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

Zinc in PDB 1ldy: Horse Liver Alcohol Dehydrogenase Complexed to Nadh and Cyclohexyl Formamide (Cxf)

Enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and Cyclohexyl Formamide (Cxf)

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and Cyclohexyl Formamide (Cxf):
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase Complexed to Nadh and Cyclohexyl Formamide (Cxf), PDB code: 1ldy 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) 12.00 / 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 (%) 20.7 / n/a

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 1ldy

Go back to Zinc Binding Sites List in 1ldy
Zinc binding site 1 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and Cyclohexyl Formamide (Cxf)


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 Cyclohexyl Formamide (Cxf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:13.5
occ:1.00
 NE2 A:HIS67 2.2 17.6 1.0
SG A:CYS174 2.2 15.1 1.0
SG A:CYS46 2.3 16.7 1.0
O9 A:CXF378 2.3 23.6 1.0
C7 A:CXF378 3.0 24.3 1.0
CD2 A:HIS67 3.1 16.7 1.0
CB A:CYS46 3.1 20.4 1.0
CE1 A:HIS67 3.2 16.1 1.0
CB A:CYS174 3.3 19.2 1.0
C5N A:NAD377 3.5 18.0 1.0
OG A:SER48 3.8 18.2 1.0
CB A:SER48 4.1 19.3 1.0
C6N A:NAD377 4.2 17.6 1.0
N8 A:CXF378 4.2 27.3 1.0
CG A:HIS67 4.3 16.9 1.0
C4N A:NAD377 4.3 18.4 1.0
ND1 A:HIS67 4.3 14.8 1.0
NH2 A:ARG369 4.4 22.3 1.0
OE2 A:GLU68 4.5 21.7 1.0
CA A:CYS46 4.6 20.9 1.0
CA A:CYS174 4.7 20.3 1.0
N A:GLY175 4.7 19.6 1.0
N A:SER48 4.8 19.9 1.0
CE2 A:PHE93 4.9 19.8 1.0
C A:CYS174 4.9 20.8 1.0

Zinc binding site 2 out of 8 in 1ldy

Go back to Zinc Binding Sites List in 1ldy
Zinc binding site 2 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and Cyclohexyl Formamide (Cxf)


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 Cyclohexyl Formamide (Cxf) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:23.2
occ:1.00
 SG A:CYS103 2.2 17.6 1.0
SG A:CYS100 2.2 27.1 1.0
SG A:CYS111 2.4 19.2 1.0
SG A:CYS97 2.5 26.8 1.0
CB A:CYS103 3.1 24.3 1.0
CB A:CYS111 3.4 21.1 1.0
CB A:CYS97 3.4 25.9 1.0
CB A:CYS100 3.5 28.7 1.0
N A:CYS97 3.5 23.8 1.0
CA A:CYS111 3.7 20.5 1.0
N A:CYS100 3.8 31.4 1.0
CA A:CYS97 3.8 25.3 1.0
N A:GLY98 3.9 28.4 1.0
N A:LEU112 3.9 22.4 1.0
N A:CYS103 4.2 24.4 1.0
CA A:CYS103 4.2 25.5 1.0
C A:CYS111 4.2 21.8 1.0
C A:CYS97 4.2 28.1 1.0
CA A:CYS100 4.2 29.9 1.0
N A:LYS99 4.5 30.4 1.0
C A:GLN96 4.6 24.0 1.0
CG A:LYS113 4.8 29.5 1.0
CA A:GLY98 4.8 28.7 1.0
O A:CYS100 4.8 29.4 1.0
N A:LYS113 4.9 25.6 1.0
C A:CYS100 4.9 29.1 1.0
CA A:GLN96 5.0 22.9 1.0
C A:LYS99 5.0 33.0 1.0

Zinc binding site 3 out of 8 in 1ldy

Go back to Zinc Binding Sites List in 1ldy
Zinc binding site 3 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and Cyclohexyl Formamide (Cxf)


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 Cyclohexyl Formamide (Cxf) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:13.4
occ:1.00
 NE2 B:HIS67 2.1 17.9 1.0
SG B:CYS174 2.1 15.3 1.0
O9 B:CXF378 2.3 23.6 1.0
SG B:CYS46 2.4 17.1 1.0
C7 B:CXF378 2.9 24.1 1.0
CD2 B:HIS67 3.1 16.7 1.0
CE1 B:HIS67 3.2 16.5 1.0
CB B:CYS46 3.2 20.2 1.0
CB B:CYS174 3.3 18.9 1.0
C5N B:NAD377 3.6 18.1 1.0
OG B:SER48 3.8 17.6 1.0
N8 B:CXF378 4.1 26.7 1.0
CB B:SER48 4.1 18.9 1.0
CG B:HIS67 4.2 16.5 1.0
ND1 B:HIS67 4.3 15.0 1.0
C6N B:NAD377 4.3 17.6 1.0
C4N B:NAD377 4.3 17.9 1.0
NH2 B:ARG369 4.5 21.6 1.0
OE2 B:GLU68 4.5 21.9 1.0
CA B:CYS174 4.6 20.3 1.0
CA B:CYS46 4.7 20.7 1.0
CE2 B:PHE93 4.7 20.1 1.0
N B:GLY175 4.7 19.4 1.0
C B:CYS174 4.8 20.2 1.0
N B:SER48 4.9 19.9 1.0
C1 B:CXF378 5.0 26.3 1.0

