Zinc in PDB 8rip: Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Malonate and Coenzyme A

The structure of Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Malonate and Coenzyme A, PDB code: 8rip 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)	29.99 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.155, 134.35, 140.848, 90, 90, 90
R / Rfree (%)	15.8 / 17.8

The binding sites of Zinc atom in the Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Malonate and Coenzyme A (pdb code 8rip). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Malonate and Coenzyme A, PDB code: 8rip:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Malonate and Coenzyme A


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 Malonate and Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:25.6 occ:1.00 NE2 A:HIS49 2.1 22.4 1.0 OE2 A:GLU258 2.1 23.8 1.0 NE2 A:HIS51 2.2 24.9 1.0 O6 A:MLI401 2.2 23.4 1.0 O8 A:MLI401 2.2 25.3 1.0 O A:HOH679 2.8 47.1 1.0 CD A:GLU258 3.0 24.8 1.0 C3 A:MLI401 3.0 29.2 1.0 CD2 A:HIS49 3.1 22.2 1.0 CE1 A:HIS49 3.1 25.9 1.0 CE1 A:HIS51 3.1 24.2 1.0 C2 A:MLI401 3.1 24.4 1.0 OE1 A:GLU258 3.2 22.5 1.0 CD2 A:HIS51 3.2 22.1 1.0 C1 A:MLI401 3.4 26.8 1.0 O A:HOH637 3.9 25.1 1.0 NH2 A:ARG254 4.0 25.8 1.0 O9 A:MLI401 4.0 32.0 1.0 OG1 A:THR85 4.2 23.2 1.0 ND1 A:HIS49 4.2 25.8 1.0 CG A:HIS49 4.2 22.9 1.0 ND1 A:HIS51 4.2 25.1 1.0 O7 A:MLI401 4.3 25.8 1.0 CG A:HIS51 4.3 24.4 1.0 CG A:GLU258 4.4 20.8 1.0 CB A:THR85 4.5 23.1 1.0 NH1 A:ARG254 4.5 24.2 1.0 CZ A:ARG254 4.7 24.1 1.0 CA A:GLY15 4.8 22.0 1.0 O A:HOH575 4.8 34.4 1.0

Zinc binding site 2 out of 4 in the Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Malonate and Coenzyme A


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 Malonate and Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:25.8 occ:1.00 OE2 B:GLU258 2.1 24.6 1.0 NE2 B:HIS51 2.1 22.2 1.0 NE2 B:HIS49 2.1 23.7 1.0 O7 B:MLI401 2.2 24.9 1.0 O9 B:MLI401 2.2 25.8 1.0 O B:HOH608 2.4 35.5 1.0 CD B:GLU258 3.0 22.1 1.0 CE1 B:HIS51 3.0 22.3 1.0 C3 B:MLI401 3.0 30.5 1.0 CD2 B:HIS49 3.0 23.2 1.0 C2 B:MLI401 3.1 24.1 1.0 CE1 B:HIS49 3.1 26.8 1.0 CD2 B:HIS51 3.1 23.4 1.0 OE1 B:GLU258 3.2 23.8 1.0 C1 B:MLI401 3.4 28.5 1.0 O B:HOH631 3.9 23.5 1.0 NH2 B:ARG254 4.0 25.8 1.0 O8 B:MLI401 4.1 32.9 1.0 OG1 B:THR85 4.1 23.7 1.0 ND1 B:HIS51 4.1 22.6 1.0 CG B:HIS49 4.2 23.6 1.0 ND1 B:HIS49 4.2 27.0 1.0 O6 B:MLI401 4.2 25.8 1.0 CG B:HIS51 4.2 22.6 1.0 CG B:GLU258 4.4 21.9 1.0 CB B:THR85 4.5 22.2 1.0 NH1 B:ARG254 4.6 26.6 1.0 CA B:GLY15 4.7 21.9 1.0 CZ B:ARG254 4.7 25.2 1.0

