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Zinc in PDB 5yat: Crystal Structure of Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115, PDB code: 5yat was solved by H.D.Zhang, Q.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.61 / 1.75
Space group P 64
Cell size a, b, c (Å), α, β, γ (°) 111.856, 111.856, 105.520, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 21.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115 (pdb code 5yat). 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 Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115, PDB code: 5yat:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5yat

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Zinc binding site 1 out of 4 in the Crystal Structure of Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115


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 Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:21.9
occ:1.00
OE2 A:GLU70 1.9 23.9 1.0
NE2 A:HIS69 2.1 24.4 1.0
SG A:CYS46 2.3 25.0 1.0
SG A:CYS156 2.3 20.0 1.0
CD A:GLU70 3.0 22.1 1.0
CD2 A:HIS69 3.0 24.9 1.0
CE1 A:HIS69 3.1 24.8 1.0
HB3 A:CYS156 3.1 26.3 1.0
HB3 A:CYS46 3.1 31.3 1.0
CB A:CYS156 3.1 21.9 1.0
HD2 A:HIS69 3.2 30.0 1.0
HB2 A:CYS156 3.2 26.3 1.0
HE1 A:HIS69 3.3 29.9 1.0
HG2 A:GLU70 3.4 24.3 1.0
CB A:CYS46 3.4 26.0 1.0
H12 A:GOL402 3.5 44.9 1.0
HG3 A:GLU70 3.5 24.3 1.0
CG A:GLU70 3.5 20.2 1.0
O A:HOH592 3.6 29.6 1.0
HB A:THR48 3.7 30.6 1.0
HB2 A:CYS46 4.0 31.3 1.0
OE1 A:GLU70 4.1 23.2 1.0
ND1 A:HIS69 4.1 23.8 1.0
CG A:HIS69 4.1 25.6 1.0
HG1 A:THR48 4.2 30.0 1.0
C1 A:GOL402 4.5 37.4 1.0
H2 A:GOL402 4.5 55.0 1.0
CA A:CYS46 4.5 24.7 1.0
HO1 A:GOL402 4.5 47.4 1.0
H A:CYS46 4.6 30.3 1.0
CB A:THR48 4.6 25.5 1.0
N A:CYS46 4.6 25.2 1.0
OG1 A:THR48 4.6 24.9 1.0
CA A:CYS156 4.6 19.3 1.0
H A:THR48 4.7 25.5 1.0
O1 A:GOL402 4.7 39.4 1.0
O A:HOH580 4.8 22.9 1.0
H A:ALA157 4.8 25.8 1.0
HD1 A:HIS69 4.9 28.6 1.0
HA A:CYS156 5.0 23.3 1.0

Zinc binding site 2 out of 4 in 5yat

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Zinc binding site 2 out of 4 in the Crystal Structure of Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115


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 Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:19.9
occ:1.00
SG A:CYS103 2.3 18.2 1.0
SG A:CYS114 2.3 16.8 1.0
SG A:CYS100 2.4 20.8 1.0
SG A:CYS106 2.4 17.7 1.0
H A:CYS100 2.9 21.1 1.0
HB2 A:CYS114 2.9 22.9 1.0
HB3 A:CYS103 3.2 30.2 1.0
CB A:CYS114 3.2 19.1 1.0
HB2 A:CYS106 3.2 23.9 1.0
H A:LEU101 3.3 24.1 1.0
CB A:CYS103 3.4 25.1 1.0
CB A:CYS100 3.4 18.9 1.0
HB3 A:CYS100 3.4 22.8 1.0
CB A:CYS106 3.4 19.9 1.0
H A:CYS103 3.6 30.9 1.0
HA A:CYS114 3.6 19.5 1.0
N A:CYS100 3.6 17.5 1.0
H A:CYS106 3.6 21.1 1.0
HB2 A:SER99 3.7 22.6 1.0
H A:ASN102 3.7 24.9 1.0
N A:LEU101 3.8 20.0 1.0
CA A:CYS100 3.9 21.4 1.0
N A:CYS103 3.9 25.7 1.0
CA A:CYS114 3.9 16.2 1.0
HB3 A:CYS114 4.0 22.9 1.0
O A:HOH617 4.1 20.2 1.0
HB2 A:CYS103 4.1 30.2 1.0
HB3 A:CYS106 4.1 23.9 1.0
C A:CYS100 4.2 25.0 1.0
CA A:CYS103 4.2 24.3 1.0
N A:CYS106 4.2 17.6 1.0
HB2 A:CYS100 4.2 22.8 1.0
N A:ASN102 4.3 20.7 1.0
CA A:CYS106 4.4 17.7 1.0
H A:LYS116 4.5 23.4 1.0
CB A:SER99 4.6 18.8 1.0
H A:ALA115 4.6 26.4 1.0
O A:HOH759 4.6 41.1 1.0
HB2 A:LYS116 4.7 28.0 1.0
O A:HOH788 4.7 33.0 1.0
C A:SER99 4.7 20.6 1.0
C A:ASN102 4.7 34.4 1.0
HB2 A:TYR105 4.7 18.7 1.0
HA A:CYS106 4.7 21.3 1.0
CA A:LEU101 4.8 21.9 1.0
HA A:LEU101 4.8 26.3 1.0
HA A:CYS100 4.8 25.7 1.0
C A:CYS114 4.8 20.9 1.0
HG A:SER99 4.9 22.4 1.0
OG A:SER99 4.9 18.6 1.0
C A:CYS103 4.9 21.7 1.0
C A:LEU101 4.9 24.6 1.0
N A:ALA115 4.9 21.9 1.0

Zinc binding site 3 out of 4 in 5yat

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Zinc binding site 3 out of 4 in the Crystal Structure of Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115


