Magnesium in PDB 9dl2: Structure of Proline Utilization A Complexed with 2,3-Dihydro-1,4- Benzodioxine-5-Carboxylic Acid

All present enzymatic activity of Structure of Proline Utilization A Complexed with 2,3-Dihydro-1,4- Benzodioxine-5-Carboxylic Acid:
1.2.1.88; 1.5.5.2;

The structure of Structure of Proline Utilization A Complexed with 2,3-Dihydro-1,4- Benzodioxine-5-Carboxylic Acid, PDB code: 9dl2 was solved by J.J.Tanner, K.R.Meeks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.90 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	100.396, 101.723, 126.293, 90, 106.23, 90
R / Rfree (%)	16.7 / 19

The binding sites of Magnesium atom in the Structure of Proline Utilization A Complexed with 2,3-Dihydro-1,4- Benzodioxine-5-Carboxylic Acid (pdb code 9dl2). 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 Complexed with 2,3-Dihydro-1,4- Benzodioxine-5-Carboxylic Acid, PDB code: 9dl2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Proline Utilization A Complexed with 2,3-Dihydro-1,4- Benzodioxine-5-Carboxylic Acid


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 Complexed with 2,3-Dihydro-1,4- Benzodioxine-5-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2014 b:45.3 occ:1.00 O A:HOH3002 2.2 48.0 1.0 O A:HOH2111 2.2 40.2 1.0 O A:HOH3001 2.2 47.8 1.0 O2A A:NAD2008 2.3 32.2 0.7 O A:HOH2962 2.3 45.5 1.0 O A:HOH2639 2.4 41.0 1.0 O A:HOH2747 3.6 37.9 1.0 PA A:NAD2008 3.7 32.6 0.7 O1N A:NAD2008 3.8 31.9 0.7 O5B A:NAD2008 3.9 32.9 0.7 O A:HOH3211 4.0 40.4 1.0 O A:HOH3136 4.2 37.6 1.0 OE2 A:GLU733 4.3 42.2 1.0 OE2 A:GLU734 4.3 37.8 1.0 O3 A:NAD2008 4.3 30.8 0.7 PN A:NAD2008 4.4 33.4 0.7 O2N A:NAD2008 4.6 26.8 0.7 NE1 A:TRP706 4.6 32.5 1.0 O1A A:NAD2008 4.7 29.8 0.7 O A:HOH2328 4.9 38.4 1.0 CD1 A:TRP706 4.9 35.3 1.0

Magnesium binding site 2 out of 2 in the Structure of Proline Utilization A Complexed with 2,3-Dihydro-1,4- Benzodioxine-5-Carboxylic Acid


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 Complexed with 2,3-Dihydro-1,4- Benzodioxine-5-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2013 b:38.7 occ:1.00 O B:HOH2128 1.9 33.6 1.0 O B:HOH2469 2.0 36.0 1.0 O2A B:NAD2010 2.1 25.1 0.8 O B:HOH2992 2.3 47.6 1.0 O B:HOH2899 2.3 41.2 1.0 O B:HOH2609 3.3 27.9 1.0 PA B:NAD2010 3.4 23.7 0.8 O5B B:NAD2010 3.7 24.6 0.8 O1N B:NAD2010 3.7 25.9 0.8 O3 B:NAD2010 4.1 19.9 0.8 OE2 B:GLU733 4.2 34.4 1.0 PN B:NAD2010 4.3 23.6 0.8 OE2 B:GLU734 4.4 31.7 1.0 O2N B:NAD2010 4.5 20.1 0.8 O1A B:NAD2010 4.5 21.5 0.8 O B:HOH3064 4.6 34.2 1.0 NE1 B:TRP706 4.9 30.7 1.0 CD B:GLU733 5.0 38.3 1.0

K.R.Meeks, A.N.Bogner, J.C.Nix, J.J.Tanner. Crystallographic Fragment Screening of A Bifunctional Proline Catabolic Enzyme Reveals New Inhibitor Templates For Proline Dehydrogenase and L-Glutamate-Gamma-Semialdehyde Dehydrogenase Molecules V. 29 2024.
ISSN: ESSN 1420-3049
DOI: 10.3390/MOLECULES29225408