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Zinc in PDB 5kj1: G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol

Enzymatic activity of G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol

All present enzymatic activity of G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol, PDB code: 5kj1 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 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.310, 51.500, 92.420, 91.82, 103.05, 110.12
R / Rfree (%) 12.4 / 17

Other elements in 5kj1:

The structure of G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol also contains other interesting chemical elements:

Fluorine (F) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol (pdb code 5kj1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol, PDB code: 5kj1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5kj1

Go back to Zinc Binding Sites List in 5kj1
Zinc binding site 1 out of 4 in the G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:10.3
occ:1.00
 O1 A:PFB378 1.9 10.2 1.0
NE2 A:HIS67 2.0 10.3 1.0
SG A:CYS174 2.3 10.0 1.0
SG A:CYS46 2.3 9.8 0.9
C7 A:PFB378 2.9 10.8 1.0
CE1 A:HIS67 3.0 9.9 1.0
CD2 A:HIS67 3.1 10.3 1.0
CB A:CYS46 3.3 11.3 0.1
CB A:CYS46 3.3 10.5 0.9
C5N A:NAJ377 3.3 9.4 1.0
CB A:CYS174 3.4 9.8 1.0
SG A:CYS46 3.5 12.0 0.1
OG A:SER48 3.8 10.1 1.0
C4N A:NAJ377 3.9 9.0 1.0
C6N A:NAJ377 3.9 8.6 1.0
CB A:SER48 4.0 10.7 1.0
F6 A:PFB378 4.1 12.2 1.0
C1 A:PFB378 4.1 10.6 1.0
ND1 A:HIS67 4.2 10.2 1.0
CG A:HIS67 4.2 9.8 1.0
C6 A:PFB378 4.6 11.8 1.0
NH2 A:ARG369 4.7 11.1 1.0
CA A:CYS174 4.7 8.7 1.0
CA A:CYS46 4.8 10.1 1.0
OE2 A:GLU68 4.8 12.4 1.0
N A:SER48 4.9 9.3 1.0
CE2 A:PHE93 4.9 10.7 1.0
N1N A:NAJ377 4.9 8.3 1.0
C3N A:NAJ377 5.0 8.4 1.0

Zinc binding site 2 out of 4 in 5kj1

Go back to Zinc Binding Sites List in 5kj1
Zinc binding site 2 out of 4 in the G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:11.3
occ:1.00
 SG A:CYS111 2.3 10.9 1.0
SG A:CYS97 2.3 12.8 1.0
SG A:CYS100 2.3 11.8 1.0
SG A:CYS103 2.4 11.0 1.0
CB A:CYS111 3.3 10.4 1.0
CB A:CYS100 3.4 12.4 1.0
CB A:CYS97 3.4 12.5 1.0
CB A:CYS103 3.4 11.1 1.0
N A:CYS97 3.5 11.2 1.0
CA A:CYS111 3.7 9.7 1.0
N A:CYS100 3.9 14.5 1.0
CA A:CYS97 3.9 12.0 1.0
N A:GLY98 3.9 13.2 1.0
N A:LEU112 4.0 10.6 1.0
N A:CYS103 4.2 11.2 1.0
CA A:CYS100 4.2 13.2 1.0
C A:CYS111 4.3 10.3 1.0
C A:CYS97 4.3 13.3 1.0
CA A:CYS103 4.4 11.4 1.0
N A:LYS99 4.5 14.6 1.0
C A:GLN96 4.6 11.0 1.0
C A:CYS100 4.8 12.7 1.0
N A:LYS113 4.9 10.3 1.0
CG A:LYS113 4.9 15.5 1.0
O A:CYS100 4.9 13.7 1.0
CA A:GLN96 4.9 10.6 1.0
CA A:GLY98 4.9 14.5 1.0
O A:HOH552 5.0 26.4 1.0

Zinc binding site 3 out of 4 in 5kj1

Go back to Zinc Binding Sites List in 5kj1
Zinc binding site 3 out of 4 in the G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:13.4
occ:1.00
 O1 B:PFB378 1.9 13.1 1.0
NE2 B:HIS67 2.0 12.7 1.0
SG B:CYS174 2.3 13.1 1.0
SG B:CYS46 2.3 13.4 1.0
C7 B:PFB378 2.9 12.8 1.0
CE1 B:HIS67 3.0 11.6 1.0
CD2 B:HIS67 3.0 12.8 1.0
CB B:CYS46 3.3 14.3 1.0
C5N B:NAJ377 3.3 11.6 1.0
CB B:CYS174 3.4 12.0 1.0
OG B:SER48 3.8 13.0 1.0
C4N B:NAJ377 3.9 12.4 1.0
C6N B:NAJ377 3.9 11.4 1.0
CB B:SER48 4.0 12.4 1.0
F6 B:PFB378 4.0 15.1 1.0
ND1 B:HIS67 4.2 13.4 1.0
C1 B:PFB378 4.2 14.1 1.0
CG B:HIS67 4.2 13.4 1.0
NH2 B:ARG369 4.6 15.0 1.0
C6 B:PFB378 4.6 14.1 1.0
CA B:CYS174 4.7 11.6 1.0
CA B:CYS46 4.8 13.2 1.0
OE2 B:GLU68 4.8 15.2 1.0
CE2 B:PHE93 4.9 12.7 1.0
N B:SER48 4.9 13.2 1.0
N1N B:NAJ377 5.0 10.9 1.0

Zinc binding site 4 out of 4 in 5kj1

Go back to Zinc Binding Sites List in 5kj1
Zinc binding site 4 out of 4 in the G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of G173A Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:14.6
occ:1.00
 SG B:CYS111 2.3 14.3 1.0
SG B:CYS100 2.3 15.2 1.0
SG B:CYS97 2.3 17.7 1.0
SG B:CYS103 2.4 13.3 1.0
CB B:CYS111 3.3 13.8 1.0
CB B:CYS100 3.4 16.9 1.0
CB B:CYS103 3.4 13.0 1.0
CB B:CYS97 3.4 16.3 1.0
N B:CYS97 3.5 13.7 1.0
CA B:CYS111 3.8 12.6 1.0
N B:CYS100 3.9 16.7 1.0
CA B:CYS97 3.9 16.0 1.0
N B:GLY98 4.0 16.7 1.0
N B:LEU112 4.0 13.7 1.0
CA B:CYS100 4.2 16.7 1.0
N B:CYS103 4.2 13.4 1.0
C B:CYS111 4.3 13.3 1.0
C B:CYS97 4.3 16.8 1.0
CA B:CYS103 4.4 12.6 1.0
N B:LYS99 4.5 17.8 1.0
C B:GLN96 4.6 13.0 1.0
N B:LYS113 4.8 14.5 1.0
C B:CYS100 4.8 15.7 1.0
CG B:LYS113 4.9 19.7 1.0
CA B:GLN96 4.9 13.3 1.0
O B:CYS100 5.0 15.2 1.0
CA B:GLY98 5.0 17.2 1.0

Reference:

K.K.Shanmuganatham, R.S.Wallace, A.Ting-I Lee, B.V.Plapp. Contribution of Buried Distal Amino Acid Residues in Horse Liver Alcohol Dehydrogenase to Structure and Catalysis. Protein Sci. V. 27 750 2018.
ISSN: ESSN 1469-896X
PubMed: 29271062
DOI: 10.1002/PRO.3370
Page generated: Sun Oct 27 20:27:08 2024

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