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Zinc in PDB 5kcz: Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol

Enzymatic activity of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol

All present enzymatic activity of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol, PDB code: 5kcz 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 / 1.14
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.400, 51.380, 92.290, 91.97, 103.03, 110.28
R / Rfree (%) 12.6 / 14.8

Other elements in 5kcz:

The structure of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol also contains other interesting chemical elements:

Fluorine (F) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol (pdb code 5kcz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol, PDB code: 5kcz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5kcz

Go back to Zinc Binding Sites List in 5kcz
Zinc binding site 1 out of 4 in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:10.1
occ:1.00
 O A:ETF378 2.0 10.6 0.5
O A:ETF378 2.0 9.9 0.5
NE2 A:HIS67 2.1 10.5 1.0
SG A:CYS174 2.3 9.5 1.0
SG A:CYS46 2.4 8.8 1.0
C2 A:ETF378 2.9 11.8 0.5
C2 A:ETF378 2.9 10.3 0.5
CE1 A:HIS67 3.0 8.5 1.0
CD2 A:HIS67 3.1 9.9 1.0
C5N A:NAJ377 3.3 8.2 1.0
CB A:CYS46 3.3 9.0 1.0
CB A:CYS174 3.4 8.4 1.0
OG1 A:THR48 3.7 8.7 1.0
C4N A:NAJ377 3.9 8.7 1.0
C6N A:NAJ377 3.9 7.7 1.0
CB A:THR48 3.9 8.8 1.0
ND1 A:HIS67 4.2 8.4 1.0
CG A:HIS67 4.2 8.2 1.0
C1 A:ETF378 4.2 11.9 0.5
C1 A:ETF378 4.3 9.7 0.5
F2 A:ETF378 4.6 15.6 0.5
NH2 A:ARG369 4.7 9.5 1.0
F1 A:ETF378 4.7 12.6 0.5
F1 A:ETF378 4.8 10.9 0.5
CG2 A:THR48 4.8 12.8 1.0
CA A:CYS174 4.8 7.8 1.0
CA A:CYS46 4.8 8.4 1.0
F3 A:ETF378 4.8 14.0 0.5
N A:THR48 4.8 7.7 1.0
CE2 A:PHE93 4.9 9.1 1.0
OE2 A:GLU68 4.9 10.2 1.0
N1N A:NAJ377 4.9 7.2 1.0
C3N A:NAJ377 5.0 7.8 1.0

Zinc binding site 2 out of 4 in 5kcz

Go back to Zinc Binding Sites List in 5kcz
Zinc binding site 2 out of 4 in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:10.6
occ:1.00
 SG A:CYS111 2.3 10.3 1.0
SG A:CYS100 2.3 11.1 1.0
SG A:CYS97 2.3 12.3 1.0
SG A:CYS103 2.4 10.4 1.0
CB A:CYS111 3.3 9.4 1.0
CB A:CYS100 3.4 12.3 1.0
CB A:CYS103 3.4 10.9 1.0
CB A:CYS97 3.4 12.7 1.0
N A:CYS97 3.5 10.5 1.0
CA A:CYS111 3.7 9.0 1.0
N A:CYS100 3.9 13.9 1.0
CA A:CYS97 3.9 11.7 1.0
N A:GLY98 4.0 11.8 1.0
N A:LEU112 4.0 10.1 1.0
N A:CYS103 4.2 9.8 1.0
CA A:CYS100 4.2 13.1 1.0
C A:CYS111 4.3 9.6 1.0
C A:CYS97 4.3 12.2 1.0
CA A:CYS103 4.3 10.1 1.0
N A:LYS99 4.5 14.3 1.0
C A:GLN96 4.6 10.6 1.0
C A:CYS100 4.8 13.4 1.0
CG A:LYS113 4.9 14.8 1.0
N A:LYS113 4.9 10.4 1.0
O A:CYS100 4.9 11.9 1.0
CA A:GLN96 4.9 10.4 1.0
O A:HOH552 5.0 28.3 1.0
CA A:GLY98 5.0 13.6 1.0

Zinc binding site 3 out of 4 in 5kcz

Go back to Zinc Binding Sites List in 5kcz
Zinc binding site 3 out of 4 in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:12.0
occ:1.00
 O B:ETF378 2.0 12.8 1.0
NE2 B:HIS67 2.1 12.4 1.0
SG B:CYS174 2.3 11.4 1.0
SG B:CYS46 2.4 10.9 1.0
C2 B:ETF378 2.9 15.9 1.0
CE1 B:HIS67 3.0 10.7 1.0
CD2 B:HIS67 3.1 11.8 1.0
C5N B:NAJ377 3.3 9.8 1.0
CB B:CYS46 3.3 10.6 1.0
CB B:CYS174 3.4 10.0 1.0
OG1 B:THR48 3.7 10.3 1.0
C4N B:NAJ377 3.9 11.4 1.0
CB B:THR48 3.9 10.4 1.0
C6N B:NAJ377 3.9 9.4 1.0
ND1 B:HIS67 4.2 10.3 1.0
CG B:HIS67 4.2 10.1 1.0
C1 B:ETF378 4.3 16.4 1.0
NH2 B:ARG369 4.7 11.7 1.0
F1 B:ETF378 4.7 20.6 1.0
CA B:CYS174 4.8 9.7 1.0
CG2 B:THR48 4.8 14.9 1.0
CA B:CYS46 4.8 10.6 1.0
F3 B:ETF378 4.9 27.8 1.0
N B:THR48 4.9 10.2 1.0
CE2 B:PHE93 4.9 10.7 1.0
OE2 B:GLU68 4.9 12.2 1.0
N1N B:NAJ377 4.9 9.7 1.0
C3N B:NAJ377 5.0 9.5 1.0

Zinc binding site 4 out of 4 in 5kcz

Go back to Zinc Binding Sites List in 5kcz
Zinc binding site 4 out of 4 in the Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Horse Liver S48T Alcohol Dehydrogenase Complexed with Nad and Trifluoroethanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:12.0
occ:1.00
 SG B:CYS111 2.3 11.6 1.0
SG B:CYS100 2.3 12.7 1.0
SG B:CYS97 2.3 14.2 1.0
SG B:CYS103 2.4 11.2 1.0
CB B:CYS111 3.3 10.8 1.0
CB B:CYS100 3.4 14.1 1.0
CB B:CYS97 3.4 13.6 1.0
CB B:CYS103 3.4 11.7 1.0
N B:CYS97 3.5 12.6 1.0
CA B:CYS111 3.8 10.4 1.0
N B:CYS100 3.9 14.4 1.0
CA B:CYS97 3.9 13.6 1.0
N B:GLY98 4.0 13.6 1.0
N B:LEU112 4.0 11.2 1.0
CA B:CYS100 4.2 14.5 1.0
N B:CYS103 4.2 11.5 1.0
C B:CYS111 4.3 10.6 1.0
C B:CYS97 4.3 13.4 1.0
CA B:CYS103 4.4 10.9 1.0
N B:LYS99 4.5 15.1 1.0
C B:GLN96 4.6 12.0 1.0
N B:LYS113 4.8 12.1 1.0
C B:CYS100 4.8 14.2 1.0
CG B:LYS113 4.9 17.2 1.0
CA B:GLN96 4.9 11.0 1.0
O B:CYS100 4.9 13.9 1.0
CA B:GLY98 5.0 14.9 1.0

Reference:

K.Kim, B.V.Plapp. Inversion of Substrate Stereoselectivity of Horse Liver Alcohol Dehydrogenase By Substitutions of Ser-48 and Phe-93. Chem. Biol. Interact. V. 276 77 2017.
ISSN: ISSN 1872-7786
PubMed: 28025168
DOI: 10.1016/J.CBI.2016.12.016
Page generated: Wed Dec 16 06:26:59 2020

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