Zinc in PDB 5svb: Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Amp Bound Structure

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

The structure of Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Amp Bound Structure, PDB code: 5svb 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)	39.62 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.928, 100.209, 441.384, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 22.7

The structure of Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Amp Bound 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 Amp Bound Structure (pdb code 5svb). 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 Amp Bound Structure, PDB code: 5svb:
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 Amp Bound 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 Amp Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:0.6 occ:0.92 SG C:CYS124 2.3 62.0 1.0 SG C:CYS74 2.3 59.1 1.0 SG C:CYS76 2.3 56.4 1.0 SG C:CYS127 2.3 70.8 1.0 HB3 C:CYS74 3.0 60.6 1.0 HB3 C:CYS124 3.0 67.7 1.0 CB C:CYS124 3.1 56.4 1.0 CB C:CYS74 3.2 50.5 1.0 HB2 C:CYS124 3.2 67.7 1.0 H C:CYS127 3.2 70.1 1.0 HB3 C:CYS76 3.4 64.0 1.0 HB2 C:CYS74 3.5 60.6 1.0 H C:CYS76 3.5 61.8 1.0 CB C:CYS76 3.5 53.3 1.0 HB3 C:CYS127 3.6 80.6 1.0 CB C:CYS127 3.6 67.2 1.0 HB3 C:HIS78 3.8 57.8 1.0 HB2 C:GLU126 3.9 77.7 1.0 N C:CYS127 4.0 58.4 1.0 HG1 C:THR129 4.1 55.0 1.0 HB C:THR129 4.2 52.6 1.0 HB2 C:CYS76 4.2 64.0 1.0 H C:HIS78 4.2 60.4 1.0 N C:CYS76 4.2 51.5 1.0 HB2 C:HIS78 4.3 57.8 1.0 H C:THR129 4.3 53.4 1.0 HB2 C:CYS127 4.3 80.6 1.0 H C:GLU126 4.4 68.7 1.0 CA C:CYS127 4.4 60.0 1.0 NE2 C:HIS131 4.4 43.2 1.0 CA C:CYS76 4.5 53.0 1.0 CB C:HIS78 4.5 48.1 1.0 CA C:CYS74 4.5 41.6 1.0 CA C:CYS124 4.6 52.3 1.0 OG1 C:THR129 4.6 45.9 1.0 H C:GLY128 4.7 57.8 1.0 H C:GLY77 4.8 62.9 1.0 C C:CYS74 4.8 41.1 1.0 CB C:THR129 4.9 43.9 1.0 CB C:GLU126 4.9 64.7 1.0 HE1 C:HIS131 4.9 51.4 1.0 H C:GLU75 4.9 58.6 1.0 HA C:CYS124 4.9 62.8 1.0 N C:GLU75 5.0 48.8 1.0 C C:CYS124 5.0 51.2 1.0

Zinc binding site 2 out of 2 in the Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Amp Bound 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 Amp Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:0.1 occ:0.51 SG F:CYS74 2.3 52.9 1.0 SG F:CYS124 2.3 65.4 1.0 SG F:CYS76 2.3 74.8 1.0 SG F:CYS127 2.3 74.6 1.0 HB3 F:CYS124 2.9 68.4 1.0 HB3 F:CYS74 3.0 59.2 1.0 H F:CYS127 3.0 76.1 1.0 CB F:CYS124 3.1 57.0 1.0 CB F:CYS74 3.2 49.3 1.0 HB2 F:CYS124 3.3 68.4 1.0 HB3 F:CYS76 3.4 83.5 1.0 HB2 F:CYS74 3.5 59.2 1.0 H F:CYS76 3.5 67.6 1.0 CB F:CYS76 3.6 69.6 1.0 HB3 F:CYS127 3.6 87.1 1.0 CB F:CYS127 3.6 72.6 1.0 N F:CYS127 3.8 63.4 1.0 HB3 F:HIS78 3.9 63.8 1.0 HB F:THR129 4.1 59.5 1.0 H F:GLU126 4.2 72.3 1.0 HG1 F:THR129 4.2 62.3 1.0 HB2 F:CYS76 4.2 83.5 1.0 N F:CYS76 4.3 56.3 1.0 H F:HIS78 4.3 66.2 1.0 CA F:CYS127 4.3 66.1 1.0 H F:THR129 4.4 60.3 1.0 HB2 F:CYS127 4.4 87.1 1.0 NE2 F:HIS131 4.4 48.0 1.0 HB2 F:HIS78 4.4 63.8 1.0 CB F:GLU126 4.4 63.2 1.0 CA F:CYS76 4.5 61.6 1.0 CA F:CYS124 4.5 50.1 1.0 CA F:CYS74 4.6 47.4 1.0 OG1 F:THR129 4.6 52.0 1.0 CB F:HIS78 4.6 53.2 1.0 H F:GLY128 4.7 65.3 1.0 H F:GLY77 4.8 68.8 1.0 C F:CYS74 4.8 49.4 1.0 CB F:THR129 4.8 49.6 1.0 C F:GLU126 4.8 67.0 1.0 N F:GLU126 4.9 60.3 1.0 HE1 F:HIS131 4.9 57.2 1.0 H F:GLU75 4.9 63.3 1.0 HA F:CYS124 4.9 60.1 1.0 C F:CYS124 4.9 51.9 1.0 N F:GLU75 5.0 52.8 1.0 CA F:GLU126 5.0 63.8 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