Manganese 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:

Zinc

(Zn)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Nucleotide-Free Structure, PDB code: 5svc:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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 A:Mn801 b:32.0 occ:1.00 NE2 A:HIS150 1.8 52.4 1.0 ND1 A:HIS175 2.1 52.8 1.0 O A:HOH942 2.2 11.1 1.0 OD1 A:ASP153 2.2 46.2 1.0 CE1 A:HIS150 2.2 48.8 1.0 OD2 A:ASP153 2.4 50.0 1.0 CG A:ASP153 2.6 44.5 1.0 CE1 A:HIS175 2.8 49.2 1.0 CD2 A:HIS150 3.2 56.0 1.0 CG A:HIS175 3.3 50.3 1.0 ND1 A:HIS150 3.5 58.0 1.0 CB A:HIS175 3.9 38.3 1.0 CG A:HIS150 4.0 50.3 1.0 CB A:ASP153 4.0 39.6 1.0 NE2 A:HIS175 4.0 48.4 1.0 NE1 A:TRP401 4.1 56.6 1.0 CD2 A:HIS175 4.3 48.8 1.0 CE A:MET187 4.4 30.9 1.0 CZ2 A:TRP401 4.4 43.4 1.0 N A:ASP153 4.6 26.9 1.0 CA A:ASP153 4.7 39.1 1.0 CE2 A:TRP401 4.7 46.1 1.0 CA A:HIS175 4.7 31.5 1.0 C A:CYS152 4.8 33.6 1.0

Manganese 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 Manganese with other atoms in the Mn 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 D:Mn801 b:28.0 occ:1.00 NE2 D:HIS150 2.0 49.6 1.0 ND1 D:HIS175 2.1 51.2 1.0 OD1 D:ASP153 2.2 42.8 1.0 O D:HOH940 2.2 15.6 1.0 CE1 D:HIS150 2.2 55.3 1.0 OD2 D:ASP153 2.4 50.4 1.0 CG D:ASP153 2.6 40.3 1.0 CE1 D:HIS175 2.8 43.9 1.0 CG D:HIS175 3.3 47.3 1.0 CD2 D:HIS150 3.3 55.7 1.0 ND1 D:HIS150 3.5 47.8 1.0 CB D:HIS175 3.8 31.7 1.0 NE2 D:HIS175 4.0 45.6 1.0 CB D:ASP153 4.0 30.8 1.0 CG D:HIS150 4.1 49.8 1.0 NE1 D:TRP401 4.1 52.9 1.0 CD2 D:HIS175 4.3 45.8 1.0 CZ2 D:TRP401 4.4 44.4 1.0 CE D:MET187 4.6 31.8 1.0 N D:ASP153 4.6 30.6 1.0 CA D:HIS175 4.6 31.6 1.0 CA D:ASP153 4.7 38.4 1.0 CE2 D:TRP401 4.7 47.7 1.0 C D:CYS152 4.8 36.2 1.0 CB D:CYS152 4.9 45.5 1.0 CZ D:PHE456 5.0 32.8 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