.3 SG X:CYS525 2.0 69.8 1.0 S4 X:BF8702 2.1 48.3 0.8 S1 X:BF8702 2.4 46.6 0.9 O X:BF8702 2.6 49.0 1.0 FE3 X:BF8702 2.7 47.4 0.8 FE5 X:BF8702 3.2 47.6 0.8 CB X:CYS525 3.5 50.5 1.0 FE1 X:BF8702 3.6 59.4 1.0 FE4 X:BF8702 3.9 47.5 0.8 S3 X:BF8702 4.1 45.3 0.7 SG X:CYS446 4.3 48.4 1.0 SG X:CYS295 4.5 51.0 1.0 NZ X:LYS562 4.6 37.4 1.0 S2 X:BF8702 4.6 45.2 0.7 NE2 X:HIS261 4.7 43.7 1.0 CE X:LYS562 4.7 44.1 1.0 CA X:CYS525 4.8 42.1 1.0 CB X:LYS562 4.9 39.0 1.0 C X:GLY445 5.0 43.9 1.0

Nickel binding site 2 out of 3 in the Carbon Monoxide Dehydrogenase IV From Carboxydothermus Hydrogenoformans


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 IV From Carboxydothermus Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni5003 b:63.5 occ:0.51 NI A:BF85003 0.0 63.5 0.5 S4 A:BF85003 2.1 49.1 1.0 S1 A:BF85003 2.4 50.9 1.0 O A:BF85003 2.6 59.6 1.0 FE3 A:BF85003 2.7 46.9 0.8 SG A:CYS525 3.0 77.5 1.0 FE5 A:BF85003 3.2 56.1 0.9 FE1 A:BF85003 3.6 50.6 0.9 CB A:CYS525 3.9 59.5 1.0 FE4 A:BF85003 3.9 50.1 0.8 S3 A:BF85003 4.1 49.7 0.8 SG A:CYS446 4.2 52.8 1.0 NZ A:LYS562 4.6 44.0 1.0 S2 A:BF85003 4.6 50.2 0.7 SG A:CYS295 4.7 57.3 1.0 CE A:LYS562 4.7 49.6 1.0 NE2 A:HIS261 4.7 49.4 1.0 CB A:LYS562 4.8 45.5 1.0 C A:GLY445 4.9 48.2 1.0 CB A:CYS446 4.9 49.9 1.0

Nickel binding site 3 out of 3 in the Carbon Monoxide Dehydrogenase IV From Carboxydothermus Hydrogenoformans


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 IV From Carboxydothermus Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni5002 b:72.1 occ:0.42 NI B:BF85002 0.0 72.1 0.4 SG B:CYS525 2.0 81.7 1.0 S4 B:BF85002 2.1 66.2 0.9 S1 B:BF85002 2.4 72.4 0.9 O B:BF85002 2.6 60.5 1.0 FE3 B:BF85002 2.7 73.3 0.8 FE5 B:BF85002 3.1 61.9 0.9 CB B:CYS525 3.4 66.3 1.0 FE1 B:BF85002 3.6 68.9 0.8 FE4 B:BF85002 3.9 64.3 0.8 S3 B:BF85002 4.1 61.1 0.8 SG B:CYS446 4.3 85.4 1.0 C B:GLY445 4.4 70.8 1.0 SG B:CYS295 4.4 69.0 1.0 CA B:GLY445 4.5 66.9 1.0 O B:GLY445 4.6 68.8 1.0 S2 B:BF85002 4.6 68.9 0.7 N B:CYS446 4.7 68.0 1.0 CA B:CYS525 4.7 61.4 1.0 CB B:CYS446 4.7 69.2 1.0 CE B:LYS562 4.9 61.3 1.0 N B:GLY445 4.9 59.9 1.0 NE2 B:HIS261 4.9 55.1 1.0 CA B:GLY475 5.0 63.1 1.0

L.Domnik, M.Merrouch, S.Goetzl, J.H.Jeoung, C.Leger, S.Dementin, V.Fourmond, H.Dobbek. Codh-IV: A High-Efficiency Co-Scavenging Co Dehydrogenase with Resistance to O2. Angew. Chem. Int. Ed. Engl. V. 56 15466 2017.
ISSN: ESSN 1521-3773
PubMed: 29024326
DOI: 10.1002/ANIE.201709261