Nickel in PDB 7nyp: Monomeric Acetyl-Coa Synthase in Closed Conformation

All present enzymatic activity of Monomeric Acetyl-Coa Synthase in Closed Conformation:
2.3.1.169;

The structure of Monomeric Acetyl-Coa Synthase in Closed Conformation, PDB code: 7nyp 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)	46.43 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.95, 99.478, 238.289, 90, 90, 90
R / Rfree (%)	19.9 / 24.4

The structure of Monomeric Acetyl-Coa Synthase in Closed Conformation also contains other interesting chemical elements:

Titanium	(Ti)	2 atoms
Iron	(Fe)	8 atoms

The binding sites of Nickel atom in the Monomeric Acetyl-Coa Synthase in Closed Conformation (pdb code 7nyp). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Monomeric Acetyl-Coa Synthase in Closed Conformation, PDB code: 7nyp:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Monomeric Acetyl-Coa Synthase in Closed Conformation


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 in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni801 b:27.2 occ:1.00 SG A:CYS512 2.2 28.7 1.0 SG A:CYS598 2.4 28.0 1.0 SG A:CYS600 2.4 29.6 1.0 O A:HOH1282 2.4 26.9 1.0 NI A:NI802 2.9 27.4 1.0 HB3 A:CYS512 2.9 36.7 1.0 HB3 A:CYS600 3.1 35.4 1.0 CB A:CYS512 3.2 30.5 1.0 HB2 A:CYS598 3.3 34.2 1.0 CB A:CYS600 3.4 29.4 1.0 CB A:CYS598 3.5 28.4 1.0 HG11 A:VAL152 3.5 36.2 1.0 HD12 A:ILE149 3.6 31.6 1.0 HB2 A:CYS512 3.7 36.7 1.0 FE4 A:SF4803 3.9 28.6 1.0 HD13 A:ILE149 4.0 31.6 1.0 HB3 A:CYS598 4.0 34.2 1.0 HB2 A:CYS600 4.0 35.4 1.0 N A:CYS600 4.2 23.6 1.0 CD1 A:ILE149 4.2 26.3 1.0 HA A:CYS512 4.3 40.1 1.0 HD1 A:PHE232 4.3 29.1 1.0 CA A:CYS512 4.4 33.4 1.0 HA A:ILE149 4.4 33.4 1.0 S1 A:SF4803 4.4 27.3 1.0 HG21 A:VAL152 4.4 37.2 1.0 CA A:CYS600 4.4 28.3 1.0 CG1 A:VAL152 4.5 30.1 1.0 HE1 A:PHE232 4.5 30.7 1.0 N A:GLY599 4.6 25.8 1.0 HG13 A:VAL152 4.7 36.2 1.0 CA A:CYS598 4.7 27.9 1.0 HD11 A:LEU530 4.7 32.8 1.0 HD11 A:ILE149 4.7 31.6 1.0 CD1 A:PHE232 4.7 24.1 1.0 CE1 A:PHE232 4.8 25.5 1.0 H A:CYS598 4.8 32.5 1.0 HG12 A:VAL152 4.9 36.2 1.0 C A:CYS598 4.9 31.2 1.0 HB A:ILE149 4.9 38.0 1.0

Nickel binding site 2 out of 4 in the Monomeric Acetyl-Coa Synthase in Closed Conformation


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 in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni802 b:27.4 occ:1.00 N A:CYS600 2.1 23.6 1.0 N A:GLY599 2.1 25.8 1.0 SG A:CYS598 2.4 28.0 1.0 SG A:CYS600 2.4 29.6 1.0 NI A:NI801 2.9 27.2 1.0 C A:GLY599 2.9 24.0 1.0 CA A:GLY599 3.0 23.7 1.0 CA A:CYS600 3.0 28.3 1.0 H A:CYS598 3.0 32.5 1.0 C A:CYS598 3.0 31.2 1.0 CB A:CYS600 3.0 29.4 1.0 CB A:CYS598 3.1 28.4 1.0 HD11 A:LEU530 3.2 32.8 1.0 HB2 A:CYS598 3.2 34.2 1.0 HB3 A:CYS600 3.2 35.4 1.0 CA A:CYS598 3.3 27.9 1.0 H A:PHE601 3.4 25.7 1.0 HA3 A:GLY599 3.5 28.6 1.0 N A:CYS598 3.5 27.0 1.0 C A:CYS600 3.7 25.0 1.0 HD1 A:PHE232 3.7 29.1 1.0 HE1 A:PHE232 3.7 30.7 1.0 HA2 A:GLY599 3.7 28.6 1.0 N A:PHE601 3.7 21.4 1.0 HA A:CYS600 3.8 34.1 1.0 CD1 A:LEU530 3.9 27.2 1.0 HB2 A:CYS600 4.0 35.4 1.0 HB3 A:CYS598 4.0 34.2 1.0 HD12 A:LEU530 4.0 32.8 1.0 O A:HOH1282 4.0 26.9 1.0 HD13 A:LEU530 4.0 32.8 1.0 O A:GLY599 4.0 21.4 1.0 O A:CYS598 4.1 27.0 1.0 HA A:CYS598 4.3 33.5 1.0 CD1 A:PHE232 4.3 24.1 1.0 CE1 A:PHE232 4.3 25.5 1.0 HD2 A:PHE601 4.5 31.3 1.0 O A:CYS600 4.6 25.4 1.0 C A:SER597 4.8 27.2 1.0 CD2 A:PHE601 4.8 26.1 1.0 SG A:CYS512 4.8 28.7 1.0 HB3 A:SER597 4.9 29.9 1.0 HB3 A:CYS512 4.9 36.7 1.0 S1 A:SF4803 5.0 27.3 1.0

