Zinc in PDB 5svc: Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Nucleotide-Free Structure

All present enzymatic activity of Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Nucleotide-Free Structure:
6.4.1.6;

The structure of Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Nucleotide-Free Structure, PDB code: 5svc was solved by B.J.Eilers, F.Mus, A.B.Alleman, B.V.Kabasakal, J.W.Murray, B.P.Nocek, J.L.Dubois, J.W.Peters, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.90 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.760, 265.159, 122.170, 90.00, 92.33, 90.00
R / Rfree (%)	20.2 / 25.5

The structure of Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Nucleotide-Free Structure also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Zinc atom in the Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Nucleotide-Free Structure (pdb code 5svc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Nucleotide-Free Structure, PDB code: 5svc:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Nucleotide-Free Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Nucleotide-Free Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:53.9 occ:0.48 SG C:CYS124 2.1 69.2 1.0 SG C:CYS127 2.2 66.1 1.0 SG C:CYS76 2.3 75.1 1.0 SG C:CYS74 2.5 61.4 1.0 CB C:CYS124 3.1 48.0 1.0 CB C:CYS74 3.3 54.8 1.0 CB C:CYS127 3.3 65.6 1.0 N C:CYS127 3.5 64.3 1.0 CB C:CYS76 3.6 69.8 1.0 CA C:CYS127 4.0 62.0 1.0 CB C:GLU126 4.2 72.3 1.0 CB C:HIS78 4.4 38.0 1.0 N C:GLU126 4.4 55.2 1.0 C C:GLU126 4.4 67.8 1.0 CA C:CYS124 4.5 44.1 1.0 CA C:GLU126 4.5 64.1 1.0 N C:CYS76 4.6 69.8 1.0 CA C:CYS76 4.7 68.5 1.0 C C:CYS124 4.8 60.2 1.0 NE2 C:HIS131 4.8 45.0 1.0 CA C:CYS74 4.8 42.4 1.0 C C:CYS127 4.9 61.8 1.0 N C:HIS78 4.9 48.1 1.0 N C:GLY77 5.0 66.3 1.0 CG C:GLU126 5.0 85.0 1.0

Zinc binding site 2 out of 2 in the Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Nucleotide-Free Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Nucleotide-Free Structure within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:52.0 occ:0.48 SG F:CYS127 2.1 80.7 1.0 SG F:CYS124 2.2 70.5 1.0 SG F:CYS74 2.3 63.1 1.0 SG F:CYS76 2.3 74.2 1.0 CB F:CYS124 3.1 53.0 1.0 CB F:CYS74 3.2 49.9 1.0 CB F:CYS127 3.5 83.9 1.0 CB F:CYS76 3.5 65.4 1.0 N F:CYS127 3.7 75.0 1.0 CA F:CYS127 4.2 74.0 1.0 N F:CYS76 4.4 58.7 1.0 CB F:GLU126 4.5 89.3 1.0 CB F:HIS78 4.5 52.7 1.0 CA F:CYS124 4.5 52.1 1.0 CA F:CYS76 4.5 63.6 1.0 NE2 F:HIS131 4.6 52.9 1.0 N F:GLU126 4.6 65.8 1.0 C F:GLU126 4.6 82.4 1.0 CA F:CYS74 4.7 45.4 1.0 CA F:GLU126 4.8 80.0 1.0 C F:CYS124 4.9 65.0 1.0 N F:HIS78 4.9 59.0 1.0 N F:GLY77 4.9 67.7 1.0 C F:CYS127 5.0 70.2 1.0

F.Mus, B.J.Eilers, A.B.Alleman, B.V.Kabasakal, J.N.Wells, J.W.Murray, B.P.Nocek, J.L.Dubois, J.W.Peters. Structural Basis For the Mechanism of Atp-Dependent Acetone Carboxylation. Sci Rep V. 7 7234 2017.
ISSN: ESSN 2045-2322
PubMed: 28775283
DOI: 10.1038/S41598-017-06973-8