Magnesium in PDB 8yav: Crystal Structure of Glucose 1-Dehydrogenase From Limosilactobacillus Fermentum

The structure of Crystal Structure of Glucose 1-Dehydrogenase From Limosilactobacillus Fermentum, PDB code: 8yav was solved by L.Cong, J.J.Wang, H.L.Wei, W.D.Liu, S.You, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.97 / 1.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.851, 58.079, 73.072, 70.58, 83.46, 78.36
R / Rfree (%)	18.9 / 21.7

The binding sites of Magnesium atom in the Crystal Structure of Glucose 1-Dehydrogenase From Limosilactobacillus Fermentum (pdb code 8yav). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Glucose 1-Dehydrogenase From Limosilactobacillus Fermentum, PDB code: 8yav:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Glucose 1-Dehydrogenase From Limosilactobacillus Fermentum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Glucose 1-Dehydrogenase From Limosilactobacillus Fermentum within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:16.0 occ:1.00 O A:HOH475 2.0 21.6 1.0 O D:HOH337 2.0 17.3 1.0 O D:GLN247 2.0 14.1 1.0 O A:HOH492 2.0 17.5 1.0 O A:HOH451 2.0 20.9 1.0 O A:GLN247 2.1 15.3 1.0 C D:GLN247 3.1 19.4 1.0 C A:GLN247 3.2 15.7 1.0 OXT D:GLN247 3.3 16.4 1.0 OXT A:GLN247 3.5 14.8 1.0 O D:TYR244 4.4 14.2 1.0 CA D:GLN247 4.4 14.7 1.0 O D:HOH415 4.4 28.4 1.0 O A:TYR244 4.4 15.0 1.0 CA A:GLN247 4.5 18.1 1.0 O A:HOH525 4.5 27.3 1.0 O A:HOH469 4.6 36.8 1.0 N D:GLN247 4.6 18.7 1.0 CG2 A:ILE144 4.7 15.4 1.0 O D:THR245 4.7 16.3 1.0 O A:THR245 4.7 17.8 1.0 N A:GLN247 4.8 17.9 1.0 CG2 D:ILE144 4.8 14.6 1.0 CA A:THR245 4.9 12.8 1.0 CA D:THR245 4.9 16.5 1.0 CG D:GLN247 4.9 14.5 1.0 C D:THR245 4.9 17.4 1.0 C A:THR245 5.0 17.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Glucose 1-Dehydrogenase From Limosilactobacillus Fermentum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Glucose 1-Dehydrogenase From Limosilactobacillus Fermentum within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:17.2 occ:1.00 O B:GLN247 2.0 16.3 1.0 O B:HOH453 2.1 15.2 1.0 O B:HOH465 2.1 18.2 1.0 O C:HOH363 2.1 18.4 1.0 O C:GLN247 2.1 16.4 1.0 O B:HOH495 2.1 19.3 1.0 C B:GLN247 3.1 19.2 1.0 C C:GLN247 3.2 21.7 1.0 OXT B:GLN247 3.5 16.2 1.0 OXT C:GLN247 3.5 18.5 1.0 O C:HOH427 4.4 29.6 1.0 CA B:GLN247 4.4 16.5 1.0 O B:TYR244 4.4 15.1 1.0 O C:TYR244 4.4 14.8 1.0 O B:HOH530 4.4 28.8 1.0 CA C:GLN247 4.5 14.5 1.0 N B:GLN247 4.6 17.0 1.0 O B:THR245 4.7 18.4 1.0 O C:THR245 4.8 16.7 1.0 N C:GLN247 4.8 17.7 1.0 CG2 C:ILE144 4.8 17.7 1.0 CG2 B:ILE144 4.8 18.9 1.0 CA B:THR245 4.9 12.8 1.0 C B:THR245 5.0 19.9 1.0 CA C:THR245 5.0 13.8 1.0 CG B:GLN247 5.0 17.2 1.0

Q.Wang, L.Cong, J.Guo, J.Wang, X.Han, W.Zhang, W.Liu, H.Wei, S.You. Structure-Guided Engineering of A Short-Chain Dehydrogenase LFSDR1 For Efficient Biosynthesis of (R)-9-(2-Hydroxypropyl)Adenine, the Key Intermediate of Tenofovir. Adv.Synth.Catal. V. N/A 2024.
ISSN: ESSN 1615-4169
DOI: 10.1002/ADSC.202400752