Magnesium in PDB 7my9: Structure of Proline Utilization A with 1,3-Dithiolane-2-Carboxylate Bound in the Proline Dehydrogenase Active Site

All present enzymatic activity of Structure of Proline Utilization A with 1,3-Dithiolane-2-Carboxylate Bound in the Proline Dehydrogenase Active Site:
1.2.1.88; 1.5.5.2;

The structure of Structure of Proline Utilization A with 1,3-Dithiolane-2-Carboxylate Bound in the Proline Dehydrogenase Active Site, PDB code: 7my9 was solved by J.J.Tanner, A.C.Campbell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	121.68 / 1.63
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	101.932, 103.094, 126.906, 90, 106.5, 90
R / Rfree (%)	16.2 / 19.2

The binding sites of Magnesium atom in the Structure of Proline Utilization A with 1,3-Dithiolane-2-Carboxylate Bound in the Proline Dehydrogenase Active Site (pdb code 7my9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Proline Utilization A with 1,3-Dithiolane-2-Carboxylate Bound in the Proline Dehydrogenase Active Site, PDB code: 7my9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Proline Utilization A with 1,3-Dithiolane-2-Carboxylate Bound in the Proline Dehydrogenase Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Proline Utilization A with 1,3-Dithiolane-2-Carboxylate Bound in the Proline Dehydrogenase Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1307 b:32.2 occ:1.00 O A:HOH1696 2.0 35.5 1.0 O2A A:NAD1303 2.0 27.9 1.0 O A:HOH1460 2.1 36.6 1.0 O A:HOH1650 2.2 32.3 1.0 O A:HOH2081 2.2 50.8 1.0 PA A:NAD1303 3.4 28.0 1.0 O A:HOH1786 3.7 35.7 1.0 O5B A:NAD1303 3.9 27.3 1.0 O1N A:NAD1303 3.9 28.1 1.0 O A:HOH2243 4.3 44.0 1.0 O3 A:NAD1303 4.3 28.0 1.0 OE2 A:GLU733 4.4 33.9 1.0 OE1 A:GLU734 4.4 37.9 1.0 O1A A:NAD1303 4.4 26.7 1.0 PN A:NAD1303 4.6 29.8 1.0 O2N A:NAD1303 4.8 30.4 1.0

Magnesium binding site 2 out of 2 in the Structure of Proline Utilization A with 1,3-Dithiolane-2-Carboxylate Bound in the Proline Dehydrogenase Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Proline Utilization A with 1,3-Dithiolane-2-Carboxylate Bound in the Proline Dehydrogenase Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1306 b:28.5 occ:1.00 O2A B:NAD1304 2.0 19.4 1.0 O B:HOH1615 2.0 24.0 1.0 O B:HOH1818 2.0 27.3 1.0 O B:HOH2315 2.1 29.4 1.0 O B:HOH1894 2.2 31.4 1.0 O B:HOH2064 2.2 33.9 1.0 PA B:NAD1304 3.4 19.4 1.0 O B:HOH1611 3.6 23.2 1.0 O5B B:NAD1304 3.9 19.3 1.0 O B:HOH1442 3.9 43.1 1.0 O1N B:NAD1304 3.9 21.4 1.0 OE2 B:GLU733 4.3 24.8 1.0 O3 B:NAD1304 4.3 17.5 1.0 O B:HOH2247 4.3 37.3 1.0 OE1 B:GLU734 4.4 26.8 1.0 O1A B:NAD1304 4.5 21.2 1.0 O B:HOH2351 4.5 34.5 1.0 PN B:NAD1304 4.5 18.6 1.0 O2N B:NAD1304 4.7 17.9 1.0 O B:HOH1684 4.8 43.7 1.0

A.C.Campbell, A.R.Prater, A.N.Bogner, T.P.Quinn, K.S.Gates, D.F.Becker, J.J.Tanner. Photoinduced Covalent Irreversible Inactivation of Proline Dehydrogenase By S-Heterocycles. Acs Chem.Biol. 2021.
ISSN: ESSN 1554-8937
PubMed: 34542291
DOI: 10.1021/ACSCHEMBIO.1C00427