Zinc binding site 4 out of 8 in 1ldy

Go back to Zinc Binding Sites List in 1ldy
Zinc binding site 4 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and Cyclohexyl Formamide (Cxf)


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 Cyclohexyl Formamide (Cxf) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:22.1
occ:1.00
 SG B:CYS103 2.1 19.2 1.0
SG B:CYS100 2.3 28.6 1.0
SG B:CYS97 2.5 28.4 1.0
SG B:CYS111 2.5 20.3 1.0
CB B:CYS103 3.2 24.4 1.0
CB B:CYS111 3.3 21.5 1.0
CB B:CYS97 3.4 25.3 1.0
N B:CYS97 3.5 24.4 1.0
CB B:CYS100 3.6 28.5 1.0
N B:CYS100 3.7 31.0 1.0
CA B:CYS111 3.8 21.0 1.0
CA B:CYS97 3.8 25.7 1.0
N B:GLY98 3.9 28.3 1.0
N B:LEU112 4.0 22.5 1.0
N B:CYS103 4.1 24.8 1.0
CA B:CYS100 4.2 29.8 1.0
CA B:CYS103 4.2 25.8 1.0
C B:CYS97 4.2 28.7 1.0
C B:CYS111 4.3 21.9 1.0
N B:LYS99 4.4 29.9 1.0
C B:GLN96 4.5 24.1 1.0
CA B:GLY98 4.8 28.9 1.0
CG B:LYS113 4.8 29.8 1.0
C B:CYS100 4.8 29.5 1.0
N B:LYS113 4.9 26.4 1.0
C B:LYS99 4.9 32.8 1.0
O B:CYS100 4.9 29.3 1.0
CA B:GLN96 4.9 23.3 1.0
C B:GLY98 5.0 30.1 1.0

Zinc binding site 5 out of 8 in 1ldy

Go back to Zinc Binding Sites List in 1ldy
Zinc binding site 5 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and Cyclohexyl Formamide (Cxf)


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 Cyclohexyl Formamide (Cxf) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn375

b:18.9
occ:1.00
 SG C:CYS174 2.1 15.8 1.0
SG C:CYS46 2.2 16.5 1.0
NE2 C:HIS67 2.3 17.6 1.0
O9 C:CXF378 2.5 23.8 1.0
CB C:CYS46 3.0 20.5 1.0
CB C:CYS174 3.2 19.6 1.0
CD2 C:HIS67 3.2 17.1 1.0
C7 C:CXF378 3.2 24.8 1.0
CE1 C:HIS67 3.2 16.8 1.0
C5N C:NAD377 3.4 17.6 1.0
OG C:SER48 3.9 18.8 1.0
C6N C:NAD377 4.1 17.6 1.0
NH2 C:ARG369 4.2 22.1 1.0
C4N C:NAD377 4.2 18.2 1.0
CB C:SER48 4.2 19.5 1.0
OE2 C:GLU68 4.3 22.7 1.0
ND1 C:HIS67 4.4 16.5 1.0
CG C:HIS67 4.4 17.2 1.0
CA C:CYS46 4.5 21.4 1.0
N8 C:CXF378 4.5 27.3 1.0
N C:GLY175 4.5 19.7 1.0
CA C:CYS174 4.6 20.1 1.0
C C:CYS174 4.8 20.6 1.0
N C:SER48 5.0 19.6 1.0
CE2 C:PHE93 5.0 20.3 1.0

Zinc binding site 6 out of 8 in 1ldy

Go back to Zinc Binding Sites List in 1ldy
Zinc binding site 6 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and Cyclohexyl Formamide (Cxf)


