Zinc in PDB 8x6m: Crystal Structure of Glycerol Dehydrogenase in the Presence of Nad+ and Glycerol

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

The structure of Crystal Structure of Glycerol Dehydrogenase in the Presence of Nad+ and Glycerol, PDB code: 8x6m was solved by T.Park, J.Y.Kang, M.Jin, J.Yang, H.Kim, C.Noh, S.H.Eom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.00
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.893, 131.893, 265.259, 90, 90, 90
R / Rfree (%)	17.6 / 21

The binding sites of Zinc atom in the Crystal Structure of Glycerol Dehydrogenase in the Presence of Nad+ and Glycerol (pdb code 8x6m). 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+ and Glycerol, PDB code: 8x6m:
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+ and Glycerol


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+ and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:81.4 occ:1.00 O1 A:GOL403 2.1 71.9 1.0 NE2 A:HIS254 2.5 56.7 1.0 NE2 A:HIS271 2.6 38.8 1.0 OD1 A:ASP171 2.7 58.3 1.0 OD2 A:ASP171 2.9 44.5 1.0 CG A:ASP171 3.0 40.8 1.0 CD2 A:HIS271 3.2 35.7 1.0 CE1 A:HIS254 3.4 46.1 1.0 OD1 A:ASP121 3.4 43.8 1.0 C1 A:GOL403 3.4 82.3 1.0 CD2 A:HIS254 3.5 54.4 1.0 CE1 A:HIS271 3.8 45.9 1.0 O2 A:GOL403 3.9 77.8 1.0 C5N A:NAD402 3.9 58.3 1.0 CG A:ASP121 4.0 45.3 1.0 OD2 A:ASP121 4.0 51.4 1.0 CG2 A:VAL275 4.1 31.1 1.0 C2 A:GOL403 4.2 81.5 1.0 O A:HOH513 4.4 48.2 1.0 CB A:ASP171 4.4 33.8 1.0 ND1 A:HIS254 4.5 45.4 1.0 CG A:HIS271 4.5 36.0 1.0 CG A:HIS254 4.6 53.7 1.0 C4N A:NAD402 4.6 57.0 1.0 ND1 A:HIS271 4.8 44.9 1.0 C6N A:NAD402 4.8 54.0 1.0 CA A:ASP171 4.9 28.1 1.0 O A:ASP171 4.9 31.1 1.0

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


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+ and Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:121.5 occ:1.00 NE2 B:HIS254 2.3 48.4 1.0 NE2 B:HIS271 2.4 38.2 1.0 OD1 B:ASP171 2.5 51.6 1.0 O B:HOH553 2.6 66.3 1.0 CD2 B:HIS271 2.9 33.3 1.0 OD2 B:ASP171 3.0 42.7 1.0 CG B:ASP171 3.1 41.5 1.0 CD2 B:HIS254 3.2 43.3 1.0 CE1 B:HIS254 3.3 48.0 1.0 OD1 B:ASP121 3.5 47.1 1.0 CE1 B:HIS271 3.6 41.2 1.0 CG2 B:VAL275 4.1 29.9 1.0 CG B:HIS271 4.2 35.1 1.0 CG B:ASP121 4.3 43.7 1.0 CG B:HIS254 4.4 48.7 1.0 ND1 B:HIS254 4.4 44.9 1.0 OD2 B:ASP121 4.4 55.1 1.0 ND1 B:HIS271 4.5 41.3 1.0 CB B:ASP171 4.5 35.5 1.0 O B:HOH501 4.9 58.5 1.0

T.Park, J.Y.Kang, M.Jin, J.Yang, H.Kim, C.Noh, C.H.Jung, S.H.Eom. Structural Insights Into the Octamerization of Glycerol Dehydrogenase. Plos One V. 19 00541 2024.
ISSN: ESSN 1932-6203
PubMed: 38483875
DOI: 10.1371/JOURNAL.PONE.0300541