Zinc in PDB 8gob: Crystal Structure of Glycerol Dehydrogenase in the Presence of Nad+

All present enzymatic activity of Crystal Structure of Glycerol Dehydrogenase in the Presence of Nad+:
1.1.1.6; 1.1.1.75;

The structure of Crystal Structure of Glycerol Dehydrogenase in the Presence of Nad+, PDB code: 8gob was solved by T.Park, H.N.Hoang, J.Y.Kang, J.Park, S.A.Mun, M.Jin, J.Yang, C.-H.Jung, S.H.Eom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.60 / 2.60
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	129.878, 129.878, 266.214, 90, 90, 90
R / Rfree (%)	18.6 / 23.1

The binding sites of Zinc atom in the Crystal Structure of Glycerol Dehydrogenase in the Presence of Nad+ (pdb code 8gob). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Glycerol Dehydrogenase in the Presence of Nad+, PDB code: 8gob:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Glycerol Dehydrogenase in the Presence of Nad+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Glycerol Dehydrogenase in the Presence of Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:46.4 occ:1.00 OD1 A:ASP171 2.3 46.1 1.0 NE2 A:HIS254 2.3 41.8 1.0 NE2 A:HIS271 2.3 54.1 1.0 O2 A:TRS403 2.5 56.5 0.8 OD2 A:ASP171 2.8 44.5 1.0 CG A:ASP171 2.8 44.5 1.0 C3 A:TRS403 3.0 88.9 0.8 C2 A:TRS403 3.1 68.0 0.8 CD2 A:HIS271 3.2 49.7 1.0 CD2 A:HIS254 3.2 43.7 1.0 CE1 A:HIS254 3.3 42.0 1.0 CE1 A:HIS271 3.3 55.7 1.0 OD1 A:ASP121 3.5 55.8 1.0 C A:TRS403 3.7 85.1 0.8 C5N A:NAD402 4.0 67.3 1.0 OD2 A:ASP121 4.0 55.9 1.0 CG A:ASP121 4.1 53.7 1.0 CG2 A:VAL275 4.2 39.9 1.0 O3 A:TRS403 4.2 94.0 0.8 CB A:ASP171 4.3 46.7 1.0 CG A:HIS271 4.4 56.9 1.0 CG A:HIS254 4.4 37.7 1.0 ND1 A:HIS271 4.4 57.7 1.0 ND1 A:HIS254 4.4 40.2 1.0 O A:HOH502 4.4 42.4 1.0 C4N A:NAD402 4.6 70.9 1.0 C1 A:TRS403 4.6 100.6 0.8 N A:TRS403 4.8 95.3 0.8 C6N A:NAD402 4.9 67.3 1.0 CA A:ASP171 4.9 40.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Glycerol Dehydrogenase in the Presence of Nad+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Glycerol Dehydrogenase in the Presence of Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:47.9 occ:1.00 OD1 B:ASP171 2.1 44.8 1.0 NE2 B:HIS254 2.3 46.1 1.0 NE2 B:HIS271 2.3 56.7 1.0 O2 B:TRS403 2.3 81.5 0.5 O2 B:TRS403 2.3 80.7 0.5 CG B:ASP171 2.7 42.4 1.0 OD2 B:ASP171 2.8 44.0 1.0 CE1 B:HIS271 3.1 56.4 1.0 CD2 B:HIS254 3.2 49.0 1.0 CE1 B:HIS254 3.3 50.1 1.0 CD2 B:HIS271 3.4 45.9 1.0 C2 B:TRS403 3.4 82.1 0.5 OD1 B:ASP121 3.6 53.3 1.0 C2 B:TRS403 3.6 84.9 0.5 C3 B:TRS403 3.7 93.9 0.5 N B:TRS403 3.8 91.5 0.5 C5N B:NAD402 4.0 60.4 1.0 OD2 B:ASP121 4.1 53.4 1.0 CG2 B:VAL275 4.1 36.9 1.0 C B:TRS403 4.2 95.2 0.5 CG B:ASP121 4.2 53.1 1.0 CB B:ASP171 4.2 41.2 1.0 C B:TRS403 4.2 96.6 0.5 ND1 B:HIS271 4.3 54.6 1.0 CG B:HIS254 4.3 43.0 1.0 ND1 B:HIS254 4.4 49.7 1.0 CG B:HIS271 4.4 53.5 1.0 O B:HOH512 4.5 44.6 1.0 C4N B:NAD402 4.7 59.5 1.0 C3 B:TRS403 4.8 94.4 0.5 CA B:ASP171 4.8 41.9 1.0 O3 B:TRS403 4.8 89.4 0.5 O3 B:TRS403 4.8 90.8 0.5 N B:TRS403 4.9 89.1 0.5 C6N B:NAD402 5.0 64.5 1.0

T.Park, H.N.Hoang, J.Y.Kang, J.Park, S.A.Mun, M.Jin, J.Yang, C.H.Jung, S.H.Eom. Structural and Functional Insights Into the Flexible Beta-Hairpin of Glycerol Dehydrogenase. Febs J. 2023.
ISSN: ISSN 1742-464X
PubMed: 37165682
DOI: 10.1111/FEBS.16813