Atomistry » Zinc » PDB 1kzo-1lfw » 1lde
Atomistry »
  Zinc »
    PDB 1kzo-1lfw »
      1lde »

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

Go back to Zinc Binding Sites List in 1lde
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

Go back to Zinc Binding Sites List in 1lde
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

Go back to Zinc Binding Sites List in 1lde
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

Go back to Zinc Binding Sites List in 1lde
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

Go back to Zinc Binding Sites List in 1lde
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

Go back to Zinc Binding Sites List in 1lde
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

Go back to Zinc Binding Sites List in 1lde
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

Go back to Zinc Binding Sites List in 1lde
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy