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Zinc in PDB 1bto: Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide

Enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide, PDB code: 1bto was solved by S.Ramaswamy, B.V.Plapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.930, 180.200, 86.800, 90.00, 106.00, 90.00
R / Rfree (%) 19 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide (pdb code 1bto). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide, PDB code: 1bto:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1bto

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Zinc binding site 1 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:12.7
occ:1.00
 SG A:CYS46 2.1 9.2 1.0
NE2 A:HIS67 2.2 8.8 1.0
SG A:CYS174 2.2 10.4 1.0
O6 A:SSB378 2.3 10.8 1.0
S1 A:SSB378 3.1 12.2 1.0
CE1 A:HIS67 3.1 8.5 1.0
CD2 A:HIS67 3.2 8.1 1.0
CB A:CYS46 3.2 11.8 1.0
CB A:CYS174 3.3 10.2 1.0
C5N A:NAD377 3.3 8.6 1.0
C6N A:NAD377 4.0 10.3 1.0
OG A:SER48 4.0 9.0 1.0
C5 A:SSB378 4.0 13.5 1.0
C4N A:NAD377 4.1 10.4 1.0
CB A:SER48 4.1 9.4 1.0
ND1 A:HIS67 4.2 8.8 1.0
CG A:HIS67 4.3 8.7 1.0
NH2 A:ARG369 4.4 13.4 1.0
OE2 A:GLU68 4.6 14.5 1.0
C2 A:SSB378 4.6 15.2 1.0
CA A:CYS46 4.6 12.5 1.0
CA A:CYS174 4.7 11.3 1.0
N A:GLY175 4.8 11.0 1.0
N A:SER48 4.9 8.7 1.0
CE2 A:PHE93 4.9 11.1 1.0
C A:CYS174 5.0 11.7 1.0

Zinc binding site 2 out of 8 in 1bto

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Zinc binding site 2 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:14.6
occ:1.00
 SG A:CYS103 2.3 9.7 1.0
SG A:CYS111 2.3 12.7 1.0
SG A:CYS97 2.4 14.6 1.0
SG A:CYS100 2.4 14.8 1.0
CB A:CYS103 3.3 12.9 1.0
CB A:CYS111 3.3 12.7 1.0
CB A:CYS97 3.4 15.6 1.0
CB A:CYS100 3.4 17.1 1.0
N A:CYS97 3.5 13.8 1.0
CA A:CYS111 3.7 12.9 1.0
N A:CYS100 3.8 19.9 1.0
N A:LEU112 3.9 13.3 1.0
CA A:CYS97 3.9 15.8 1.0
N A:GLY98 3.9 17.5 1.0
N A:CYS103 4.1 15.3 1.0
CA A:CYS100 4.2 18.6 1.0
C A:CYS111 4.2 13.0 1.0
CA A:CYS103 4.3 14.2 1.0
C A:CYS97 4.3 17.9 1.0
N A:LYS99 4.5 19.9 1.0
C A:GLN96 4.6 14.1 1.0
O A:HOH597 4.8 30.6 1.0
C A:CYS100 4.8 18.6 1.0
N A:LYS113 4.9 16.8 1.0
O A:CYS100 4.9 16.4 1.0
CA A:GLY98 4.9 17.3 1.0
CA A:GLN96 4.9 12.5 1.0
CG A:LYS113 5.0 22.2 1.0
CA A:LEU112 5.0 14.9 1.0

Zinc binding site 3 out of 8 in 1bto

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Zinc binding site 3 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:12.2
occ:1.00
 SG B:CYS46 2.1 10.5 1.0
SG B:CYS174 2.2 10.5 1.0
NE2 B:HIS67 2.2 8.4 1.0
O6 B:SSB378 2.3 11.2 1.0
S1 B:SSB378 3.1 12.6 1.0
CE1 B:HIS67 3.1 8.7 1.0
CB B:CYS46 3.2 11.9 1.0
CD2 B:HIS67 3.2 8.2 1.0
C5N B:NAD377 3.3 8.6 1.0
CB B:CYS174 3.3 10.1 1.0
C6N B:NAD377 3.9 10.3 1.0
OG B:SER48 4.0 8.6 1.0
C5 B:SSB378 4.0 13.2 1.0
C4N B:NAD377 4.0 10.1 1.0
CB B:SER48 4.1 9.2 1.0
ND1 B:HIS67 4.3 8.9 1.0
CG B:HIS67 4.3 8.5 1.0
NH2 B:ARG369 4.4 12.8 1.0
OE2 B:GLU68 4.6 14.6 1.0
C2 B:SSB378 4.6 15.1 1.0
CA B:CYS46 4.7 12.6 1.0
CA B:CYS174 4.7 11.2 1.0
N B:GLY175 4.8 11.5 1.0
C B:CYS174 5.0 11.3 1.0
CE2 B:PHE93 5.0 11.0 1.0
N B:SER48 5.0 8.4 1.0

Zinc binding site 4 out of 8 in 1bto

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Zinc binding site 4 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:15.1
occ:1.00
 SG B:CYS103 2.3 10.6 1.0
SG B:CYS111 2.3 13.7 1.0
SG B:CYS97 2.4 15.1 1.0
SG B:CYS100 2.4 14.9 1.0
CB B:CYS111 3.3 12.8 1.0
CB B:CYS97 3.4 15.7 1.0
CB B:CYS103 3.4 13.1 1.0
CB B:CYS100 3.5 17.0 1.0
N B:CYS97 3.5 14.2 1.0
CA B:CYS111 3.7 13.3 1.0
N B:CYS100 3.8 19.5 1.0
CA B:CYS97 3.9 16.1 1.0
N B:GLY98 3.9 17.4 1.0
N B:LEU112 3.9 13.3 1.0
N B:CYS103 4.2 15.2 1.0
CA B:CYS100 4.2 18.7 1.0
C B:CYS111 4.3 13.2 1.0
C B:CYS97 4.3 17.9 1.0
CA B:CYS103 4.3 14.2 1.0
N B:LYS99 4.5 19.4 1.0
C B:GLN96 4.6 14.1 1.0
O B:HOH596 4.8 38.9 1.0
N B:LYS113 4.8 16.4 1.0
C B:CYS100 4.9 18.4 1.0
CA B:GLN96 4.9 12.8 1.0
CA B:GLY98 4.9 17.2 1.0
CG B:LYS113 4.9 22.2 1.0
O B:CYS100 5.0 16.4 1.0
C B:LYS99 5.0 22.2 1.0

Zinc binding site 5 out of 8 in 1bto

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Zinc binding site 5 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn375

b:15.3
occ:1.00
 SG C:CYS174 2.2 12.0 1.0
O6 C:SSB378 2.2 11.7 1.0
NE2 C:HIS67 2.2 9.0 1.0
SG C:CYS46 2.3 9.7 1.0
S1 C:SSB378 3.0 13.3 1.0
CD2 C:HIS67 3.2 8.9 1.0
CE1 C:HIS67 3.2 8.7 1.0
CB C:CYS46 3.2 12.2 1.0
C5N C:NAD377 3.3 8.9 1.0
CB C:CYS174 3.3 10.6 1.0
OG C:SER48 4.0 8.3 1.0
C6N C:NAD377 4.0 9.9 1.0
C4N C:NAD377 4.0 10.0 1.0
C5 C:SSB378 4.0 13.6 1.0
CB C:SER48 4.2 9.5 1.0
ND1 C:HIS67 4.3 9.5 1.0
CG C:HIS67 4.3 8.9 1.0
NH2 C:ARG369 4.5 13.7 1.0
C2 C:SSB378 4.6 15.3 1.0
OE2 C:GLU68 4.6 15.0 1.0
CA C:CYS174 4.7 11.3 1.0
CA C:CYS46 4.7 12.4 1.0
N C:GLY175 4.8 12.0 1.0
CE2 C:PHE93 4.9 11.3 1.0
N C:SER48 4.9 8.9 1.0
C C:CYS174 5.0 11.8 1.0

Zinc binding site 6 out of 8 in 1bto

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Zinc binding site 6 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn376

b:15.3
occ:1.00
 SG C:CYS103 2.1 10.0 1.0
SG C:CYS111 2.3 13.2 1.0
SG C:CYS100 2.4 14.8 1.0
SG C:CYS97 2.5 14.9 1.0
CB C:CYS103 3.2 12.9 1.0
CB C:CYS111 3.3 12.8 1.0
CB C:CYS97 3.4 15.5 1.0
N C:CYS97 3.4 13.9 1.0
CB C:CYS100 3.5 17.0 1.0
N C:GLY98 3.7 18.0 1.0
N C:CYS100 3.8 19.8 1.0
CA C:CYS111 3.8 12.7 1.0
CA C:CYS97 3.8 15.8 1.0
N C:LEU112 4.1 13.3 1.0
N C:CYS103 4.1 15.2 1.0
CA C:CYS100 4.2 18.6 1.0
CA C:CYS103 4.2 14.1 1.0
C C:CYS97 4.2 18.1 1.0
C C:CYS111 4.4 13.2 1.0
N C:LYS99 4.4 19.8 1.0
C C:GLN96 4.5 14.1 1.0
CA C:GLY98 4.8 17.4 1.0
C C:CYS100 4.8 18.3 1.0
CA C:GLN96 4.9 12.9 1.0
O C:CYS100 4.9 16.4 1.0
C C:LYS99 4.9 22.1 1.0
C C:GLY98 5.0 18.9 1.0
O C:HOH977 5.0 32.5 1.0

Zinc binding site 7 out of 8 in 1bto

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Zinc binding site 7 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn375

b:14.1
occ:1.00
 O6 D:SSB378 2.1 11.6 1.0
NE2 D:HIS67 2.2 9.4 1.0
SG D:CYS174 2.2 10.6 1.0
SG D:CYS46 2.3 11.2 1.0
S1 D:SSB378 3.1 14.1 1.0
CD2 D:HIS67 3.1 8.6 1.0
CE1 D:HIS67 3.1 9.0 1.0
CB D:CYS46 3.2 11.8 1.0
C5N D:NAD377 3.3 8.8 1.0
CB D:CYS174 3.3 10.6 1.0
C6N D:NAD377 3.9 10.2 1.0
OG D:SER48 4.0 9.2 1.0
C4N D:NAD377 4.0 9.8 1.0
C5 D:SSB378 4.1 13.5 1.0
CB D:SER48 4.1 9.3 1.0
ND1 D:HIS67 4.2 9.7 1.0
CG D:HIS67 4.3 8.8 1.0
NH2 D:ARG369 4.5 13.7 1.0
C2 D:SSB378 4.6 15.1 1.0
OE2 D:GLU68 4.6 14.7 1.0
CA D:CYS174 4.7 11.5 1.0
CA D:CYS46 4.7 12.5 1.0
N D:GLY175 4.8 11.8 1.0
CE2 D:PHE93 4.9 11.0 1.0
N D:SER48 4.9 8.8 1.0
C D:CYS174 5.0 11.6 1.0

Zinc binding site 8 out of 8 in 1bto

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Zinc binding site 8 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and (1S, 3R)3-Butylthiolane 1-Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn376

b:15.5
occ:1.00
 SG D:CYS103 2.1 10.2 1.0
SG D:CYS111 2.4 13.6 1.0
SG D:CYS97 2.4 15.5 1.0
SG D:CYS100 2.4 16.0 1.0
CB D:CYS111 3.3 12.9 1.0
CB D:CYS103 3.3 13.0 1.0
CB D:CYS97 3.4 15.5 1.0
CB D:CYS100 3.5 17.3 1.0
N D:CYS97 3.5 14.1 1.0
CA D:CYS111 3.7 13.5 1.0
N D:CYS100 3.8 19.6 1.0
N D:GLY98 3.8 17.6 1.0
CA D:CYS97 3.9 15.7 1.0
N D:LEU112 3.9 12.9 1.0
N D:CYS103 4.1 15.0 1.0
CA D:CYS100 4.2 18.9 1.0
CA D:CYS103 4.2 13.9 1.0
C D:CYS111 4.3 13.4 1.0
C D:CYS97 4.3 18.3 1.0
N D:LYS99 4.5 19.5 1.0
C D:GLN96 4.5 14.1 1.0
O D:HOH587 4.5 26.6 1.0
C D:CYS100 4.8 18.1 1.0
CA D:GLY98 4.8 17.6 1.0
CA D:GLN96 4.9 12.8 1.0
N D:LYS113 4.9 16.5 1.0
O D:CYS100 4.9 16.6 1.0
C D:LYS99 5.0 22.2 1.0

Reference:

H.Cho, S.Ramaswamy, B.V.Plapp. Flexibility of Liver Alcohol Dehydrogenase in Stereoselective Binding of 3-Butylthiolane 1-Oxides. Biochemistry V. 36 382 1997.
ISSN: ISSN 0006-2960
PubMed: 9003191
DOI: 10.1021/BI9624604
Page generated: Wed Dec 16 02:46:04 2020

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