Magnesium in PDB 9e5w: Proline Utilization A (Puta) From Sinorhizobium Meliloti Inactivated By N-Propargylglycine

All present enzymatic activity of Proline Utilization A (Puta) From Sinorhizobium Meliloti Inactivated By N-Propargylglycine:
1.2.1.88; 1.5.5.2;

The structure of Proline Utilization A (Puta) From Sinorhizobium Meliloti Inactivated By N-Propargylglycine, PDB code: 9e5w was solved by J.J.Tanner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.00 / 1.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	100.848, 101.967, 126.567, 90, 106.5, 90
R / Rfree (%)	19.1 / 21.1

The binding sites of Magnesium atom in the Proline Utilization A (Puta) From Sinorhizobium Meliloti Inactivated By N-Propargylglycine (pdb code 9e5w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Proline Utilization A (Puta) From Sinorhizobium Meliloti Inactivated By N-Propargylglycine, PDB code: 9e5w:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Proline Utilization A (Puta) From Sinorhizobium Meliloti Inactivated By N-Propargylglycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Proline Utilization A (Puta) From Sinorhizobium Meliloti Inactivated By N-Propargylglycine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1308 b:26.1 occ:1.00 O A:HOH1432 1.9 28.1 1.0 O A:HOH1831 2.0 30.6 1.0 O2A A:NAD1302 2.0 22.8 1.0 O A:HOH1439 2.1 27.8 1.0 O A:HOH1838 2.1 28.7 1.0 O A:HOH2034 2.1 30.8 1.0 PA A:NAD1302 3.4 24.9 1.0 O A:HOH1570 3.8 25.1 1.0 O5B A:NAD1302 3.9 25.0 1.0 O1N A:NAD1302 3.9 25.1 1.0 O A:HOH2081 4.1 28.8 1.0 OE2 A:GLU733 4.3 28.0 1.0 OE2 A:GLU734 4.3 29.4 1.0 O A:HOH2063 4.4 31.7 1.0 O3 A:NAD1302 4.4 22.9 1.0 O1A A:NAD1302 4.4 24.5 1.0 PN A:NAD1302 4.6 23.1 1.0 O A:HOH1555 4.7 32.5 1.0 O2N A:NAD1302 4.8 23.3 1.0

Magnesium binding site 2 out of 2 in the Proline Utilization A (Puta) From Sinorhizobium Meliloti Inactivated By N-Propargylglycine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Proline Utilization A (Puta) From Sinorhizobium Meliloti Inactivated By N-Propargylglycine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1305 b:27.6 occ:1.00 O B:HOH1481 1.8 23.4 1.0 O B:HOH2035 2.0 32.5 1.0 O B:HOH1775 2.0 25.8 1.0 O2A B:NAD1302 2.1 16.7 1.0 O B:HOH1766 2.4 32.7 1.0 O B:HOH1903 2.4 32.9 1.0 O B:HOH1642 3.3 19.1 1.0 PA B:NAD1302 3.5 16.9 1.0 O1N B:NAD1302 3.7 17.1 1.0 O5B B:NAD1302 3.8 16.9 1.0 OE2 B:GLU734 4.2 23.7 1.0 OE2 B:GLU733 4.2 25.1 1.0 O3 B:NAD1302 4.3 15.2 1.0 PN B:NAD1302 4.3 17.6 1.0 O2N B:NAD1302 4.4 17.0 1.0 O B:HOH2048 4.6 28.5 1.0 O1A B:NAD1302 4.6 15.9 1.0 CD B:GLU733 4.9 23.6 1.0 OE1 B:GLU734 5.0 17.0 1.0

K.R.Meeks, J.Ji, G.K.Scott, A.C.Campbell, J.C.Nix, A.Tadeo, L.M.Ellerby, C.C.Benz, J.J.Tanner. Biochemical, Structural, and Cellular Characterization of S-But-3-Yn-2-Ylglycine As A Mechanism-Based Covalent Inactivator of the Flavoenzyme Proline Dehydrogenase. Arch.Biochem.Biophys. 10319 2025.
ISSN: ESSN 1096-0384
PubMed: 39870289
DOI: 10.1016/J.ABB.2025.110319