Nickel in PDB 8cja: A225L/F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans

All present enzymatic activity of A225L/F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans:
1.2.7.4; 2.3.1.169;

The structure of A225L/F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 8cja was solved by J.Ruickoldt, J.Jeoung, F.Lennartz, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.55 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.219, 142.219, 290.773, 90, 90, 120
R / Rfree (%)	17.8 / 20.9

The structure of A225L/F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans also contains other interesting chemical elements:

Iron

(Fe)

14 atoms

The binding sites of Nickel atom in the A225L/F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans (pdb code 8cja). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the A225L/F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 8cja:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the A225L/F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of A225L/F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni700 b:49.6 occ:0.24 NI A:RQM700 0.0 49.6 0.2 SG A:CYS546 1.9 44.8 0.2 CB A:CYS546 2.0 41.2 0.3 CB A:CYS546 2.0 41.1 0.5 CB A:CYS546 2.1 41.2 0.2 O A:OH704 2.2 49.1 1.0 S4 A:RQM700 2.3 55.0 0.7 FE2 A:RQM700 2.5 43.5 0.8 SG A:CYS546 2.6 41.7 0.3 S1 A:RQM700 2.6 55.7 0.7 O A:OH705 2.9 47.1 1.0 SG A:CYS546 2.9 44.3 0.5 CA A:CYS546 3.4 39.7 0.5 FE3 A:RQM700 3.4 48.5 0.4 CA A:CYS546 3.5 39.8 0.3 SG A:CYS316 3.6 46.5 1.0 CA A:CYS546 3.6 39.7 0.2 O A:HOH785 3.6 38.4 1.0 FE1 A:RQM700 3.9 50.4 0.4 S3 A:RQM700 3.9 58.0 0.7 N A:CYS546 4.1 39.5 0.5 N A:CYS546 4.1 39.6 0.3 N A:CYS546 4.1 38.6 0.2 FE4 A:RQM700 4.3 56.0 0.9 NZ A:LYS583 4.4 52.9 1.0 NE2 A:HIS282 4.5 48.4 1.0 C A:CYS546 4.5 39.2 0.3 C A:CYS546 4.5 39.3 0.5 C A:CYS546 4.6 40.2 0.2 CA A:GLY496 4.9 39.5 1.0

Nickel binding site 2 out of 3 in the A225L/F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of A225L/F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni801 b:35.4 occ:1.00 N B:CYS600 1.9 35.0 1.0 N B:GLY599 2.0 34.0 1.0 SG B:CYS598 2.2 36.5 1.0 SG B:CYS600 2.3 39.1 1.0 C B:GLY599 2.8 33.7 1.0 NI B:NI803 2.8 28.7 0.7 CA B:CYS600 2.9 36.5 1.0 CA B:GLY599 2.9 30.9 1.0 CB B:CYS600 3.0 38.5 1.0 CB B:CYS598 3.0 33.8 1.0 C B:CYS598 3.0 36.1 1.0 CA B:CYS598 3.3 36.3 1.0 N B:CYS598 3.6 34.5 1.0 C B:CYS600 3.6 34.0 1.0 O B:ACT804 3.7 39.8 1.0 N B:PHE601 3.7 28.8 1.0 OXT B:ACT804 3.8 38.4 1.0 CD1 B:LEU530 3.9 32.0 1.0 C B:ACT804 4.0 37.4 1.0 O B:GLY599 4.0 34.7 1.0 O B:CYS598 4.2 35.4 1.0 O B:CYS600 4.6 34.6 1.0 CD1 B:PHE232 4.6 35.8 1.0 C B:SER597 4.8 35.5 1.0 CE1 B:PHE232 4.9 37.5 1.0 S3 B:SF4802 4.9 35.7 1.0 SG B:CYS512 4.9 40.2 1.0 CA B:PHE601 5.0 34.1 1.0 CD2 B:PHE601 5.0 33.0 1.0

Nickel binding site 3 out of 3 in the A225L/F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of A225L/F231A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni803 b:28.7 occ:0.70 O B:ACT804 2.0 39.8 1.0 OXT B:ACT804 2.1 38.4 1.0 SG B:CYS512 2.3 40.2 1.0 C B:ACT804 2.3 37.4 1.0 SG B:CYS598 2.3 36.5 1.0 SG B:CYS600 2.3 39.1 1.0 NI B:NI801 2.8 35.4 1.0 CB B:CYS512 3.2 35.0 1.0 CB B:CYS598 3.3 33.8 1.0 CB B:CYS600 3.4 38.5 1.0 FE1 B:SF4802 3.8 38.1 1.0 CH3 B:ACT804 3.9 39.7 1.0 N B:CYS600 4.1 35.0 1.0 S3 B:SF4802 4.3 35.7 1.0 CD1 B:ILE149 4.3 44.2 1.0 N B:GLY599 4.4 34.0 1.0 CA B:CYS600 4.4 36.5 1.0 CA B:CYS512 4.5 40.5 1.0 CG1 B:VAL152 4.5 42.1 1.0 CA B:CYS598 4.6 36.3 1.0 C B:CYS598 4.9 36.1 1.0

J.Ruickoldt, J.Jeoung, F.Lennartz, H.Dobbek. A225L Variant of the Codh/Acs Complex of C. Hydrogenoformans To Be Published.