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Zinc in PDB 5yln: Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form

Enzymatic activity of Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form

All present enzymatic activity of Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form:
1.1.1.1;

Protein crystallography data

The structure of Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form, PDB code: 5yln was solved by S.Donghyuk, H.Seungsu, L.Sangho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.10 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.177, 123.245, 130.356, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form (pdb code 5yln). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form, PDB code: 5yln:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5yln

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Zinc binding site 1 out of 8 in the Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:47.2
occ:1.00
 N A:TRS403 2.0 53.1 1.0
NE2 A:HIS60 2.1 38.0 1.0
SG A:CYS38 2.5 37.2 1.0
CD2 A:HIS60 3.0 36.4 1.0
CE1 A:HIS60 3.1 38.6 1.0
C A:TRS403 3.1 46.0 1.0
CB A:CYS38 3.2 32.1 1.0
C3 A:TRS403 3.4 41.5 1.0
C2 A:TRS403 3.7 33.2 1.0
O3 A:TRS403 3.7 39.9 1.0
O2 A:TRS403 3.9 34.1 1.0
ND1 A:HIS60 4.2 35.0 1.0
CG A:HIS60 4.2 29.4 1.0
C1 A:TRS403 4.3 47.8 1.0
OG1 A:THR40 4.4 41.5 1.0
OE2 A:GLU61 4.6 44.8 1.0
CB A:THR40 4.6 39.7 1.0
CA A:CYS38 4.7 31.4 1.0
O A:HOH530 4.7 50.5 1.0
CD A:GLU61 4.7 33.8 1.0
CG A:GLU61 5.0 29.6 1.0

Zinc binding site 2 out of 8 in 5yln

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Zinc binding site 2 out of 8 in the Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:39.8
occ:0.71
 SG A:CYS96 2.2 35.4 1.0
SG A:CYS90 2.3 39.5 1.0
SG A:CYS93 2.4 36.9 1.0
SG A:CYS104 2.4 36.3 1.0
CB A:CYS104 3.1 27.1 1.0
CB A:CYS96 3.2 35.2 1.0
CB A:CYS93 3.4 33.7 1.0
CB A:CYS90 3.5 28.8 1.0
N A:CYS90 3.5 35.9 1.0
CA A:CYS104 3.6 33.1 1.0
N A:CYS93 3.7 45.2 1.0
N A:GLY91 3.9 36.0 1.0
CA A:CYS90 3.9 35.6 1.0
N A:GLU105 4.0 27.1 1.0
CA A:CYS93 4.1 39.5 1.0
N A:CYS96 4.1 34.5 1.0
C A:CYS104 4.2 33.8 1.0
CA A:CYS96 4.2 35.9 1.0
C A:CYS90 4.3 41.2 1.0
N A:LYS92 4.3 49.4 1.0
N A:ASP106 4.6 43.7 1.0
C A:ALA89 4.6 37.4 1.0
C A:CYS93 4.8 36.4 1.0
C A:LYS92 4.9 45.2 1.0
CA A:GLY91 4.9 44.1 1.0
N A:CYS104 4.9 34.1 1.0
CA A:ALA89 4.9 37.5 1.0

Zinc binding site 3 out of 8 in 5yln

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Zinc binding site 3 out of 8 in the Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:48.8
occ:0.76
 N B:TRS403 2.0 44.1 1.0
NE2 B:HIS60 2.1 43.8 1.0
SG B:CYS38 2.4 41.0 1.0
CD2 B:HIS60 3.0 42.3 1.0
C B:TRS403 3.1 45.7 1.0
CE1 B:HIS60 3.1 41.1 1.0
CB B:CYS38 3.3 41.1 1.0
C3 B:TRS403 3.3 51.9 1.0
C2 B:TRS403 3.6 37.9 1.0
O3 B:TRS403 3.7 58.1 1.0
O2 B:TRS403 4.0 43.7 1.0
CG B:HIS60 4.2 46.1 1.0
ND1 B:HIS60 4.2 47.8 1.0
OG1 B:THR40 4.2 52.4 1.0
C1 B:TRS403 4.3 51.0 1.0
CB B:THR40 4.4 45.9 1.0
OE2 B:GLU61 4.5 47.4 1.0
CA B:CYS38 4.6 43.4 1.0
CD B:GLU61 4.7 46.8 1.0

