Nickel in PDB 7nz5: Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A

All present enzymatic activity of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A:
2.3.1.169;

The structure of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A, PDB code: 7nz5 was solved by J.Kreibich, J.H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.19 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.246, 98.811, 238.875, 90, 90, 90
R / Rfree (%)	19.3 / 22.4

The structure of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Iron	(Fe)	8 atoms
Titanium	(Ti)	1 atom

The binding sites of Nickel atom in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A (pdb code 7nz5). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A, PDB code: 7nz5:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni803 b:15.0 occ:0.90 N A:CYS600 2.1 14.1 1.0 N A:GLY599 2.2 15.5 1.0 SG A:CYS598 2.2 19.7 1.0 SG A:CYS600 2.3 16.9 1.0 CB A:CYS600 2.8 17.0 1.0 HB2 A:CYS598 2.8 18.1 1.0 ZN A:ZN802 2.9 9.2 0.6 C A:GLY599 2.9 13.8 1.0 CA A:GLY599 2.9 14.2 1.0 CA A:CYS600 2.9 12.5 1.0 CB A:CYS598 2.9 15.0 1.0 HB3 A:CYS600 3.0 20.5 1.0 C A:CYS598 3.1 19.0 1.0 H A:CYS598 3.1 19.7 1.0 HD11 A:LEU530 3.2 22.1 1.0 H A:PHE601 3.3 12.6 1.0 CA A:CYS598 3.3 16.6 1.0 HA3 A:GLY599 3.5 17.2 1.0 N A:CYS598 3.6 16.4 1.0 HA2 A:GLY599 3.6 17.2 1.0 C A:CYS600 3.7 12.8 1.0 N A:PHE601 3.7 10.4 1.0 HA A:CYS600 3.7 15.1 1.0 HD13 A:LEU530 3.8 22.1 1.0 HB2 A:CYS600 3.8 20.5 1.0 CD1 A:LEU530 3.8 18.4 1.0 HB3 A:CYS598 3.9 18.1 1.0 HD12 A:LEU530 4.0 22.1 1.0 HD1 A:PHE232 4.0 25.4 1.0 O A:GLY599 4.0 12.4 1.0 HE1 A:PHE232 4.1 22.1 1.0 O A:CYS598 4.2 18.5 1.0 HA A:CYS598 4.3 20.1 1.0 HB3 A:SER597 4.5 13.5 1.0 O A:CYS600 4.6 16.9 1.0 CD1 A:PHE232 4.7 21.1 1.0 CE1 A:PHE232 4.7 18.3 1.0 C A:SER597 4.8 16.9 1.0 HD2 A:PHE601 4.8 16.7 1.0 HD21 A:LEU530 4.9 22.7 1.0 CA A:PHE601 5.0 8.5 1.0 S1 A:SF4801 5.0 16.9 1.0 SG A:CYS512 5.0 18.2 1.0 CD2 A:PHE601 5.0 13.8 1.0

Nickel binding site 2 out of 2 in the Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Monomeric Acetyl-Coa Synthase with Zn at the Proximal Position of Cluster A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni803 b:12.2 occ:0.84 N B:CYS600 1.9 13.6 1.0 N B:GLY599 2.1 13.6 1.0 SG B:CYS598 2.2 17.3 1.0 SG B:CYS600 2.3 15.3 1.0 C B:GLY599 2.8 15.4 1.0 CA B:CYS600 2.9 15.7 1.0 ZN B:ZN802 2.9 6.3 0.5 CA B:GLY599 2.9 13.2 1.0 CB B:CYS600 2.9 13.2 1.0 CB B:CYS598 3.1 11.9 1.0 HD11 B:LEU530 3.1 17.0 1.0 C B:CYS598 3.2 13.8 1.0 HB3 B:CYS600 3.2 15.9 1.0 HB2 B:CYS598 3.2 14.4 1.0 H B:CYS598 3.4 16.7 1.0 H B:PHE601 3.4 19.2 1.0 CA B:CYS598 3.5 7.4 1.0 HA3 B:GLY599 3.5 16.0 1.0 HA2 B:GLY599 3.6 16.0 1.0 HA B:CYS600 3.6 19.0 1.0 C B:CYS600 3.7 15.0 1.0 N B:PHE601 3.8 15.9 1.0 N B:CYS598 3.8 13.8 1.0 HB2 B:CYS600 3.8 15.9 1.0 CD1 B:LEU530 3.9 14.1 1.0 HD1 B:PHE232 3.9 19.2 1.0 O B:GLY599 4.0 15.4 1.0 HD13 B:LEU530 4.0 17.0 1.0 HB3 B:CYS598 4.0 14.4 1.0 HD12 B:LEU530 4.0 17.0 1.0 O B:CYS598 4.3 14.0 1.0 HE1 B:PHE232 4.4 23.3 1.0 HA B:CYS598 4.4 9.0 1.0 HD2 B:PHE601 4.6 13.8 1.0 CD1 B:PHE232 4.6 15.9 1.0 O B:CYS600 4.6 17.2 1.0 HB3 B:SER597 4.7 16.7 1.0 CD2 B:PHE601 4.8 11.4 1.0 CE1 B:PHE232 4.9 19.3 1.0 S1 B:SF4801 4.9 16.5 1.0 CA B:PHE601 5.0 13.9 1.0 C B:SER597 5.0 15.3 1.0

J.Kreibich, J.H.Jeoung, H.Dobbek. Ligand Binding at the Ni,Ni-[4FE-4S] Cluster of Acetyl-Coa Synthase To Be Published.