Zinc in PDB 7yxm: Benzoylsuccinyl-Coa Thiolase with Coenzyme A

The structure of Benzoylsuccinyl-Coa Thiolase with Coenzyme A, PDB code: 7yxm was solved by U.Ermler, J.Heider, S.Weidenweber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.67 / 1.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.34, 117.34, 228, 90, 90, 90
R / Rfree (%)	15.8 / 18.1

The structure of Benzoylsuccinyl-Coa Thiolase with Coenzyme A also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Zinc atom in the Benzoylsuccinyl-Coa Thiolase with Coenzyme A (pdb code 7yxm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Benzoylsuccinyl-Coa Thiolase with Coenzyme A, PDB code: 7yxm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Benzoylsuccinyl-Coa Thiolase with Coenzyme A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Benzoylsuccinyl-Coa Thiolase with Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:36.9 occ:1.00 SG A:CYS58 2.1 37.5 1.0 SG A:CYS45 2.3 38.6 1.0 SG A:CYS42 2.4 38.2 1.0 SG A:CYS55 2.4 34.2 1.0 CB A:CYS42 3.1 36.6 1.0 CB A:CYS55 3.2 32.6 1.0 CB A:CYS45 3.2 37.8 1.0 CB A:CYS58 3.3 40.6 1.0 N A:CYS45 3.8 40.9 1.0 N A:CYS58 3.8 36.0 1.0 CA A:CYS45 4.0 38.4 1.0 CA A:CYS58 4.1 34.8 1.0 CB A:SER60 4.5 42.8 1.0 CB A:ASN57 4.5 37.9 1.0 CA A:CYS42 4.6 36.6 1.0 ND2 A:ASN57 4.6 40.9 1.0 CA A:CYS55 4.6 31.6 1.0 C A:CYS58 4.6 36.9 1.0 C A:CYS45 4.7 44.5 1.0 CB A:GLN47 4.7 38.1 1.0 N A:GLY46 4.7 38.6 1.0 C A:ASN57 4.8 38.1 1.0 CB A:LYS44 4.8 43.0 1.0 N A:TRP59 4.8 33.5 1.0 N A:GLN47 4.8 38.8 1.0 N A:SER60 4.8 36.9 1.0 C A:LYS44 4.8 45.7 1.0 O A:HOH366 4.9 42.5 1.0

Zinc binding site 2 out of 2 in the Benzoylsuccinyl-Coa Thiolase with Coenzyme A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Benzoylsuccinyl-Coa Thiolase with Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:31.0 occ:1.00 SG C:CYS45 2.3 30.9 1.0 SG C:CYS58 2.3 30.2 1.0 SG C:CYS42 2.3 33.1 1.0 SG C:CYS55 2.4 30.5 1.0 CB C:CYS55 3.1 27.6 1.0 CB C:CYS42 3.2 31.0 1.0 CB C:CYS45 3.2 34.7 1.0 CB C:CYS58 3.4 31.1 1.0 N C:CYS58 3.8 30.9 1.0 N C:CYS45 3.9 33.5 1.0 CA C:CYS45 4.1 35.9 1.0 CA C:CYS58 4.1 35.0 1.0 CB C:SER60 4.5 48.5 1.0 CB C:ASN57 4.5 30.0 1.0 CA C:CYS55 4.6 29.5 1.0 CA C:CYS42 4.6 32.1 1.0 C C:CYS58 4.7 30.1 1.0 C C:ASN57 4.7 28.8 1.0 N C:SER60 4.8 33.3 1.0 C C:CYS45 4.8 33.0 1.0 CB C:LYS44 4.8 40.9 1.0 N C:TRP59 4.8 29.8 1.0 ND2 C:ASN57 4.8 38.5 1.0 CB C:GLN47 4.9 26.6 1.0 O C:HOH360 4.9 29.9 1.0 C C:LYS44 4.9 33.2 1.0 N C:GLY46 4.9 30.6 1.0 N C:ASN57 5.0 31.0 1.0 CA C:ASN57 5.0 28.7 1.0

S.Weidenweber, K.Schuhle, M.L.Lippert, J.Mock, A.Seubert, U.Demmer, U.Ermler, J.Heider. Finis Tolueni: A New Type of Thiolase with An Integrated Zn-Finger Subunit Catalyzes the Final Step of Anaerobic Toluene Metabolism. Febs J. V. 289 5599 2022.
ISSN: ISSN 1742-464X
PubMed: 35313080
DOI: 10.1111/FEBS.16443