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 Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:28.1
occ:1.00
OE2 B:GLU70 1.9 29.5 1.0
NE2 B:HIS69 2.0 31.7 1.0
SG B:CYS156 2.3 26.7 1.0
SG B:CYS46 2.3 32.4 1.0
CE1 B:HIS69 2.9 34.6 1.0
CD B:GLU70 3.0 33.9 1.0
HE1 B:HIS69 3.0 41.6 1.0
CD2 B:HIS69 3.1 34.5 1.0
HB3 B:CYS46 3.2 46.5 1.0
CB B:CYS156 3.2 31.3 1.0
HB3 B:CYS156 3.2 37.6 1.0
HB2 B:CYS156 3.2 37.6 1.0
H12 B:GOL402 3.3 52.1 1.0
HD2 B:HIS69 3.3 41.5 1.0
CB B:CYS46 3.4 38.7 1.0
HG2 B:GLU70 3.4 41.3 1.0
HG3 B:GLU70 3.5 41.3 1.0
CG B:GLU70 3.6 34.4 1.0
O B:HOH609 3.8 36.2 1.0
HB B:THR48 3.9 47.3 1.0
ND1 B:HIS69 4.0 34.7 1.0
HB2 B:CYS46 4.0 46.5 1.0
OE1 B:GLU70 4.1 32.1 1.0
CG B:HIS69 4.1 28.0 1.0
C1 B:GOL402 4.2 43.4 1.0
H2 B:GOL402 4.2 56.5 1.0
HG1 B:THR48 4.3 39.9 1.0
HO1 B:GOL402 4.4 54.8 1.0
H B:CYS46 4.4 43.3 1.0
N B:CYS46 4.5 36.0 1.0
CA B:CYS46 4.5 36.1 1.0
O1 B:GOL402 4.5 45.6 1.0
OG1 B:THR48 4.6 33.2 1.0
CB B:THR48 4.7 39.3 1.0
CA B:CYS156 4.7 29.2 1.0
O B:HOH584 4.7 31.5 1.0
HD1 B:HIS69 4.7 41.7 1.0
H B:THR48 4.7 41.8 1.0
C2 B:GOL402 4.8 47.1 1.0
H B:ALA157 4.9 29.9 1.0
HA B:CYS156 5.0 35.0 1.0

Zinc binding site 4 out of 4 in 5yat

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Zinc binding site 4 out of 4 in the Crystal Structure of Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115


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 Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn405

b:21.4
occ:1.00
SG B:CYS100 2.3 23.8 1.0
SG B:CYS114 2.3 22.6 1.0
SG B:CYS106 2.3 22.7 1.0
SG B:CYS103 2.4 21.3 1.0
HB2 B:CYS114 2.9 21.9 1.0
H B:CYS100 3.0 26.9 1.0
HB3 B:CYS103 3.0 27.5 1.0
HB2 B:CYS106 3.1 25.6 1.0
CB B:CYS114 3.1 18.2 1.0
H B:LEU101 3.3 28.6 1.0
CB B:CYS103 3.3 22.9 1.0
CB B:CYS106 3.4 21.3 1.0
CB B:CYS100 3.4 23.8 1.0
HB3 B:CYS100 3.5 28.6 1.0
H B:CYS103 3.6 28.4 1.0
H B:CYS106 3.6 18.9 1.0
HA B:CYS114 3.6 28.1 1.0
N B:CYS100 3.6 22.4 1.0
HB2 B:SER99 3.7 30.9 1.0
H B:ASN102 3.7 29.7 1.0
N B:LEU101 3.8 23.8 1.0
N B:CYS103 3.9 23.6 1.0
HB3 B:CYS114 3.9 21.9 1.0
CA B:CYS100 3.9 25.5 1.0
CA B:CYS114 4.0 23.3 1.0
HB3 B:CYS106 4.0 25.6 1.0
HB2 B:CYS103 4.1 27.5 1.0
CA B:CYS103 4.2 24.2 1.0
C B:CYS100 4.2 25.4 1.0
N B:CYS106 4.2 15.7 1.0
HB2 B:CYS100 4.3 28.6 1.0
N B:ASN102 4.3 24.7 1.0
O B:HOH634 4.3 26.2 1.0
CA B:CYS106 4.4 18.5 1.0
O B:HOH708 4.5 35.3 1.0
CB B:SER99 4.6 25.7 1.0
C B:ASN102 4.6 24.0 1.0
H B:LYS116 4.6 32.9 1.0
H B:ALA115 4.6 31.3 1.0
O B:HOH694 4.7 37.1 1.0
HA B:CYS106 4.7 22.2 1.0
HB2 B:TYR105 4.7 20.2 1.0
CA B:LEU101 4.7 24.0 1.0
HA B:LEU101 4.7 28.8 1.0
C B:SER99 4.7 22.3 1.0
HG B:SER99 4.9 31.2 1.0
HB2 B:LYS116 4.9 39.6 1.0
HA B:CYS100 4.9 30.6 1.0
OG B:SER99 4.9 26.0 1.0
C B:LEU101 4.9 22.3 1.0
C B:CYS114 4.9 26.3 1.0
H B:TYR105 4.9 21.2 1.0
C B:CYS103 4.9 21.6 1.0
HA B:GLU111 4.9 28.7 1.0
HA B:CYS103 5.0 29.1 1.0

Reference:

H.Zhang, Q.Li, L.Wang, Y.Chen. Investigation of Structure and Function of Mitochondrial Alcohol Dehydrogenase Isozyme III From Komagataella Phaffii GS115. Biochim. Biophys. Acta V.1862 1199 2018.
ISSN: ISSN 0006-3002
PubMed: 29474823
DOI: 10.1016/J.BBAGEN.2018.02.012
Page generated: Wed Dec 16 11:22:23 2020

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