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Zinc in PDB 4w6z: Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme

Enzymatic activity of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme

All present enzymatic activity of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme:
1.1.1.1;

Protein crystallography data

The structure of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme, PDB code: 4w6z was solved by B.V.Plapp, B.R.Savarimuthu, S.Ramaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.09 / 2.40
Space group P 3 2 1
Cell size a, b, c (Å), α, β, γ (°) 144.338, 144.338, 128.204, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 22.2

Other elements in 4w6z:

The structure of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Iodine (I) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme (pdb code 4w6z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme, PDB code: 4w6z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4w6z

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Zinc binding site 1 out of 8 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


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 I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:33.1
occ:1.00
 O A:ETF404 1.8 27.0 1.0
NE2 A:HIS66 2.0 29.0 1.0
SG A:CYS43 2.2 27.4 1.0
SG A:CYS153 2.4 26.8 1.0
CE1 A:HIS66 2.8 30.8 1.0
C2 A:ETF404 3.0 31.8 1.0
CD2 A:HIS66 3.1 30.2 1.0
CB A:CYS43 3.2 29.5 1.0
C5N A:8ID403 3.3 39.2 1.0
CB A:CYS153 3.4 25.1 1.0
OG1 A:THR45 3.6 27.5 1.0
CB A:THR45 3.7 28.1 1.0
C6N A:8ID403 3.8 34.9 1.0
ND1 A:HIS66 4.0 30.1 1.0
C4N A:8ID403 4.1 35.0 1.0
CG A:HIS66 4.1 29.3 1.0
C1 A:ETF404 4.2 31.3 1.0
CG2 A:THR45 4.3 28.6 1.0
F3 A:ETF404 4.4 31.5 1.0
F2 A:ETF404 4.7 34.8 1.0
CA A:CYS153 4.7 24.5 1.0
NH2 A:ARG340 4.7 32.8 1.0
CA A:CYS43 4.7 29.6 1.0
OE2 A:GLU67 4.8 28.2 1.0
N1N A:8ID403 4.9 33.4 1.0
CA A:THR45 5.0 29.7 1.0
N A:THR45 5.0 30.2 1.0
C A:CYS153 5.0 24.6 1.0

Zinc binding site 2 out of 8 in 4w6z

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Zinc binding site 2 out of 8 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


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 I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:35.3
occ:1.00
 SG A:CYS97 2.3 30.4 1.0
SG A:CYS100 2.3 40.9 1.0
SG A:CYS103 2.4 29.4 1.0
SG A:CYS111 2.4 34.0 1.0
CB A:CYS111 3.1 34.3 1.0
CB A:CYS97 3.3 34.1 1.0
CB A:CYS100 3.3 40.0 1.0
CB A:CYS103 3.5 30.4 1.0
N A:MET98 3.6 38.6 1.0
N A:CYS97 3.8 36.5 1.0
N A:CYS100 3.8 39.3 1.0
CA A:CYS97 3.9 35.2 1.0
CA A:CYS111 4.0 35.5 1.0
C A:CYS97 4.1 36.8 1.0
CA A:CYS100 4.1 39.7 1.0
N A:ALA99 4.2 40.6 1.0
N A:CYS103 4.3 30.4 1.0
CA A:CYS103 4.5 29.8 1.0
CA A:MET98 4.6 41.2 1.0
CD A:PRO112 4.8 41.4 1.0
CB A:SER96 4.8 37.8 1.0
C A:ALA99 4.8 40.3 1.0
ND1 A:HIS113 4.8 53.0 1.0
C A:CYS100 4.8 39.0 1.0
C A:CYS111 4.9 38.1 1.0
O A:CYS100 4.9 37.7 1.0
C A:SER96 4.9 36.1 1.0
C A:MET98 5.0 42.1 1.0

Zinc binding site 3 out of 8 in 4w6z

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Zinc binding site 3 out of 8 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