Zinc binding site 4 out of 8 in 5yln

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Zinc binding site 4 out of 8 in the Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:40.6
occ:0.75
 SG B:CYS96 2.2 38.0 1.0
SG B:CYS104 2.3 35.9 1.0
SG B:CYS93 2.4 39.2 1.0
SG B:CYS90 2.5 40.5 1.0
CB B:CYS104 3.1 31.2 1.0
CB B:CYS96 3.3 28.9 1.0
CB B:CYS90 3.3 42.3 1.0
CB B:CYS93 3.5 41.8 1.0
N B:CYS90 3.5 35.2 1.0
CA B:CYS104 3.5 35.4 1.0
CA B:CYS90 3.8 39.2 1.0
N B:GLU105 3.8 44.0 1.0
N B:GLY91 3.9 41.3 1.0
N B:CYS93 3.9 43.6 1.0
C B:CYS104 4.1 39.3 1.0
C B:CYS90 4.2 47.8 1.0
N B:CYS96 4.2 33.3 1.0
CA B:CYS93 4.3 41.7 1.0
CA B:CYS96 4.3 33.3 1.0
N B:LYS92 4.5 47.5 1.0
N B:ASP106 4.5 51.4 1.0
C B:ALA89 4.6 40.1 1.0
CB B:ASP106 4.8 52.8 1.0
N B:CYS104 4.8 42.1 1.0
CA B:GLY91 4.9 33.6 1.0
C B:CYS93 4.9 35.1 1.0

Zinc binding site 5 out of 8 in 5yln

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Zinc binding site 5 out of 8 in the Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:49.7
occ:0.89
 N C:TRS403 2.0 44.1 1.0
NE2 C:HIS60 2.1 37.0 1.0
SG C:CYS38 2.6 39.8 1.0
C C:TRS403 2.9 51.9 1.0
CD2 C:HIS60 3.1 33.1 1.0
CE1 C:HIS60 3.1 36.3 1.0
C3 C:TRS403 3.1 56.2 1.0
CB C:CYS38 3.4 37.7 1.0
C2 C:TRS403 3.4 45.8 1.0
O3 C:TRS403 3.6 55.0 1.0
O2 C:TRS403 4.1 49.5 1.0
C1 C:TRS403 4.2 49.0 1.0
ND1 C:HIS60 4.2 35.8 1.0
CG C:HIS60 4.3 35.7 1.0
O1 C:TRS403 4.3 60.0 1.0
OE2 C:GLU61 4.7 45.1 1.0
CB C:THR40 4.7 43.1 1.0
OG1 C:THR40 4.7 49.5 1.0
CD C:GLU61 4.8 43.7 1.0
CA C:CYS38 4.8 39.6 1.0

