Nickel in PDB 3s2x: Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain

All present enzymatic activity of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain:
2.3.1.169;

The structure of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain, PDB code: 3s2x was solved by P.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.60 / 2.35
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	129.040, 129.040, 46.030, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 26.4

The binding sites of Nickel atom in the Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain (pdb code 3s2x). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain, PDB code: 3s2x:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni200 b:61.9 occ:1.00 N A:CYS4 1.9 55.2 1.0 SG A:CYS2 2.2 57.8 1.0 N A:GLY3 2.2 59.0 1.0 SG A:CYS4 2.4 57.1 1.0 CA A:CYS4 2.8 53.8 1.0 CB A:CYS4 2.8 54.2 1.0 C A:GLY3 2.9 57.6 1.0 CB A:CYS2 2.9 59.1 1.0 CA A:GLY3 3.1 57.9 1.0 C A:CYS2 3.2 59.4 1.0 N A:PHE5 3.4 51.7 1.0 CA A:CYS2 3.5 60.4 1.0 C A:CYS4 3.5 53.0 1.0 NI A:NI201 3.6 66.8 1.0 N A:CYS2 3.8 62.2 1.0 O A:HOH139 3.8 46.0 1.0 O A:GLY3 4.0 58.4 1.0 CD1 A:PHE5 4.1 53.8 1.0 O A:CYS2 4.4 61.3 1.0 CE1 A:PHE5 4.6 54.4 1.0 O A:CYS4 4.6 53.0 1.0 CA A:PHE5 4.6 51.8 1.0 CG A:PHE5 4.9 53.2 1.0 CB A:PHE5 4.9 51.8 1.0 C A:SER1 5.0 63.2 1.0

Nickel binding site 2 out of 4 in the Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:66.8 occ:1.00 N A:CYS2 2.1 62.2 1.0 N A:SER1 2.2 61.1 1.0 SG A:CYS2 2.4 57.8 1.0 O A:HOH139 2.7 46.0 1.0 CA A:SER1 2.8 62.9 1.0 C A:SER1 2.8 63.2 1.0 CA A:CYS2 3.2 60.4 1.0 CB A:CYS2 3.4 59.1 1.0 CD1 A:PHE5 3.5 53.8 1.0 NI A:NI200 3.6 61.9 1.0 O A:SER1 4.0 64.4 1.0 C A:CYS2 4.1 59.4 1.0 N A:GLY3 4.1 59.0 1.0 CB A:SER1 4.2 63.5 1.0 CE1 A:PHE5 4.2 54.4 1.0 O A:GLY53 4.4 53.6 1.0 CG A:PHE5 4.4 53.2 1.0 CB A:PHE5 4.5 51.8 1.0 SG A:CYS4 4.7 57.1 1.0 N A:PHE5 4.8 51.7 1.0 OG A:SER1 4.9 64.3 1.0 C A:GLY53 5.0 54.1 1.0

Nickel binding site 3 out of 4 in the Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni202 b:61.6 occ:1.00 N B:CYS4 2.1 57.3 1.0 SG B:CYS2 2.2 60.5 1.0 SG B:CYS4 2.4 61.2 1.0 N B:GLY3 2.4 59.8 1.0 CB B:CYS4 2.9 56.1 1.0 CA B:CYS4 2.9 56.0 1.0 CB B:CYS2 3.0 60.8 1.0 C B:GLY3 3.1 58.0 1.0 CA B:GLY3 3.3 58.4 1.0 C B:CYS2 3.3 61.2 1.0 N B:PHE5 3.4 53.4 1.0 NI B:NI203 3.4 70.9 1.0 CA B:CYS2 3.4 62.0 1.0 C B:CYS4 3.6 54.4 1.0 N B:CYS2 3.6 65.0 1.0 CD1 B:PHE5 4.0 53.9 1.0 O B:GLY3 4.2 57.2 1.0 O B:CYS2 4.4 61.4 1.0 CE1 B:PHE5 4.6 54.2 1.0 CA B:PHE5 4.7 53.7 1.0 O B:CYS4 4.7 52.8 1.0 CG B:PHE5 4.9 53.3 1.0 C B:SER1 4.9 66.4 1.0

Nickel binding site 4 out of 4 in the Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of Acetyl-Coenzyme A Synthase Alpha Subunit C-Terminal Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni203 b:70.9 occ:1.00 N B:SER1 2.1 66.4 1.0 N B:CYS2 2.2 65.0 1.0 SG B:CYS2 2.4 60.5 1.0 CA B:SER1 2.9 66.5 1.0 C B:SER1 2.9 66.4 1.0 CA B:CYS2 3.3 62.0 1.0 CB B:CYS2 3.3 60.8 1.0 CD1 B:PHE5 3.4 53.9 1.0 NI B:NI202 3.4 61.6 1.0 O B:SER1 4.0 68.2 1.0 CE1 B:PHE5 4.1 54.2 1.0 N B:GLY3 4.1 59.8 1.0 C B:CYS2 4.2 61.2 1.0 CB B:SER1 4.3 68.2 1.0 CG B:PHE5 4.4 53.3 1.0 CB B:PHE5 4.5 53.2 1.0 O B:GLY53 4.5 48.1 1.0 SG B:CYS4 4.5 61.2 1.0 N B:PHE5 4.7 53.4 1.0

Y.Liu, F.Wang, P.Li, X.Tan. Insights Into the Mechanistic Role of the [Fe(4) S(4) ] Cubane in the A-Cluster {[Fe(4) S(4) ]-(Sr)-[Ni(P) Ni(D) ]} of Acetyl-Coenzyme A Synthase. Chembiochem V. 12 1417 2011.
ISSN: ISSN 1439-4227
PubMed: 21626638
DOI: 10.1002/CBIC.201100101