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 I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:49.6
occ:1.00
 NE2 B:HIS66 2.2 43.8 1.0
OE2 B:GLU67 2.3 37.3 1.0
SG B:CYS43 2.5 49.5 1.0
SG B:CYS153 2.6 41.9 1.0
CE1 B:HIS66 2.7 45.1 1.0
CB B:CYS43 3.0 49.7 1.0
O B:ETF404 3.1 61.3 1.0
CD B:GLU67 3.2 35.3 1.0
CD2 B:HIS66 3.3 40.4 1.0
CB B:CYS153 3.4 35.4 1.0
CG B:GLU67 3.7 34.7 1.0
ND1 B:HIS66 3.9 44.2 1.0
CG B:HIS66 4.2 40.9 1.0
CA B:CYS43 4.2 52.6 1.0
OE1 B:GLU67 4.2 36.0 1.0
N B:CYS43 4.2 51.5 1.0
C2 B:ETF404 4.4 71.3 1.0
CB B:THR45 4.6 48.1 1.0
CA B:CYS153 4.8 33.4 1.0
O B:HOH532 4.9 29.5 1.0
C B:CYS43 4.9 53.5 1.0

Zinc binding site 4 out of 8 in 4w6z

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Zinc binding site 4 out of 8 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


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 I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:37.7
occ:1.00
 SG B:CYS97 2.2 39.8 1.0
SG B:CYS103 2.3 35.6 1.0
SG B:CYS100 2.3 33.5 1.0
SG B:CYS111 2.3 42.9 1.0
CB B:CYS111 3.2 42.8 1.0
CB B:CYS103 3.4 32.6 1.0
CB B:CYS100 3.4 35.7 1.0
CB B:CYS97 3.4 42.6 1.0
N B:CYS97 3.8 40.5 1.0
N B:MET98 3.8 43.3 1.0
N B:CYS100 4.0 36.6 1.0
CA B:CYS111 4.0 44.3 1.0
CA B:CYS97 4.0 41.8 1.0
N B:CYS103 4.2 31.5 1.0
CA B:CYS100 4.2 36.0 1.0
C B:CYS97 4.3 42.6 1.0
N B:ALA99 4.3 39.6 1.0
CA B:CYS103 4.3 31.2 1.0
CB B:SER96 4.5 39.2 1.0
CD B:PRO112 4.5 51.7 1.0
CA B:MET98 4.7 43.0 1.0
C B:SER96 4.7 41.3 1.0
C B:ALA99 4.7 38.7 1.0
OG B:SER96 4.8 35.2 1.0
O B:CYS100 4.8 33.7 1.0
C B:CYS111 4.8 46.5 1.0
N B:PRO112 4.8 51.9 1.0
C B:CYS100 4.9 35.0 1.0

Zinc binding site 5 out of 8 in 4w6z

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Zinc binding site 5 out of 8 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:25.9
occ:1.00
 O C:ETF404 1.9 18.2 1.0
NE2 C:HIS66 2.1 29.5 1.0
SG C:CYS43 2.3 25.2 1.0
SG C:CYS153 2.5 23.1 1.0
C2 C:ETF404 2.9 22.9 1.0
CD2 C:HIS66 3.0 30.0 1.0
CE1 C:HIS66 3.1 32.0 1.0
CB C:CYS43 3.1 26.3 1.0
OG1 C:THR45 3.5 22.1 1.0
CB C:CYS153 3.5 22.0 1.0
C5N C:8ID403 3.5 24.2 1.0
CB C:THR45 3.6 23.4 1.0
C6N C:8ID403 4.0 23.6 1.0
CG C:HIS66 4.2 28.8 1.0
ND1 C:HIS66 4.2 30.6 1.0
C1 C:ETF404 4.3 23.9 1.0
CG2 C:THR45 4.3 23.8 1.0
C4N C:8ID403 4.4 23.8 1.0
CA C:CYS43 4.6 26.9 1.0
F3 C:ETF404 4.6 25.8 1.0
F1 C:ETF404 4.7 24.9 1.0
CA C:CYS153 4.8 21.6 1.0
CA C:THR45 4.9 26.7 1.0
N C:THR45 4.9 27.5 1.0
N1N C:8ID403 5.0 22.2 1.0
OE2 C:GLU67 5.0 21.1 1.0
NH2 C:ARG340 5.0 23.2 1.0

