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Zinc in PDB 6cy3: Horse Liver E267N Alcohol Dehydrogenase Complex with 3'- Dephosphocoenzyme A

Protein crystallography data

The structure of Horse Liver E267N Alcohol Dehydrogenase Complex with 3'- Dephosphocoenzyme A, PDB code: 6cy3 was solved by B.V.Plapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 55.510, 74.010, 182.460, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 31

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver E267N Alcohol Dehydrogenase Complex with 3'- Dephosphocoenzyme A (pdb code 6cy3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Horse Liver E267N Alcohol Dehydrogenase Complex with 3'- Dephosphocoenzyme A, PDB code: 6cy3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6cy3

Go back to Zinc Binding Sites List in 6cy3
Zinc binding site 1 out of 2 in the Horse Liver E267N Alcohol Dehydrogenase Complex with 3'- Dephosphocoenzyme A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Horse Liver E267N Alcohol Dehydrogenase Complex with 3'- Dephosphocoenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:58.0
occ:1.00
SG A:CYS174 2.2 42.6 1.0
NE2 A:HIS67 2.3 40.0 1.0
S44 A:COD403 2.5 51.6 1.0
SG A:CYS46 2.6 55.2 1.0
CD2 A:HIS67 3.1 44.4 1.0
CB A:CYS174 3.2 38.0 1.0
C43 A:COD403 3.3 52.9 1.0
CE1 A:HIS67 3.4 42.0 1.0
CB A:CYS46 3.4 46.1 1.0
CG A:HIS67 4.3 40.7 1.0
ND1 A:HIS67 4.4 41.3 1.0
CA A:CYS174 4.6 41.1 1.0
OG A:SER48 4.6 35.9 1.0
CB A:SER48 4.8 39.9 1.0
N A:GLY175 4.8 42.3 1.0
C42 A:COD403 4.8 53.7 1.0
C A:CYS174 4.8 40.5 1.0
OE2 A:GLU68 4.9 50.1 1.0
CA A:CYS46 4.9 48.0 1.0
CE2 A:PHE93 4.9 42.8 1.0

Zinc binding site 2 out of 2 in 6cy3

Go back to Zinc Binding Sites List in 6cy3
Zinc binding site 2 out of 2 in the Horse Liver E267N Alcohol Dehydrogenase Complex with 3'- Dephosphocoenzyme A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Horse Liver E267N Alcohol Dehydrogenase Complex with 3'- Dephosphocoenzyme A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:52.2
occ:1.00
SG A:CYS100 2.1 46.5 1.0
SG A:CYS103 2.3 45.6 1.0
SG A:CYS111 2.3 49.2 1.0
SG A:CYS97 2.6 53.7 1.0
CB A:CYS111 3.3 49.3 1.0
CB A:CYS100 3.3 52.0 1.0
CB A:CYS103 3.4 50.1 1.0
CA A:CYS111 3.6 48.7 1.0
CB A:CYS97 3.6 49.0 1.0
N A:LEU112 3.7 54.6 1.0
N A:CYS97 3.8 46.5 1.0
N A:CYS100 3.9 52.8 1.0
C A:CYS111 4.1 56.3 1.0
CA A:CYS97 4.1 50.5 1.0
CA A:CYS100 4.2 54.7 1.0
N A:CYS103 4.2 44.2 1.0
N A:GLY98 4.2 64.3 1.0
CA A:CYS103 4.4 47.3 1.0
N A:LYS113 4.5 52.2 1.0
C A:CYS97 4.6 58.3 1.0
N A:LYS99 4.7 61.2 1.0
C A:GLN96 4.8 47.8 1.0
CG A:LYS113 4.8 52.8 1.0
CA A:LEU112 4.9 56.0 1.0
N A:CYS111 4.9 48.1 1.0
C A:CYS100 5.0 56.4 1.0

Reference:

Y.H.Kim, D.S.Gogerty, B.V.Plapp. Substitutions of A Buried Glutamate Residue Hinder the Conformational Change in Horse Liver Alcohol Dehydrogenase and Yield A Surprising Complex with Endogenous 3'-Dephosphocoenzyme A. Arch. Biochem. Biophys. V. 653 97 2018.
ISSN: ESSN 1096-0384
PubMed: 30018019
DOI: 10.1016/J.ABB.2018.07.003
Page generated: Wed Dec 16 11:38:31 2020

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