Manganese 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:

Zinc

(Zn)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Mechanism of Atp-Dependent Acetone Carboxylation, Acetone Carboxylase Amp Bound Structure, PDB code: 5svb:
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 Amp Bound 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 Amp Bound Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn801 b:55.5 occ:1.00 HD2 A:HIS175 1.3 62.7 1.0 OE1 A:GLU89 2.1 59.3 1.0 ND1 A:HIS150 2.1 48.8 1.0 OD1 A:ASP153 2.1 57.4 1.0 OD2 A:ASP153 2.2 53.0 1.0 CD2 A:HIS175 2.2 52.2 1.0 CG A:ASP153 2.5 51.9 1.0 CE1 A:HIS150 2.9 49.8 1.0 HB2 A:HIS175 3.0 59.6 1.0 HB2 A:HIS150 3.0 58.6 1.0 CD A:GLU89 3.0 59.2 1.0 HE1 A:HIS150 3.1 59.7 1.0 CG A:HIS150 3.1 49.4 1.0 CG A:HIS175 3.1 52.5 1.0 NE2 A:HIS175 3.3 54.1 1.0 OE2 A:GLU89 3.5 60.3 1.0 HE2 A:HIS175 3.5 64.9 1.0 CB A:HIS150 3.5 48.9 1.0 CB A:HIS175 3.6 49.7 1.0 HE1 A:HIS111 3.8 52.1 1.0 NE2 A:HIS150 3.9 51.1 1.0 CB A:ASP153 4.0 45.2 1.0 HB3 A:HIS150 4.0 58.6 1.0 CD2 A:HIS150 4.0 50.9 1.0 HA A:HIS175 4.1 58.3 1.0 HG2 A:GLU89 4.2 70.1 1.0 CG A:GLU89 4.2 58.4 1.0 ND1 A:HIS175 4.3 55.7 1.0 HB3 A:HIS175 4.3 59.6 1.0 HE2 A:HIS111 4.3 51.8 1.0 HB2 A:ASP153 4.3 54.2 1.0 CE1 A:HIS175 4.3 56.1 1.0 SG A:CYS152 4.4 56.4 1.0 HD11 A:ILE110 4.4 63.1 1.0 CA A:HIS175 4.4 48.6 1.0 HB3 A:ASP153 4.4 54.2 1.0 O A:HOH938 4.5 48.0 1.0 CE1 A:HIS111 4.5 43.5 1.0 HA A:ASP153 4.5 54.1 1.0 H A:HIS150 4.6 56.1 1.0 HE2 A:HIS150 4.7 61.3 1.0 HB A:VAL149 4.7 54.4 1.0 CA A:ASP153 4.7 45.0 1.0 H A:ASP153 4.7 55.5 1.0 NE2 A:HIS111 4.8 43.2 1.0 N A:ASP153 4.8 46.2 1.0 HG A:CYS152 4.8 67.7 1.0 CA A:HIS150 4.8 48.0 1.0 HD12 A:ILE110 4.8 63.1 1.0 HD2 A:HIS150 4.9 61.1 1.0 N A:HIS150 4.9 46.7 1.0 HG3 A:GLU89 4.9 70.1 1.0 HE1 A:TRP401 5.0 62.8 1.0 HG12 A:VAL149 5.0 56.1 1.0

Manganese 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 Manganese with other atoms in the Mn 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 D:Mn801 b:55.9 occ:1.00 OD1 D:ASP153 2.1 46.9 1.0 OE1 D:GLU89 2.2 66.2 1.0 OE2 D:GLU89 2.2 68.0 1.0 OD2 D:ASP153 2.2 46.6 1.0 ND1 D:HIS175 2.2 49.4 1.0 ND1 D:HIS150 2.2 49.0 1.0 CD D:GLU89 2.4 66.2 1.0 CG D:ASP153 2.4 45.2 1.0 HB2 D:HIS150 3.0 58.4 1.0 CE1 D:HIS175 3.0 51.0 1.0 HE1 D:HIS175 3.0 61.2 1.0 CE1 D:HIS150 3.1 50.2 1.0 HB2 D:HIS175 3.2 57.9 1.0 HE1 D:HIS150 3.2 60.2 1.0 CG D:HIS150 3.3 50.0 1.0 CG D:HIS175 3.3 49.6 1.0 HE2 D:HIS111 3.6 51.3 1.0 CB D:HIS150 3.6 48.6 1.0 CB D:HIS175 3.7 48.2 1.0 CG D:GLU89 3.9 65.3 1.0 CB D:ASP153 4.0 44.0 1.0 HB3 D:HIS150 4.1 58.4 1.0 HB2 D:GLU89 4.2 79.5 1.0 NE2 D:HIS175 4.2 52.2 1.0 HA D:HIS175 4.2 57.0 1.0 NE2 D:HIS150 4.2 53.4 1.0 CD2 D:HIS175 4.3 51.3 1.0 CD2 D:HIS150 4.3 52.6 1.0 NE2 D:HIS111 4.3 42.7 1.0 HB D:VAL149 4.3 54.0 1.0 HG2 D:GLU89 4.4 78.3 1.0 HB2 D:ASP153 4.4 52.9 1.0 HB3 D:ASP153 4.4 52.9 1.0 HG3 D:GLU89 4.4 78.3 1.0 H D:HIS150 4.4 55.6 1.0 HB3 D:HIS175 4.5 57.9 1.0 CB D:GLU89 4.5 66.3 1.0 HE1 D:HIS111 4.6 50.7 1.0 HA D:ASP153 4.6 53.4 1.0 CA D:HIS175 4.6 47.5 1.0 HD11 D:ILE110 4.6 58.7 1.0 HB3 D:GLU89 4.6 79.5 1.0 SG D:CYS152 4.6 62.7 1.0 CA D:ASP153 4.7 44.5 1.0 N D:HIS150 4.7 46.4 1.0 CA D:HIS150 4.8 47.7 1.0 HG12 D:VAL149 4.8 55.8 1.0 CE1 D:HIS111 4.9 42.3 1.0 H D:ASP153 4.9 56.8 1.0 N D:ASP153 4.9 47.4 1.0 HE2 D:HIS175 4.9 62.6 1.0 HE1 D:TRP401 4.9 54.6 1.0 HG11 D:VAL149 5.0 55.8 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