Zinc binding site 6 out of 8 in 4w6z

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Zinc binding site 6 out of 8 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:30.5
occ:1.00
 SG C:CYS97 2.1 31.5 1.0
SG C:CYS100 2.2 31.5 1.0
SG C:CYS111 2.3 31.0 1.0
SG C:CYS103 2.3 24.5 1.0
CB C:CYS111 3.1 28.2 1.0
CB C:CYS100 3.3 32.9 1.0
CB C:CYS97 3.5 35.7 1.0
CB C:CYS103 3.6 25.8 1.0
N C:MET98 3.8 38.9 1.0
N C:CYS97 3.9 36.1 1.0
N C:CYS100 3.9 33.6 1.0
CA C:CYS111 4.0 27.9 1.0
N C:CYS103 4.0 26.5 1.0
CA C:CYS97 4.1 36.2 1.0
CA C:CYS100 4.2 33.9 1.0
CA C:CYS103 4.4 25.8 1.0
C C:CYS97 4.4 37.8 1.0
N C:ALA99 4.4 37.2 1.0
CD C:PRO112 4.5 34.7 1.0
CB C:SER96 4.6 32.3 1.0
CA C:MET98 4.6 40.9 1.0
C C:CYS111 4.8 29.9 1.0
C C:SER96 4.8 35.0 1.0
OG C:SER96 4.8 34.7 1.0
N C:PRO112 4.9 33.6 1.0
ND1 C:HIS113 4.9 39.9 1.0
C C:CYS100 4.9 34.4 1.0
C C:ALA99 4.9 35.8 1.0
C C:MET98 4.9 39.5 1.0

Zinc binding site 7 out of 8 in 4w6z

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Zinc binding site 7 out of 8 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:48.2
occ:1.00
 OE2 D:GLU67 2.0 40.6 1.0
NE2 D:HIS66 2.2 44.8 1.0
SG D:CYS43 2.3 54.7 1.0
SG D:CYS153 2.7 44.8 1.0
CE1 D:HIS66 2.8 45.9 1.0
O D:ETF404 2.9 52.8 1.0
CD D:GLU67 3.2 38.4 1.0
CB D:CYS43 3.4 53.8 1.0
CD2 D:HIS66 3.4 41.4 1.0
CB D:CYS153 3.5 36.0 1.0
CG D:GLU67 3.9 38.0 1.0
ND1 D:HIS66 4.0 45.0 1.0
OE1 D:GLU67 4.1 37.9 1.0
C2 D:ETF404 4.2 56.4 1.0
CG D:HIS66 4.3 40.8 1.0
OG1 D:THR45 4.3 59.9 1.0
CA D:CYS43 4.5 55.6 1.0
N D:CYS43 4.5 53.2 1.0
O D:HOH520 4.5 18.7 1.0
CB D:THR45 4.9 58.7 1.0
OD2 D:ASP46 4.9 64.5 1.0
CA D:CYS153 4.9 33.8 1.0
NH1 D:ARG340 5.0 86.2 1.0

Zinc binding site 8 out of 8 in 4w6z

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Zinc binding site 8 out of 8 in the Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Yeast Alcohol Dehydrogenase I, Saccharomyces Cerevisiae Fermentative Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:33.8
occ:1.00
 SG D:CYS97 2.2 35.2 1.0
SG D:CYS100 2.3 31.2 1.0
SG D:CYS103 2.4 30.5 1.0
SG D:CYS111 2.6 42.0 1.0
CB D:CYS111 3.1 38.3 1.0
CB D:CYS103 3.4 29.3 1.0
CB D:CYS100 3.5 32.7 1.0
CB D:CYS97 3.5 37.3 1.0
N D:MET98 3.6 36.3 1.0
N D:CYS97 3.6 37.0 1.0
CA D:CYS111 3.9 40.3 1.0
CA D:CYS97 3.9 37.1 1.0
N D:CYS100 4.1 33.2 1.0
C D:CYS97 4.2 36.9 1.0
N D:CYS103 4.3 29.3 1.0
CA D:CYS100 4.3 33.0 1.0
N D:ALA99 4.4 34.9 1.0
CA D:CYS103 4.4 28.3 1.0
CA D:MET98 4.5 37.4 1.0
CB D:SER96 4.5 35.4 1.0
CD D:PRO112 4.5 46.1 1.0
C D:SER96 4.7 35.4 1.0
OG D:SER96 4.7 38.6 1.0
O D:CYS100 4.7 29.5 1.0
C D:CYS111 4.8 42.3 1.0
C D:CYS100 4.8 31.2 1.0
C D:ALA99 4.9 35.2 1.0
N D:PRO112 4.9 45.3 1.0

Reference:

S.B.Raj, S.Ramaswamy, B.V.Plapp. Yeast Alcohol Dehydrogenase Structure and Catalysis. Biochemistry V. 53 5791 2014.
ISSN: ISSN 0006-2960
PubMed: 25157460
DOI: 10.1021/BI5006442
Page generated: Sun Oct 27 09:43:50 2024

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