Nickel binding site 3 out of 4 in the Monomeric Acetyl-Coa Synthase in Closed Conformation


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Monomeric Acetyl-Coa Synthase in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni802 b:29.6 occ:1.00 SG B:CYS512 2.2 25.8 1.0 O B:HOH1309 2.4 19.7 1.0 SG B:CYS598 2.4 29.4 1.0 SG B:CYS600 2.4 28.1 1.0 NI B:NI803 2.8 20.8 1.0 HB3 B:CYS512 3.0 31.5 1.0 HB3 B:CYS600 3.1 38.3 1.0 HB2 B:CYS598 3.2 31.6 1.0 CB B:CYS512 3.3 26.2 1.0 CB B:CYS600 3.4 31.8 1.0 CB B:CYS598 3.5 26.3 1.0 HG11 B:VAL152 3.5 31.1 1.0 HD12 B:ILE149 3.6 40.5 1.0 HD13 B:ILE149 3.7 40.5 1.0 HB2 B:CYS512 3.8 31.5 1.0 FE4 B:SF4804 3.9 29.4 1.0 HB3 B:CYS598 4.0 31.6 1.0 HB2 B:CYS600 4.0 38.3 1.0 CD1 B:ILE149 4.1 33.7 1.0 HD1 B:PHE232 4.2 27.1 1.0 N B:CYS600 4.2 26.8 1.0 S1 B:SF4804 4.3 26.8 1.0 HA B:CYS512 4.3 26.8 1.0 HG21 B:VAL152 4.4 29.7 1.0 HE1 B:PHE232 4.4 27.9 1.0 CG1 B:VAL152 4.4 25.8 1.0 CA B:CYS600 4.4 27.4 1.0 HA B:ILE149 4.4 34.2 1.0 CA B:CYS512 4.5 22.2 1.0 HD11 B:ILE149 4.5 40.5 1.0 HG13 B:VAL152 4.5 31.1 1.0 H B:GLY599 4.6 27.0 1.0 N B:GLY599 4.6 22.4 1.0 CD1 B:PHE232 4.7 22.5 1.0 CA B:CYS598 4.7 27.1 1.0 CE1 B:PHE232 4.8 23.1 1.0 C B:CYS598 4.9 23.0 1.0 HG12 B:VAL152 4.9 31.1 1.0 H B:CYS598 4.9 34.0 1.0 HB3 B:CYS531 5.0 38.6 1.0 HD11 B:LEU530 5.0 30.1 1.0 HB B:ILE149 5.0 38.4 1.0

Nickel binding site 4 out of 4 in the Monomeric Acetyl-Coa Synthase in Closed Conformation


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Monomeric Acetyl-Coa Synthase in Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni803 b:20.8 occ:1.00 H B:GLY599 2.0 27.0 1.0 N B:CYS600 2.1 26.8 1.0 SG B:CYS598 2.2 29.4 1.0 N B:GLY599 2.3 22.4 1.0 SG B:CYS600 2.4 28.1 1.0 NI B:NI802 2.8 29.6 1.0 C B:GLY599 2.9 25.2 1.0 CB B:CYS600 2.9 31.8 1.0 CA B:CYS600 3.0 27.4 1.0 CA B:GLY599 3.0 26.1 1.0 C B:CYS598 3.1 23.0 1.0 HB3 B:CYS600 3.1 38.3 1.0 CB B:CYS598 3.1 26.3 1.0 H B:CYS598 3.2 34.0 1.0 HB2 B:CYS598 3.2 31.6 1.0 HD11 B:LEU530 3.3 30.1 1.0 CA B:CYS598 3.4 27.1 1.0 H B:PHE601 3.4 29.3 1.0 HA3 B:GLY599 3.5 31.4 1.0 C B:CYS600 3.6 27.3 1.0 N B:CYS598 3.7 28.2 1.0 HD1 B:PHE232 3.7 27.1 1.0 N B:PHE601 3.7 24.4 1.0 HE1 B:PHE232 3.7 27.9 1.0 HA B:CYS600 3.8 33.0 1.0 HA2 B:GLY599 3.8 31.4 1.0 HB2 B:CYS600 3.9 38.3 1.0 HD12 B:LEU530 3.9 30.1 1.0 HB3 B:CYS598 4.0 31.6 1.0 CD1 B:LEU530 4.0 25.0 1.0 O B:HOH1309 4.0 19.7 1.0 O B:GLY599 4.1 24.8 1.0 O B:CYS598 4.2 24.9 1.0 HD13 B:LEU530 4.3 30.1 1.0 HA B:CYS598 4.3 32.7 1.0 CD1 B:PHE232 4.4 22.5 1.0 CE1 B:PHE232 4.4 23.1 1.0 O B:CYS600 4.5 28.2 1.0 SG B:CYS512 4.7 25.8 1.0 S1 B:SF4804 4.8 26.8 1.0 HD2 B:PHE601 4.8 31.1 1.0 C B:SER597 4.9 30.1 1.0 CA B:PHE601 4.9 25.2 1.0 HA B:PHE601 4.9 30.3 1.0 HB3 B:CYS512 5.0 31.5 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.