Zinc in PDB 9hnf: Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Acetoacetate and Acetyl-Coa

The structure of Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Acetoacetate and Acetyl-Coa, PDB code: 9hnf was solved by D.G.Marchal, J.Zarzycki, T.J.Erb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.69 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	80.9, 138.48, 136.36, 90, 90, 90
R / Rfree (%)	17.5 / 19.2

The binding sites of Zinc atom in the Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Acetoacetate and Acetyl-Coa (pdb code 9hnf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Acetoacetate and Acetyl-Coa, PDB code: 9hnf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Acetoacetate and Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Acetoacetate and Acetyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:33.8 occ:1.00 O1 A:AAE402 2.0 31.5 1.0 OE2 A:GLU258 2.0 30.0 1.0 O8 A:AAE402 2.1 34.7 1.0 NE2 A:HIS51 2.3 33.0 1.0 NE2 A:HIS49 2.3 31.0 1.0 O A:ACO401 2.8 40.6 0.9 CD2 A:HIS49 3.0 30.3 1.0 CD A:GLU258 3.0 31.1 1.0 C5 A:AAE402 3.0 36.1 1.0 C2 A:AAE402 3.1 34.6 1.0 CE1 A:HIS51 3.2 34.6 1.0 CD2 A:HIS51 3.2 31.2 1.0 OE1 A:GLU258 3.3 31.5 1.0 CE1 A:HIS49 3.4 35.1 1.0 C4 A:AAE402 3.5 37.2 1.0 C A:ACO401 3.8 39.6 0.9 NH2 A:ARG254 4.0 28.2 1.0 O A:HOH524 4.0 30.3 1.0 OG1 A:THR85 4.0 35.2 1.0 O3 A:AAE402 4.2 35.4 1.0 NH1 A:ARG254 4.2 30.1 1.0 CG A:HIS49 4.2 33.1 1.0 ND1 A:HIS51 4.3 35.2 1.0 CG A:HIS51 4.3 33.6 1.0 C2P A:ACO401 4.4 37.7 0.9 C9 A:AAE402 4.4 34.4 1.0 CG A:GLU258 4.4 32.0 1.0 ND1 A:HIS49 4.4 34.6 1.0 CB A:THR85 4.5 34.5 1.0 CZ A:ARG254 4.6 34.3 1.0 S1P A:ACO401 4.7 42.3 0.9 CA A:GLY15 4.9 29.0 1.0 CH3 A:ACO401 4.9 37.8 0.9

Zinc binding site 2 out of 2 in the Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Acetoacetate and Acetyl-Coa


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Acetoacetate and Acetyl-Coa within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:37.3 occ:1.00 OE2 B:GLU258 2.0 34.3 1.0 O1 B:AAE402 2.1 37.2 1.0 O8 B:AAE402 2.2 37.7 1.0 NE2 B:HIS49 2.3 36.1 1.0 NE2 B:HIS51 2.3 33.7 1.0 CD B:GLU258 3.0 34.3 1.0 C2 B:AAE402 3.1 41.4 1.0 CE1 B:HIS51 3.1 38.9 1.0 C5 B:AAE402 3.1 41.3 1.0 CD2 B:HIS49 3.2 34.1 1.0 CD2 B:HIS51 3.3 35.6 1.0 OE1 B:GLU258 3.3 32.0 1.0 CE1 B:HIS49 3.3 39.8 1.0 C4 B:AAE402 3.6 45.7 1.0 NH2 B:ARG254 3.9 33.1 1.0 O B:HOH552 4.0 37.7 1.0 OG1 B:THR85 4.1 37.2 1.0 O3 B:AAE402 4.2 40.8 1.0 ND1 B:HIS51 4.3 37.2 1.0 CG B:HIS49 4.3 36.0 1.0 CG B:HIS51 4.4 37.1 1.0 ND1 B:HIS49 4.4 40.6 1.0 CG B:GLU258 4.4 32.3 1.0 C2P B:ACO401 4.4 54.5 0.8 O B:ACO401 4.5 59.4 0.8 C9 B:AAE402 4.5 42.5 1.0 NH1 B:ARG254 4.5 34.5 1.0 CB B:THR85 4.5 38.6 1.0 CZ B:ARG254 4.7 35.0 1.0 C B:ACO401 4.8 59.8 0.8 CA B:GLY15 4.8 31.2 1.0 S1P B:ACO401 4.9 61.2 0.8

A.Satanowski, D.G.Marchal, A.Perret, J.L.Petit, M.Bouzon, V.Doring, I.Dubois, H.He, E.N.Smith, V.Pellouin, H.M.Petri, V.Rainaldi, M.Nattermann, S.Burgener, N.Paczia, J.Zarzycki, M.Heinemann, A.Bar-Even, T.J.Erb. Design and Implementation of Aerobic and Ambient Co 2 -Reduction As An Entry-Point For Enhanced Carbon Fixation. Nat Commun V. 16 3134 2025.
ISSN: ESSN 2041-1723
PubMed: 40169551
DOI: 10.1038/S41467-025-57549-4