Magnesium in PDB 7myb: Structure of Proline Utilization A with Tetrahydrothiophene-2- Carboxylate Bound in the Proline Dehydrogenase Active Site

All present enzymatic activity of Structure of Proline Utilization A with Tetrahydrothiophene-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 Tetrahydrothiophene-2- Carboxylate Bound in the Proline Dehydrogenase Active Site, PDB code: 7myb 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)	97.72 / 1.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	101.884, 103.024, 127.062, 90, 106.44, 90
R / Rfree (%)	16.4 / 18.6

The binding sites of Magnesium atom in the Structure of Proline Utilization A with Tetrahydrothiophene-2- Carboxylate Bound in the Proline Dehydrogenase Active Site (pdb code 7myb). 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 Tetrahydrothiophene-2- Carboxylate Bound in the Proline Dehydrogenase Active Site, PDB code: 7myb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Proline Utilization A with Tetrahydrothiophene-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 Tetrahydrothiophene-2- Carboxylate Bound in the Proline Dehydrogenase Active Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1309 b:26.4 occ:1.00 O A:HOH1824 2.0 27.8 1.0 O2A A:NAD1305 2.1 23.3 1.0 O A:HOH1502 2.1 27.9 1.0 O A:HOH1623 2.1 27.5 1.0 O A:HOH2095 2.2 41.2 1.0 PA A:NAD1305 3.5 22.1 1.0 O A:HOH1827 3.6 26.2 1.0 O A:HOH2094 3.9 43.5 1.0 O5B A:NAD1305 3.9 20.4 1.0 O1N A:NAD1305 4.0 22.7 1.0 O A:HOH2220 4.3 47.3 1.0 OE2 A:GLU733 4.3 28.0 1.0 O3 A:NAD1305 4.4 20.9 1.0 OE1 A:GLU734 4.4 27.1 1.0 O1A A:NAD1305 4.5 21.2 1.0 O A:HOH1643 4.5 30.8 1.0 O A:HOH2446 4.5 31.5 1.0 PN A:NAD1305 4.6 22.0 1.0 O2N A:NAD1305 4.9 23.6 1.0

Magnesium binding site 2 out of 2 in the Structure of Proline Utilization A with Tetrahydrothiophene-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 Tetrahydrothiophene-2- Carboxylate Bound in the Proline Dehydrogenase Active Site within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1307 b:22.6 occ:1.00 O2A B:NAD1305 2.0 15.9 1.0 O B:HOH1824 2.0 21.3 1.0 O B:HOH2453 2.1 23.3 1.0 O B:HOH1531 2.1 21.4 1.0 O B:HOH2086 2.2 28.7 1.0 O B:HOH2212 2.2 28.8 1.0 PA B:NAD1305 3.4 14.4 1.0 O B:HOH1708 3.6 19.8 1.0 O5B B:NAD1305 3.9 13.8 1.0 O1N B:NAD1305 3.9 15.6 1.0 O B:HOH1770 4.1 34.5 1.0 O B:HOH2353 4.3 32.5 1.0 OE2 B:GLU733 4.3 21.1 1.0 O3 B:NAD1305 4.3 13.5 1.0 O1A B:NAD1305 4.4 15.1 1.0 OE1 B:GLU734 4.5 20.7 1.0 PN B:NAD1305 4.5 14.7 1.0 O B:HOH2465 4.6 30.4 1.0 O2N B:NAD1305 4.8 15.0 1.0 O B:HOH1837 4.8 35.5 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