Nickel in PDB 8cjc: F515A Variant of the Codh/Acs Complex of C. Hydrogenoformans

All present enzymatic activity of F515A Variant of the Codh/Acs Complex of C. Hydrogenoformans:
1.2.7.4; 2.3.1.169;

The structure of F515A Variant of the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 8cjc 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)	45.00 / 2.22
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	142.13, 142.13, 290.72, 90, 90, 120
R / Rfree (%)	15.8 / 20.2

The structure of F515A Variant of the Codh/Acs Complex of C. Hydrogenoformans also contains other interesting chemical elements:

Iron	(Fe)	14 atoms
Sodium	(Na)	1 atom

The binding sites of Nickel atom in the F515A Variant of the Codh/Acs Complex of C. Hydrogenoformans (pdb code 8cjc). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the F515A Variant of the Codh/Acs Complex of C. Hydrogenoformans, PDB code: 8cjc:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the F515A 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 F515A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni701 b:33.8 occ:0.18 NI A:RQM701 0.0 33.8 0.2 SG A:CYS546 1.9 34.8 0.6 O A:OH705 2.0 28.2 1.0 CB A:CYS546 2.0 29.4 0.4 O A:OH704 2.4 39.0 1.0 FE2 A:RQM701 2.4 36.5 0.8 S4 A:RQM701 2.4 45.0 0.8 CB A:CYS546 2.4 28.6 0.6 SG A:CYS546 2.5 35.4 0.4 S1 A:RQM701 2.6 39.8 0.7 SG A:CYS316 3.5 33.2 1.0 FE3 A:RQM701 3.6 31.1 0.5 CA A:CYS546 3.6 27.7 0.4 O A:HOH802 3.8 37.5 1.0 CA A:CYS546 3.9 27.5 0.6 FE1 A:RQM701 3.9 28.5 0.5 NZ A:LYS583 4.0 39.1 1.0 S3 A:RQM701 4.0 37.1 0.8 NE2 A:HIS282 4.2 37.1 1.0 FE4 A:RQM701 4.2 37.7 0.8 O A:HOH987 4.2 26.3 1.0 N A:CYS546 4.2 26.9 0.4 N A:CYS546 4.3 26.9 0.6 C A:CYS546 4.6 27.5 0.4 CE A:LYS583 4.9 34.0 1.0 C A:CYS546 4.9 27.3 0.6

Nickel binding site 2 out of 3 in the F515A 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 F515A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni801 b:25.9 occ:1.00 N B:CYS600 2.0 29.8 1.0 N B:GLY599 2.1 29.1 1.0 SG B:CYS598 2.2 27.9 1.0 SG B:CYS600 2.3 30.9 1.0 C B:GLY599 2.8 25.9 1.0 NI B:NI803 2.9 39.2 1.0 CA B:CYS600 2.9 30.1 1.0 CA B:GLY599 2.9 26.8 1.0 CB B:CYS600 2.9 31.2 1.0 CB B:CYS598 3.0 31.5 1.0 C B:CYS598 3.1 28.9 1.0 CA B:CYS598 3.3 30.7 1.0 N B:CYS598 3.6 28.1 1.0 C B:CYS600 3.7 27.6 1.0 N B:PHE601 3.8 21.7 1.0 CD1 B:LEU530 4.0 20.0 1.0 O B:GLY599 4.0 28.2 1.0 OXT B:ACT804 4.0 35.8 1.0 O B:ACT804 4.2 41.0 1.0 O B:CYS598 4.2 28.8 1.0 C B:ACT804 4.4 37.9 1.0 CD1 B:PHE232 4.5 29.2 1.0 O B:CYS600 4.6 26.1 1.0 CE1 B:PHE232 4.6 29.2 1.0 C B:SER597 4.8 28.6 1.0 CD2 B:PHE601 4.8 24.5 1.0 S3 B:SF4802 5.0 25.5 1.0

Nickel binding site 3 out of 3 in the F515A 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 F515A Variant of the Codh/Acs Complex of C. Hydrogenoformans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni803 b:39.2 occ:1.00 OXT B:ACT804 2.3 35.8 1.0 SG B:CYS512 2.4 34.5 1.0 SG B:CYS600 2.4 30.9 1.0 SG B:CYS598 2.4 27.9 1.0 O B:ACT804 2.5 41.0 1.0 C B:ACT804 2.7 37.9 1.0 NI B:NI801 2.9 25.9 1.0 CB B:CYS512 3.2 31.1 1.0 CB B:CYS598 3.3 31.5 1.0 CB B:CYS600 3.4 31.2 1.0 CD1 B:ILE149 3.7 41.4 1.0 FE1 B:SF4802 3.7 29.1 1.0 S3 B:SF4802 4.2 25.5 1.0 N B:CYS600 4.2 29.8 1.0 CH3 B:ACT804 4.2 37.5 1.0 CG1 B:ILE149 4.3 47.4 1.0 CA B:CYS512 4.5 33.2 1.0 CA B:CYS600 4.5 30.1 1.0 N B:GLY599 4.5 29.1 1.0 CA B:CYS598 4.6 30.7 1.0 C B:CYS598 5.0 28.9 1.0

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