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Zinc in PDB 1y9a: Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate

Enzymatic activity of Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate

All present enzymatic activity of Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate:
1.1.1.2;

Protein crystallography data

The structure of Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate, PDB code: 1y9a was solved by L.J.Shimon, M.Peretz, E.Goihberg, Y.Burstein, F.Frolow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 117.04 / 1.81
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 76.891, 234.139, 96.241, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 17.7

Other elements in 1y9a:

The structure of Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Arsenic (As) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate (pdb code 1y9a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate, PDB code: 1y9a:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1y9a

Go back to Zinc Binding Sites List in 1y9a
Zinc binding site 1 out of 4 in the Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1000

b:24.0
occ:1.00
 O2 A:CAC1001 2.0 23.6 1.0
OD2 A:ASP150 2.0 22.3 1.0
NE2 A:HIS59 2.1 22.9 1.0
SG A:CYS37 2.3 24.5 1.0
CD2 A:HIS59 3.0 21.8 1.0
CE1 A:HIS59 3.1 24.2 1.0
CG A:ASP150 3.1 22.9 1.0
CB A:CYS37 3.2 23.1 1.0
AS A:CAC1001 3.2 26.8 1.0
O1 A:CAC1001 3.6 29.0 1.0
OD1 A:ASP150 3.6 26.3 1.0
OG A:SER39 3.7 23.0 1.0
CB A:SER39 3.8 25.1 1.0
C2 A:CAC1001 3.8 23.6 1.0
CG A:HIS59 4.1 23.7 1.0
ND1 A:HIS59 4.2 22.1 1.0
CB A:ASP150 4.3 21.0 1.0
OE2 A:GLU60 4.3 26.8 1.0
CE A:MET151 4.4 22.5 1.0
CA A:CYS37 4.6 23.7 1.0
CD A:GLU60 4.7 22.8 1.0
C1 A:CAC1001 4.8 29.0 1.0
N A:SER39 4.9 25.1 1.0
CA A:SER39 4.9 23.9 1.0

Zinc binding site 2 out of 4 in 1y9a

Go back to Zinc Binding Sites List in 1y9a
Zinc binding site 2 out of 4 in the Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:44.7
occ:1.00
 O A:HOH1330 2.0 39.0 1.0
OD2 A:ASP51 2.0 40.8 1.0
NE2 A:HIS53 2.0 36.2 1.0
CE1 A:HIS53 2.6 36.8 1.0
CG A:ASP51 2.8 35.2 1.0
OD1 A:ASP51 2.9 35.4 1.0
CD2 A:HIS53 3.3 33.1 1.0
ND1 A:HIS53 3.8 36.2 1.0
CA A:GLY8 4.1 35.0 1.0
CB A:ASP51 4.1 32.7 1.0
CG A:HIS53 4.2 33.6 1.0
N A:ILE9 4.6 37.4 1.0
C A:GLY8 4.9 35.7 1.0

Zinc binding site 3 out of 4 in 1y9a

Go back to Zinc Binding Sites List in 1y9a
Zinc binding site 3 out of 4 in the Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2000

b:19.8
occ:1.00
 O2 C:CAC2001 2.0 22.6 1.0
OD2 C:ASP150 2.0 22.0 1.0
NE2 C:HIS59 2.0 15.3 1.0
SG C:CYS37 2.2 19.3 1.0
CE1 C:HIS59 3.0 20.6 1.0
CD2 C:HIS59 3.0 18.4 1.0
CB C:CYS37 3.1 19.9 1.0
CG C:ASP150 3.2 21.8 1.0
AS C:CAC2001 3.3 22.9 1.0
OG C:SER39 3.6 20.2 1.0
OD1 C:ASP150 3.7 22.5 1.0
O1 C:CAC2001 3.7 21.4 1.0
C2 C:CAC2001 3.8 20.2 1.0
CB C:SER39 3.8 21.1 1.0
ND1 C:HIS59 4.1 19.3 1.0
CG C:HIS59 4.2 18.0 1.0
CB C:ASP150 4.3 16.5 1.0
OE2 C:GLU60 4.4 23.3 1.0
CE C:MET151 4.4 22.5 1.0
CA C:CYS37 4.6 21.3 1.0
CD C:GLU60 4.7 19.6 1.0
N C:SER39 4.8 21.2 1.0
O C:HOH2204 4.9 34.2 1.0
C1 C:CAC2001 4.9 22.1 1.0
CA C:SER39 4.9 21.2 1.0

Zinc binding site 4 out of 4 in 1y9a

Go back to Zinc Binding Sites List in 1y9a
Zinc binding site 4 out of 4 in the Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Alcohol Dehydrogenase From Entamoeba Histolotica in Complex with Cacodylate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2002

b:23.4
occ:0.50
 NE2 C:HIS53 1.8 19.4 1.0
OD2 C:ASP51 2.1 21.2 1.0
CE1 C:HIS53 2.8 25.0 1.0
CD2 C:HIS53 2.8 24.3 1.0
CG C:ASP51 2.9 22.1 1.0
OD1 C:ASP51 3.0 20.5 1.0
ND1 C:HIS53 3.9 24.5 1.0
CG C:HIS53 4.0 21.7 1.0
CB C:ASP51 4.3 20.5 1.0
CA C:GLY8 4.4 25.4 1.0
O C:HOH2185 4.5 42.7 1.0
O C:ARG52 5.0 21.4 1.0

Reference:

L.J.Shimon, E.Goihberg, M.Peretz, Y.Burstein, F.Frolow. Structure of Alcohol Dehydrogenase From Entamoeba Histolytica. Acta Crystallogr.,Sect.D V. 62 541 2006.
ISSN: ISSN 0907-4449
PubMed: 16627948
DOI: 10.1107/S0907444906009292
Page generated: Wed Dec 16 03:13:55 2020

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