Zinc in PDB 8goa: Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+

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

The structure of Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+, PDB code: 8goa 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)	49.24 / 2.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	161.47, 161.47, 291.907, 90, 90, 90
R / Rfree (%)	19.2 / 22

The binding sites of Zinc atom in the Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+ (pdb code 8goa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+, PDB code: 8goa:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Glycerol Dehydrogenase in the Absence 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 Absence of Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:49.3 occ:1.00 NE2 A:HIS254 2.2 53.3 1.0 OD1 A:ASP171 2.3 51.1 1.0 NE2 A:HIS271 2.3 54.9 1.0 O1 A:TRS402 2.3 75.7 0.7 C3 A:TRS402 2.8 74.8 0.7 OD2 A:ASP171 2.8 49.9 1.0 CG A:ASP171 2.8 50.1 1.0 CD2 A:HIS254 3.0 56.9 1.0 CD2 A:HIS271 3.1 54.6 1.0 C1 A:TRS402 3.3 75.6 0.7 O3 A:TRS402 3.3 82.0 0.7 CE1 A:HIS271 3.3 58.4 1.0 CE1 A:HIS254 3.4 58.2 1.0 OD1 A:ASP121 3.4 58.8 1.0 C A:TRS402 3.4 75.5 0.7 OD2 A:ASP121 3.4 56.4 1.0 C2 A:TRS402 3.6 82.6 0.7 CG A:ASP121 3.7 57.3 1.0 CG A:HIS254 4.2 56.7 1.0 CG2 A:VAL275 4.3 50.4 1.0 CG A:HIS271 4.3 56.7 1.0 CB A:ASP171 4.3 47.0 1.0 ND1 A:HIS254 4.4 59.7 1.0 ND1 A:HIS271 4.4 61.0 1.0 O2 A:TRS402 4.5 88.4 0.7 OG1 A:THR120 4.7 65.8 1.0 N A:TRS402 4.8 95.1 0.7 O A:HOH509 4.9 50.6 1.0 CA A:ASP171 4.9 45.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Glycerol Dehydrogenase in the Absence 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 Absence of Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:44.7 occ:1.00 OD1 B:ASP171 2.1 51.8 1.0 NE2 B:HIS254 2.2 51.7 1.0 NE2 B:HIS271 2.3 59.3 1.0 O3 B:TRS402 2.4 88.9 0.9 N B:TRS402 2.4 91.5 0.9 OD2 B:ASP171 2.8 49.5 1.0 CG B:ASP171 2.8 49.8 1.0 CD2 B:HIS254 3.0 51.4 1.0 CD2 B:HIS271 3.1 57.6 1.0 C3 B:TRS402 3.2 87.9 0.9 C B:TRS402 3.2 89.5 0.9 CE1 B:HIS271 3.3 65.3 1.0 CE1 B:HIS254 3.3 56.4 1.0 OD1 B:ASP121 3.5 61.3 1.0 C1 B:TRS402 3.5 89.2 0.9 OD2 B:ASP121 3.5 65.7 1.0 O1 B:TRS402 3.7 88.7 0.9 CG B:ASP121 3.9 64.4 1.0 CG2 B:VAL275 4.2 53.0 1.0 CG B:HIS271 4.2 55.0 1.0 CG B:HIS254 4.2 49.2 1.0 ND1 B:HIS271 4.3 62.2 1.0 CB B:ASP171 4.3 47.3 1.0 ND1 B:HIS254 4.4 53.4 1.0 C2 B:TRS402 4.6 119.9 0.9 O B:HOH510 4.8 52.1 1.0 O B:ASP171 4.9 42.4 1.0 CA B:ASP171 4.9 46.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:53.2 occ:1.00 OD1 C:ASP171 2.1 51.0 1.0 NE2 C:HIS254 2.2 49.5 1.0 NE2 C:HIS271 2.3 64.1 1.0 C2 C:TRS402 2.5 59.5 0.8 O2 C:TRS402 2.6 52.9 0.8 CG C:ASP171 2.8 52.2 1.0 OD2 C:ASP171 2.8 48.8 1.0 CD2 C:HIS271 3.0 60.9 1.0 CE1 C:HIS254 3.1 51.7 1.0 CD2 C:HIS254 3.2 54.0 1.0 O1 C:TRS402 3.2 73.8 0.8 OD1 C:ASP121 3.4 55.8 1.0 CE1 C:HIS271 3.4 70.8 1.0 OD2 C:ASP121 3.7 63.4 1.0 C C:TRS402 3.8 74.7 0.8 CG C:ASP121 4.0 57.5 1.0 C1 C:TRS402 4.0 73.7 0.8 ND1 C:HIS254 4.2 51.8 1.0 CG C:HIS271 4.2 63.9 1.0 CG2 C:VAL275 4.2 53.4 1.0 CG C:HIS254 4.3 49.8 1.0 CB C:ASP171 4.3 50.5 1.0 ND1 C:HIS271 4.4 70.1 1.0 C3 C:TRS402 4.6 83.2 0.8 N C:TRS402 4.8 69.2 0.8 CA C:ASP171 4.9 48.4 1.0 O C:HOH542 5.0 52.7 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Glycerol Dehydrogenase in the Absence of Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:57.5 occ:1.00 O2 D:TRS402 2.1 130.2 0.9 OD1 D:ASP171 2.2 59.5 1.0 NE2 D:HIS254 2.2 66.7 1.0 NE2 D:HIS271 2.3 63.0 1.0 O3 D:TRS402 2.5 86.7 0.9 OD2 D:ASP171 2.6 60.9 1.0 CG D:ASP171 2.7 60.5 1.0 CD2 D:HIS254 3.1 67.1 1.0 CE1 D:HIS271 3.2 70.5 1.0 C3 D:TRS402 3.2 91.1 0.9 CD2 D:HIS271 3.2 62.0 1.0 CE1 D:HIS254 3.3 64.0 1.0 C2 D:TRS402 3.3 94.5 0.9 O1 D:TRS402 3.4 90.3 0.9 OD1 D:ASP121 3.6 68.1 1.0 C D:TRS402 3.7 91.4 0.9 C1 D:TRS402 3.8 94.7 0.9 OD2 D:ASP121 4.0 70.9 1.0 CB D:ASP171 4.2 57.4 1.0 CG D:ASP121 4.2 69.8 1.0 CG D:HIS254 4.3 62.2 1.0 ND1 D:HIS271 4.3 70.4 1.0 CG2 D:VAL275 4.3 61.6 1.0 CG D:HIS271 4.3 64.3 1.0 ND1 D:HIS254 4.4 62.6 1.0 CA D:ASP171 4.9 55.1 1.0 CG1 D:VAL275 4.9 60.7 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