Zinc binding site 3 out of 4 in the Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Malonate and Coenzyme A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Malonate and Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:27.4 occ:1.00 OE2 C:GLU258 2.1 26.6 1.0 NE2 C:HIS49 2.1 26.8 1.0 NE2 C:HIS51 2.2 24.6 1.0 O8 C:MLI401 2.3 29.6 1.0 O6 C:MLI401 2.3 27.2 1.0 O C:HOH557 2.3 35.0 1.0 CD C:GLU258 3.0 26.5 1.0 CE1 C:HIS49 3.0 31.5 1.0 C3 C:MLI401 3.0 34.0 1.0 CE1 C:HIS51 3.1 25.6 1.0 CD2 C:HIS49 3.1 26.1 1.0 C2 C:MLI401 3.2 30.3 1.0 OE1 C:GLU258 3.2 26.4 1.0 CD2 C:HIS51 3.2 24.8 1.0 C1 C:MLI401 3.4 31.1 1.0 NH2 C:ARG254 3.8 27.1 1.0 O C:HOH610 4.0 28.1 1.0 O9 C:MLI401 4.0 36.9 1.0 OG1 C:THR85 4.1 26.0 1.0 ND1 C:HIS49 4.2 32.9 1.0 CG C:HIS49 4.2 27.3 1.0 ND1 C:HIS51 4.2 25.5 1.0 CG C:HIS51 4.3 24.9 1.0 O7 C:MLI401 4.3 29.6 1.0 CG C:GLU258 4.4 23.3 1.0 CB C:THR85 4.5 27.5 1.0 NH1 C:ARG254 4.7 27.6 1.0 CZ C:ARG254 4.7 26.1 1.0 CA C:GLY15 4.7 23.4 1.0 O C:HOH585 4.9 43.5 1.0 O C:HOH696 4.9 43.3 1.0

Zinc binding site 4 out of 4 in the Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Malonate and Coenzyme A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Beta-Keto Acid Cleavage Enzyme From Paracoccus Denitrificans with Bound Malonate and Coenzyme A within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:25.9 occ:1.00 OE2 D:GLU258 2.1 27.3 1.0 NE2 D:HIS49 2.1 23.9 1.0 NE2 D:HIS51 2.2 25.0 1.0 O8 D:MLI401 2.2 28.5 1.0 O7 D:MLI401 2.2 24.3 1.0 O D:HOH551 2.5 35.2 1.0 CD D:GLU258 2.9 23.9 1.0 C3 D:MLI401 3.0 33.4 1.0 CE1 D:HIS49 3.1 29.2 1.0 CE1 D:HIS51 3.1 23.6 1.0 CD2 D:HIS49 3.1 23.6 1.0 C2 D:MLI401 3.1 27.0 1.0 OE1 D:GLU258 3.1 24.4 1.0 CD2 D:HIS51 3.2 23.1 1.0 C1 D:MLI401 3.4 29.9 1.0 NH2 D:ARG254 3.9 26.9 1.0 O D:HOH623 4.0 27.3 1.0 OG1 D:THR85 4.1 23.9 1.0 O9 D:MLI401 4.1 34.5 1.0 ND1 D:HIS49 4.2 30.1 1.0 ND1 D:HIS51 4.2 23.9 1.0 CG D:HIS49 4.2 26.0 1.0 O6 D:MLI401 4.3 25.1 1.0 CG D:HIS51 4.3 23.8 1.0 CG D:GLU258 4.4 25.6 1.0 CB D:THR85 4.4 23.7 1.0 NH1 D:ARG254 4.6 26.5 1.0 CA D:GLY15 4.7 23.0 1.0 CZ D:ARG254 4.7 24.8 1.0 O D:HOH689 4.8 44.2 1.0 O D:HOH559 5.0 37.1 1.0

A.G.Satanowski, D.G.Marchal, A.Perret, J.-L.Petit, M.Bouzon, V.Doering, 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, Ambient CO2-Reduction As An Entry-Point For Enhanced Carbon Fixation Nat Commun.
ISSN: ESSN 2041-1723