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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

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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

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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

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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

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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

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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

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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

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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

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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: Wed Dec 16 02:56:15 2020

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