Zinc in PDB 5env: Yeast Alcohol Dehydrogenase with Bound Coenzyme

All present enzymatic activity of Yeast Alcohol Dehydrogenase with Bound Coenzyme:
1.1.1.1;

The structure of Yeast Alcohol Dehydrogenase with Bound Coenzyme, PDB code: 5env was solved by B.V.Plapp, H.A.Charlier Jr., S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 3.00
Space group	P 3 2 1
Cell size a, b, c (Å), α, β, γ (°)	146.256, 146.256, 65.980, 90.00, 90.00, 120.00
R / Rfree (%)	13.2 / 19.7

The structure of Yeast Alcohol Dehydrogenase with Bound Coenzyme also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Zinc atom in the Yeast Alcohol Dehydrogenase with Bound Coenzyme (pdb code 5env). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Yeast Alcohol Dehydrogenase with Bound Coenzyme, PDB code: 5env:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Yeast Alcohol Dehydrogenase with Bound Coenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Alcohol Dehydrogenase with Bound Coenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:51.0 occ:1.00 O A:ETF404 2.1 53.2 1.0 NE2 A:HIS66 2.2 49.5 1.0 SG A:CYS43 2.4 52.1 1.0 SG A:CYS153 2.4 45.0 1.0 CE1 A:HIS66 3.1 51.4 1.0 CD2 A:HIS66 3.2 48.7 1.0 C2 A:ETF404 3.3 52.9 1.0 C5N A:NAD403 3.4 42.1 1.0 CB A:CYS43 3.4 53.1 1.0 CB A:CYS153 3.5 43.7 1.0 OG1 A:THR45 3.6 48.1 1.0 CB A:THR45 3.8 50.0 1.0 C6N A:NAD403 3.9 43.2 1.0 ND1 A:HIS66 4.2 51.4 1.0 C4N A:NAD403 4.3 40.7 1.0 CG A:HIS66 4.3 49.6 1.0 F3 A:ETF404 4.4 55.0 1.0 C1 A:ETF404 4.5 54.1 1.0 CG2 A:THR45 4.6 50.2 1.0 CA A:CYS153 4.8 41.2 1.0 CA A:CYS43 4.8 54.8 1.0 NH2 A:ARG340 4.9 50.2 1.0 N A:THR45 5.0 52.8 1.0 C A:CYS153 5.0 40.8 1.0

Zinc binding site 2 out of 4 in the Yeast Alcohol Dehydrogenase with Bound Coenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Alcohol Dehydrogenase with Bound Coenzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:47.6 occ:1.00 SG A:CYS103 2.3 44.6 1.0 SG A:CYS111 2.3 47.4 1.0 SG A:CYS100 2.3 45.0 1.0 SG A:CYS97 2.4 49.9 1.0 CB A:CYS111 3.3 44.9 1.0 CB A:CYS97 3.4 51.8 1.0 CB A:CYS103 3.5 42.8 1.0 CB A:CYS100 3.5 46.8 1.0 N A:CYS97 3.7 49.9 1.0 N A:CYS100 3.9 47.0 1.0 CA A:CYS97 4.0 51.6 1.0 CA A:CYS111 4.1 44.2 1.0 N A:MET98 4.2 50.7 1.0 N A:CYS103 4.2 40.3 1.0 C A:CYS97 4.3 51.8 1.0 CA A:CYS100 4.3 46.4 1.0 N A:ALA99 4.4 49.0 1.0 CA A:CYS103 4.4 40.7 1.0 CD A:PRO112 4.7 46.5 1.0 CB A:SER96 4.8 46.6 1.0 C A:SER96 4.9 49.6 1.0 C A:CYS100 4.9 44.6 1.0 CA A:MET98 4.9 50.4 1.0 C A:ALA99 4.9 48.9 1.0 O A:CYS100 5.0 43.2 1.0

Zinc binding site 3 out of 4 in the Yeast Alcohol Dehydrogenase with Bound Coenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Alcohol Dehydrogenase with Bound Coenzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:67.6 occ:1.00 NE2 B:HIS66 2.3 64.8 1.0 SG B:CYS43 2.3 72.4 1.0 SG B:CYS153 2.4 59.5 1.0 OE2 B:GLU67 2.6 65.3 1.0 CE1 B:HIS66 3.2 67.3 1.0 CD2 B:HIS66 3.2 61.8 1.0 CD B:GLU67 3.3 61.8 1.0 CB B:CYS153 3.3 55.3 1.0 O B:ETF404 3.4 61.4 0.5 CB B:CYS43 3.5 75.3 1.0 CG B:GLU67 3.9 59.1 1.0 OE1 B:GLU67 4.1 61.2 1.0 ND1 B:HIS66 4.3 65.9 1.0 OG1 B:THR45 4.3 80.5 1.0 CG B:HIS66 4.3 62.5 1.0 C2 B:ETF404 4.5 59.2 0.5 NH2 B:ARG340 4.6 74.0 1.0 CA B:CYS43 4.7 79.0 1.0 N B:CYS43 4.8 77.3 1.0 CA B:CYS153 4.8 51.3 1.0 CB B:THR45 4.9 81.7 1.0 O B:HOH507 4.9 38.6 1.0

Zinc binding site 4 out of 4 in the Yeast Alcohol Dehydrogenase with Bound Coenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Alcohol Dehydrogenase with Bound Coenzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:48.8 occ:1.00 SG B:CYS103 2.3 43.9 1.0 SG B:CYS97 2.3 52.2 1.0 SG B:CYS111 2.3 51.0 1.0 SG B:CYS100 2.4 47.8 1.0 CB B:CYS97 3.4 53.8 1.0 CB B:CYS111 3.4 49.6 1.0 CB B:CYS100 3.4 48.9 1.0 CB B:CYS103 3.5 42.2 1.0 N B:CYS97 3.6 51.9 1.0 N B:MET98 3.8 48.3 1.0 CA B:CYS97 3.9 52.6 1.0 N B:CYS100 4.0 47.0 1.0 C B:CYS97 4.2 50.8 1.0 N B:ALA99 4.2 47.6 1.0 CA B:CYS100 4.3 47.5 1.0 CA B:CYS111 4.3 51.2 1.0 N B:CYS103 4.4 41.6 1.0 CA B:CYS103 4.5 40.7 1.0 C B:SER96 4.6 51.2 1.0 CB B:SER96 4.7 48.9 1.0 C B:ALA99 4.7 48.8 1.0 CA B:MET98 4.7 46.5 1.0 O B:CYS100 4.8 44.0 1.0 C B:CYS100 4.9 45.5 1.0

B.V.Plapp, H.A.Charlier, S.Ramaswamy. Mechanistic Implications From Structures of Yeast Alcohol Dehydrogenase Complexed with Coenzyme and An Alcohol. Arch.Biochem.Biophys. V. 591 35 2015.
ISSN: ESSN 1096-0384
PubMed: 26743849
DOI: 10.1016/J.ABB.2015.12.009