Zinc binding site 6 out of 8 in 5yln

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Zinc binding site 6 out of 8 in the Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:53.3
occ:0.86
 SG C:CYS104 2.3 36.5 1.0
SG C:CYS93 2.3 44.1 1.0
SG C:CYS96 2.4 43.0 1.0
SG C:CYS90 2.6 41.2 1.0
CB C:CYS104 3.1 43.7 1.0
CB C:CYS96 3.2 44.2 1.0
CB C:CYS93 3.4 39.0 1.0
CB C:CYS90 3.5 37.7 1.0
CA C:CYS104 3.5 44.8 1.0
N C:CYS90 3.6 41.1 1.0
N C:CYS93 3.7 46.7 1.0
N C:GLY91 3.9 49.3 1.0
N C:GLU105 3.9 52.1 1.0
CA C:CYS90 3.9 41.5 1.0
C C:CYS104 4.2 43.6 1.0
CA C:CYS93 4.2 43.5 1.0
N C:LYS92 4.2 52.9 1.0
N C:CYS96 4.3 41.4 1.0
C C:CYS90 4.3 49.0 1.0
CA C:CYS96 4.3 41.9 1.0
N C:ASP106 4.5 42.9 1.0
C C:ALA89 4.7 41.5 1.0
N C:CYS104 4.8 38.9 1.0
C C:LYS92 4.8 54.1 1.0
CA C:GLY91 4.8 48.7 1.0
CB C:ASP106 4.9 48.0 1.0
C C:CYS93 4.9 48.3 1.0
C C:GLY91 4.9 54.5 1.0
CA C:ALA89 5.0 41.8 1.0

Zinc binding site 7 out of 8 in 5yln

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Zinc binding site 7 out of 8 in the Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:51.3
occ:1.00
 N D:TRS403 1.8 44.1 1.0
NE2 D:HIS60 2.2 29.3 1.0
SG D:CYS38 2.5 40.0 1.0
C D:TRS403 3.1 45.3 1.0
CD2 D:HIS60 3.1 29.4 1.0
CE1 D:HIS60 3.2 31.8 1.0
CB D:CYS38 3.3 37.7 1.0
C2 D:TRS403 3.5 36.3 1.0
C3 D:TRS403 3.6 46.6 1.0
O3 D:TRS403 3.8 46.8 1.0
C1 D:TRS403 4.2 48.1 1.0
O2 D:TRS403 4.2 40.7 1.0
CG D:HIS60 4.3 35.8 1.0
ND1 D:HIS60 4.3 34.0 1.0
OG1 D:THR40 4.4 48.0 1.0
CB D:THR40 4.6 43.5 1.0
OE2 D:GLU61 4.6 36.6 1.0
CD D:GLU61 4.7 44.1 1.0
CA D:CYS38 4.7 42.3 1.0
OE1 D:GLU61 5.0 42.1 1.0
CG D:GLU61 5.0 38.5 1.0

Zinc binding site 8 out of 8 in 5yln

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Zinc binding site 8 out of 8 in the Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:42.4
occ:0.84
 SG D:CYS104 2.3 35.2 1.0
SG D:CYS93 2.3 36.6 1.0
SG D:CYS90 2.4 36.4 1.0
SG D:CYS96 2.4 36.3 1.0
CB D:CYS104 3.0 28.1 1.0
CB D:CYS90 3.3 34.9 1.0
CB D:CYS96 3.3 33.6 1.0
CB D:CYS93 3.3 33.8 1.0
CA D:CYS104 3.5 30.0 1.0
N D:CYS90 3.6 30.8 1.0
N D:GLU105 3.7 42.0 1.0
N D:CYS93 3.8 38.6 1.0
CA D:CYS90 3.8 35.2 1.0
N D:GLY91 3.9 37.0 1.0
C D:CYS104 4.0 38.1 1.0
CA D:CYS93 4.1 39.0 1.0
C D:CYS90 4.2 31.6 1.0
N D:CYS96 4.2 28.1 1.0
CA D:CYS96 4.4 33.5 1.0
N D:LYS92 4.4 41.8 1.0
N D:ASP106 4.5 36.8 1.0
C D:ALA89 4.7 39.4 1.0
N D:CYS104 4.8 31.1 1.0
CB D:ASP106 4.8 40.2 1.0
C D:CYS93 4.9 34.5 1.0
CA D:GLY91 4.9 39.2 1.0
C D:LYS92 4.9 43.6 1.0
CA D:GLU105 4.9 42.0 1.0

Reference:

S.Donghyuk, H.Seungsu, L.Sangho. Zinc Dependent Alcohol Dehydrogenase 2 From Streptococcus Pneumonia - Apo Form To Be Published.
Page generated: Mon Oct 28 15:59:47 2024

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