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 Cyclohexyl Formamide (Cxf) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn376

b:26.3
occ:1.00
 SG C:CYS103 2.2 18.6 1.0
SG C:CYS100 2.2 26.1 1.0
SG C:CYS111 2.5 21.8 1.0
SG C:CYS97 2.5 26.1 1.0
CB C:CYS103 2.9 25.1 1.0
CB C:CYS111 3.4 21.2 1.0
N C:CYS97 3.4 23.8 1.0
CB C:CYS97 3.5 26.4 1.0
CB C:CYS100 3.6 28.6 1.0
N C:GLY98 3.6 28.6 1.0
CA C:CYS97 3.8 25.9 1.0
CA C:CYS111 3.8 20.7 1.0
N C:CYS100 3.8 31.2 1.0
CA C:CYS103 4.0 26.1 1.0
C C:CYS97 4.0 28.5 1.0
N C:LEU112 4.1 23.0 1.0
N C:CYS103 4.1 24.9 1.0
CA C:CYS100 4.3 29.7 1.0
C C:CYS111 4.3 21.7 1.0
N C:LYS99 4.4 30.4 1.0
C C:GLN96 4.5 23.8 1.0
CA C:GLY98 4.7 28.9 1.0
O C:HOH553 4.8 31.8 1.0
C C:GLY98 4.9 29.7 1.0
CG C:LYS113 4.9 29.9 1.0
CA C:GLN96 4.9 23.8 1.0
C C:CYS100 4.9 29.0 1.0
C C:LYS99 4.9 32.6 1.0
O C:CYS100 4.9 29.1 1.0
N C:LYS113 5.0 26.2 1.0

Zinc binding site 7 out of 8 in 1ldy

Go back to Zinc Binding Sites List in 1ldy
Zinc binding site 7 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and Cyclohexyl Formamide (Cxf)


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 Cyclohexyl Formamide (Cxf) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn375

b:17.1
occ:1.00
 NE2 D:HIS67 2.1 17.9 1.0
SG D:CYS174 2.1 17.4 1.0
SG D:CYS46 2.3 18.6 1.0
O9 D:CXF378 2.4 24.5 1.0
C7 D:CXF378 3.0 24.6 1.0
CD2 D:HIS67 3.1 17.2 1.0
CE1 D:HIS67 3.1 16.8 1.0
CB D:CYS46 3.2 20.9 1.0
CB D:CYS174 3.3 19.3 1.0
C5N D:NAD377 3.5 18.3 1.0
OG D:SER48 4.0 18.6 1.0
N8 D:CXF378 4.2 27.4 1.0
CB D:SER48 4.2 19.4 1.0
C6N D:NAD377 4.2 17.7 1.0
ND1 D:HIS67 4.2 16.6 1.0
CG D:HIS67 4.2 17.3 1.0
C4N D:NAD377 4.3 18.1 1.0
NH2 D:ARG369 4.4 22.3 1.0
OE2 D:GLU68 4.5 22.7 1.0
CA D:CYS174 4.6 20.4 1.0
CA D:CYS46 4.6 21.2 1.0
N D:GLY175 4.7 20.3 1.0
CE2 D:PHE93 4.8 20.5 1.0
N D:SER48 4.8 19.4 1.0
C D:CYS174 4.9 20.7 1.0
C1 D:CXF378 5.0 26.8 1.0

Zinc binding site 8 out of 8 in 1ldy

Go back to Zinc Binding Sites List in 1ldy
Zinc binding site 8 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed to Nadh and Cyclohexyl Formamide (Cxf)


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 Cyclohexyl Formamide (Cxf) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn376

b:24.2
occ:1.00
 SG D:CYS103 2.1 21.6 1.0
SG D:CYS100 2.2 29.0 1.0
SG D:CYS97 2.4 28.5 1.0
SG D:CYS111 2.4 21.9 1.0
CB D:CYS103 3.3 25.5 1.0
CB D:CYS97 3.4 25.4 1.0
CB D:CYS111 3.4 21.7 1.0
CB D:CYS100 3.5 28.6 1.0
N D:CYS97 3.5 24.4 1.0
N D:CYS100 3.7 31.1 1.0
N D:GLY98 3.7 28.8 1.0
CA D:CYS111 3.8 21.2 1.0
CA D:CYS97 3.8 25.7 1.0
N D:LEU112 4.0 22.9 1.0
N D:CYS103 4.1 25.3 1.0
C D:CYS97 4.1 28.7 1.0
CA D:CYS100 4.2 29.8 1.0
CA D:CYS103 4.2 25.9 1.0
C D:CYS111 4.3 22.1 1.0
N D:LYS99 4.4 30.2 1.0
O D:HOH553 4.5 22.8 1.0
C D:GLN96 4.6 24.0 1.0
CA D:GLY98 4.8 29.5 1.0
C D:CYS100 4.8 29.1 1.0
CG D:LYS113 4.8 30.2 1.0
C D:LYS99 4.9 32.8 1.0
N D:LYS113 4.9 26.0 1.0
O D:CYS100 4.9 28.7 1.0
CA D:GLN96 5.0 23.8 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 05:01:06 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy