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Zinc in PDB 1lde: Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine

Enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine, PDB code: 1lde 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 / 2.50
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 (%) 20.5 / 25.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine (pdb code 1lde). 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 N-Formyl Piperdine, PDB code: 1lde:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1lde

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Zinc binding site 1 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine


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 N-Formyl Piperdine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:12.4
occ:1.00
 SG A:CYS46 2.1 8.3 1.0
SG A:CYS174 2.2 12.2 1.0
NE2 A:HIS67 2.2 9.4 1.0
O A:FPI378 2.3 8.0 1.0
CE1 A:HIS67 3.0 7.2 1.0
CB A:CYS46 3.1 11.7 1.0
C7 A:FPI378 3.3 8.9 1.0
CD2 A:HIS67 3.4 7.0 1.0
CB A:CYS174 3.4 13.7 1.0
C5N A:NAD377 3.5 9.3 1.0
OG A:SER48 3.7 12.9 1.0
C6N A:NAD377 4.1 9.7 1.0
CB A:SER48 4.1 11.3 1.0
C4N A:NAD377 4.2 9.8 1.0
ND1 A:HIS67 4.2 7.9 1.0
CG A:HIS67 4.4 9.3 1.0
NH2 A:ARG369 4.4 10.2 1.0
N A:FPI378 4.5 8.6 1.0
CA A:CYS46 4.6 13.0 1.0
OE2 A:GLU68 4.7 12.8 1.0
CA A:CYS174 4.8 12.5 1.0
CE2 A:PHE93 4.8 10.2 1.0
N A:GLY175 4.8 13.0 1.0
N A:SER48 4.9 8.6 1.0
C A:CYS174 5.0 14.9 1.0

Zinc binding site 2 out of 8 in 1lde

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Zinc binding site 2 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine


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 N-Formyl Piperdine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:20.2
occ:1.00
 SG A:CYS103 2.2 13.6 1.0
SG A:CYS97 2.4 17.1 1.0
SG A:CYS111 2.4 10.9 1.0
SG A:CYS100 2.4 19.6 1.0
CB A:CYS97 3.3 12.8 1.0
CB A:CYS103 3.4 16.7 1.0
N A:CYS97 3.4 11.8 1.0
CB A:CYS100 3.5 17.3 1.0
CB A:CYS111 3.5 11.2 1.0
CA A:CYS97 3.8 13.6 1.0
CA A:CYS111 3.8 8.6 1.0
N A:GLY98 3.8 15.2 1.0
N A:CYS100 3.9 22.6 1.0
N A:LEU112 4.1 12.5 1.0
C A:CYS97 4.1 14.7 1.0
CA A:CYS100 4.3 20.9 1.0
N A:CYS103 4.3 17.7 1.0
C A:CYS111 4.3 10.3 1.0
CA A:CYS103 4.4 18.1 1.0
N A:LYS99 4.4 18.4 1.0
C A:GLN96 4.5 13.9 1.0
CA A:GLY98 4.8 16.7 1.0
N A:LYS113 4.9 18.4 1.0
C A:GLY98 4.9 17.4 1.0
C A:LYS99 5.0 23.1 1.0
CA A:GLN96 5.0 13.0 1.0
C A:CYS100 5.0 21.7 1.0

Zinc binding site 3 out of 8 in 1lde

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Zinc binding site 3 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine


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 N-Formyl Piperdine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:12.9
occ:1.00
 O B:FPI378 2.2 7.1 1.0
SG B:CYS46 2.2 10.1 1.0
NE2 B:HIS67 2.2 9.7 1.0
SG B:CYS174 2.2 11.6 1.0
CE1 B:HIS67 3.0 8.4 1.0
CB B:CYS46 3.1 12.0 1.0
C7 B:FPI378 3.2 8.8 1.0
CD2 B:HIS67 3.4 6.5 1.0
CB B:CYS174 3.4 13.3 1.0
C5N B:NAD377 3.4 8.6 1.0
OG B:SER48 3.7 12.9 1.0
C6N B:NAD377 4.1 10.5 1.0
CB B:SER48 4.1 11.2 1.0
C4N B:NAD377 4.2 9.1 1.0
ND1 B:HIS67 4.2 7.9 1.0
CG B:HIS67 4.4 8.7 1.0
N B:FPI378 4.4 8.2 1.0
NH2 B:ARG369 4.5 9.7 1.0
CA B:CYS46 4.6 12.8 1.0
OE2 B:GLU68 4.8 12.4 1.0
N B:SER48 4.8 8.8 1.0
CA B:CYS174 4.8 12.7 1.0
CE2 B:PHE93 4.9 10.4 1.0
N B:GLY175 4.9 13.6 1.0

Zinc binding site 4 out of 8 in 1lde

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Zinc binding site 4 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine


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 N-Formyl Piperdine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:19.4
occ:1.00
 SG B:CYS103 2.3 13.8 1.0
SG B:CYS97 2.4 16.1 1.0
SG B:CYS111 2.4 10.1 1.0
SG B:CYS100 2.4 19.9 1.0
CB B:CYS97 3.2 13.4 1.0
CB B:CYS103 3.4 15.6 1.0
N B:CYS97 3.5 12.6 1.0
CB B:CYS111 3.6 10.9 1.0
CB B:CYS100 3.6 17.4 1.0
CA B:CYS97 3.7 14.1 1.0
N B:CYS100 3.8 21.5 1.0
N B:GLY98 3.9 14.7 1.0
CA B:CYS111 3.9 9.0 1.0
C B:CYS97 4.1 14.9 1.0
N B:LEU112 4.1 12.0 1.0
CA B:CYS100 4.3 21.1 1.0
N B:CYS103 4.4 18.0 1.0
CA B:CYS103 4.4 18.5 1.0
N B:LYS99 4.4 17.9 1.0
C B:CYS111 4.4 10.5 1.0
C B:GLN96 4.6 14.0 1.0
N B:LYS113 4.8 17.8 1.0
CA B:GLY98 4.8 16.5 1.0
C B:LYS99 4.9 22.6 1.0
CG B:LYS113 4.9 25.9 1.0
CA B:GLN96 5.0 12.5 1.0
C B:GLY98 5.0 17.8 1.0

Zinc binding site 5 out of 8 in 1lde

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Zinc binding site 5 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine


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 N-Formyl Piperdine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn375

b:13.5
occ:1.00
 O C:FPI378 2.0 8.0 1.0
NE2 C:HIS67 2.1 9.1 1.0
SG C:CYS174 2.2 13.8 1.0
SG C:CYS46 2.2 11.2 1.0
CE1 C:HIS67 2.9 9.0 1.0
C7 C:FPI378 3.1 8.3 1.0
CD2 C:HIS67 3.2 8.3 1.0
CB C:CYS46 3.3 11.8 1.0
CB C:CYS174 3.4 14.3 1.0
C5N C:NAD377 3.5 9.3 1.0
OG C:SER48 3.9 14.4 1.0
C6N C:NAD377 4.1 10.1 1.0
C4N C:NAD377 4.2 11.7 1.0
ND1 C:HIS67 4.2 10.4 1.0
CB C:SER48 4.3 11.6 1.0
N C:FPI378 4.3 8.4 1.0
CG C:HIS67 4.3 9.8 1.0
NH2 C:ARG369 4.5 10.9 1.0
CA C:CYS174 4.7 12.8 1.0
CA C:CYS46 4.7 13.2 1.0
OE2 C:GLU68 4.8 13.7 1.0
CE2 C:PHE93 4.8 10.8 1.0
N C:GLY175 4.8 14.2 1.0
N C:SER48 4.9 9.5 1.0
C2 C:FPI378 4.9 9.0 1.0

Zinc binding site 6 out of 8 in 1lde

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Zinc binding site 6 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine


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 N-Formyl Piperdine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn376

b:21.3
occ:1.00
 SG C:CYS103 2.1 12.2 1.0
SG C:CYS100 2.4 19.4 1.0
SG C:CYS97 2.5 16.5 1.0
SG C:CYS111 2.5 13.1 1.0
CB C:CYS103 3.1 18.0 1.0
CB C:CYS97 3.5 13.9 1.0
N C:CYS97 3.5 11.0 1.0
CB C:CYS100 3.5 17.5 1.0
CB C:CYS111 3.5 11.1 1.0
CA C:CYS97 3.8 14.1 1.0
N C:CYS100 3.8 21.7 1.0
CA C:CYS111 3.9 7.7 1.0
N C:GLY98 3.9 15.7 1.0
C C:CYS97 4.0 15.4 1.0
N C:LEU112 4.1 11.7 1.0
CA C:CYS100 4.2 20.3 1.0
N C:CYS103 4.2 17.8 1.0
CA C:CYS103 4.3 17.9 1.0
N C:LYS99 4.3 18.2 1.0
C C:CYS111 4.3 9.4 1.0
C C:GLN96 4.5 13.1 1.0
O C:CYS100 4.8 19.8 1.0
C C:CYS100 4.9 21.1 1.0
CA C:GLY98 4.9 16.1 1.0
C C:LYS99 4.9 23.0 1.0
C C:GLY98 4.9 18.0 1.0
O C:CYS97 5.0 17.8 1.0

Zinc binding site 7 out of 8 in 1lde

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Zinc binding site 7 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine


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 N-Formyl Piperdine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn375

b:14.4
occ:1.00
 O D:FPI378 1.9 8.7 1.0
NE2 D:HIS67 2.1 10.5 1.0
SG D:CYS174 2.2 11.7 1.0
SG D:CYS46 2.3 12.0 1.0
CE1 D:HIS67 3.0 8.1 1.0
C7 D:FPI378 3.1 9.9 1.0
CD2 D:HIS67 3.2 8.7 1.0
CB D:CYS46 3.3 12.5 1.0
CB D:CYS174 3.3 13.7 1.0
C5N D:NAD377 3.5 9.3 1.0
OG D:SER48 3.8 14.9 1.0
C6N D:NAD377 4.1 10.0 1.0
ND1 D:HIS67 4.1 9.4 1.0
C4N D:NAD377 4.2 11.0 1.0
N D:FPI378 4.2 9.0 1.0
CB D:SER48 4.3 11.7 1.0
CG D:HIS67 4.3 10.3 1.0
NH2 D:ARG369 4.6 10.7 1.0
CA D:CYS174 4.7 13.1 1.0
OE2 D:GLU68 4.7 12.7 1.0
CA D:CYS46 4.8 12.7 1.0
CE2 D:PHE93 4.8 11.1 1.0
N D:GLY175 4.8 14.0 1.0
N D:SER48 4.8 9.5 1.0
C2 D:FPI378 4.9 10.3 1.0

Zinc binding site 8 out of 8 in 1lde

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Zinc binding site 8 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and N-Formyl Piperdine


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 N-Formyl Piperdine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn376

b:20.2
occ:1.00
 SG D:CYS103 2.2 13.0 1.0
SG D:CYS100 2.3 21.1 1.0
SG D:CYS111 2.5 13.3 1.0
SG D:CYS97 2.6 17.6 1.0
CB D:CYS103 3.4 17.4 1.0
CB D:CYS97 3.5 13.7 1.0
CB D:CYS100 3.5 17.6 1.0
CB D:CYS111 3.5 11.5 1.0
N D:CYS97 3.6 12.2 1.0
N D:CYS100 3.8 21.7 1.0
CA D:CYS111 3.8 9.1 1.0
CA D:CYS97 3.9 14.5 1.0
N D:GLY98 3.9 16.0 1.0
N D:LEU112 4.0 12.0 1.0
C D:CYS97 4.2 15.5 1.0
C D:CYS111 4.2 10.8 1.0
CA D:CYS100 4.2 20.8 1.0
N D:CYS103 4.3 18.3 1.0
CA D:CYS103 4.4 18.2 1.0
N D:LYS99 4.5 18.9 1.0
C D:GLN96 4.6 13.8 1.0
CA D:GLY98 4.9 17.8 1.0
N D:LYS113 4.9 19.1 1.0
C D:CYS100 4.9 21.4 1.0
C D:LYS99 5.0 23.2 1.0

Reference:

S.Ramaswamy, M.Scholze, B.V.Plapp. Binding of Formamides to Liver Alcohol Dehydrogenase. Biochemistry V. 36 3522 1997.
ISSN: ISSN 0006-2960
PubMed: 9132002
DOI: 10.1021/BI962491Z
Page generated: Sun Oct 13 04:58:26 2024

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