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Zinc in PDB 1p1r: Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide

Enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide, PDB code: 1p1r was solved by T.H.Venkataramaiah, B.V.Plapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.57
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.095, 180.340, 87.000, 90.00, 106.36, 90.00
R / Rfree (%) 15.2 / 20

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide (pdb code 1p1r). 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 with Nadh and R- N-1-Methylhexylformamide, PDB code: 1p1r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1p1r

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Zinc binding site 1 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide


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 with Nadh and R- N-1-Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:13.0
occ:1.00
 NE2 A:HIS67 2.1 11.2 1.0
O A:NMH378 2.2 13.3 1.0
SG A:CYS174 2.2 11.8 1.0
SG A:CYS46 2.3 12.6 1.0
C A:NMH378 2.9 14.1 1.0
CE1 A:HIS67 3.0 11.0 1.0
CD2 A:HIS67 3.1 11.0 1.0
CB A:CYS46 3.2 11.3 1.0
CB A:CYS174 3.3 10.0 1.0
C5N A:NAI377 3.5 11.2 1.0
OG A:SER48 4.0 11.8 1.0
C6N A:NAI377 4.1 11.5 1.0
CB A:SER48 4.1 9.9 1.0
C4N A:NAI377 4.1 11.1 1.0
ND1 A:HIS67 4.1 10.4 1.0
N A:NMH378 4.2 14.5 1.0
CG A:HIS67 4.2 10.5 1.0
NH2 A:ARG369 4.4 16.2 1.0
OE2 A:GLU68 4.5 13.7 1.0
CA A:CYS174 4.7 10.7 1.0
CA A:CYS46 4.7 11.2 1.0
N A:GLY175 4.9 10.6 1.0
N A:SER48 4.9 10.7 1.0
CE2 A:PHE93 4.9 9.8 1.0
C A:CYS174 4.9 10.7 1.0

Zinc binding site 2 out of 8 in 1p1r

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Zinc binding site 2 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide


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 with Nadh and R- N-1-Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:14.3
occ:1.00
 SG A:CYS103 2.3 13.5 1.0
SG A:CYS111 2.3 12.4 1.0
SG A:CYS97 2.3 15.5 1.0
SG A:CYS100 2.4 14.6 1.0
CB A:CYS111 3.3 12.5 1.0
CB A:CYS103 3.4 13.1 1.0
CB A:CYS97 3.4 15.3 1.0
CB A:CYS100 3.4 16.4 1.0
N A:CYS97 3.5 12.8 1.0
CA A:CYS111 3.7 12.4 1.0
N A:CYS100 3.8 18.3 1.0
CA A:CYS97 3.9 14.4 1.0
N A:LEU112 3.9 12.6 1.0
N A:GLY98 4.0 15.6 1.0
CA A:CYS100 4.2 17.2 1.0
N A:CYS103 4.2 13.4 1.0
C A:CYS111 4.3 12.4 1.0
C A:CYS97 4.3 15.4 1.0
CA A:CYS103 4.4 13.7 1.0
N A:LYS99 4.5 18.6 1.0
C A:GLN96 4.6 13.2 1.0
CG A:LYS113 4.8 17.3 1.0
N A:LYS113 4.8 13.5 1.0
C A:CYS100 4.9 17.7 1.0
CA A:GLN96 4.9 12.2 1.0
O A:HOH7170 4.9 32.1 1.0
O A:CYS100 5.0 17.2 1.0
CA A:GLY98 5.0 16.9 1.0

Zinc binding site 3 out of 8 in 1p1r

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Zinc binding site 3 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide


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 with Nadh and R- N-1-Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:15.7
occ:1.00
 NE2 B:HIS67 2.1 13.6 1.0
O B:NMH378 2.1 17.4 1.0
SG B:CYS174 2.2 14.3 1.0
SG B:CYS46 2.3 14.7 1.0
C B:NMH378 2.9 18.5 1.0
CE1 B:HIS67 3.0 12.9 1.0
CD2 B:HIS67 3.1 13.8 1.0
CB B:CYS46 3.2 14.6 1.0
CB B:CYS174 3.3 14.3 1.0
C5N B:NAI377 3.5 11.4 1.0
OG B:SER48 4.0 14.0 1.0
CB B:SER48 4.1 14.3 1.0
C4N B:NAI377 4.1 13.2 1.0
C6N B:NAI377 4.1 10.5 1.0
ND1 B:HIS67 4.1 14.3 1.0
N B:NMH378 4.2 19.3 1.0
CG B:HIS67 4.2 15.3 1.0
NH2 B:ARG369 4.5 16.1 1.0
OE2 B:GLU68 4.5 18.8 1.0
CA B:CYS46 4.7 14.4 1.0
CA B:CYS174 4.7 13.3 1.0
N B:SER48 4.9 13.3 1.0
N B:GLY175 4.9 13.2 1.0
CE2 B:PHE93 4.9 14.2 1.0
C B:CYS174 5.0 13.2 1.0

Zinc binding site 4 out of 8 in 1p1r

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Zinc binding site 4 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide


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 with Nadh and R- N-1-Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:18.9
occ:1.00
 SG B:CYS97 2.3 19.4 1.0
SG B:CYS103 2.3 17.9 1.0
SG B:CYS111 2.4 16.5 1.0
SG B:CYS100 2.4 18.2 1.0
CB B:CYS111 3.3 16.7 1.0
CB B:CYS97 3.4 17.6 1.0
CB B:CYS103 3.4 18.0 1.0
CB B:CYS100 3.4 19.1 1.0
N B:CYS97 3.6 16.8 1.0
CA B:CYS111 3.8 16.1 1.0
N B:CYS100 3.8 21.9 1.0
CA B:CYS97 3.9 18.1 1.0
N B:GLY98 3.9 19.7 1.0
N B:LEU112 4.0 17.1 1.0
CA B:CYS100 4.2 20.2 1.0
N B:CYS103 4.2 17.4 1.0
C B:CYS111 4.3 16.8 1.0
C B:CYS97 4.3 18.9 1.0
CA B:CYS103 4.4 17.9 1.0
N B:LYS99 4.5 22.2 1.0
C B:GLN96 4.6 17.2 1.0
O B:HOH7863 4.7 32.8 1.0
C B:CYS100 4.8 20.5 1.0
N B:LYS113 4.9 18.3 1.0
CA B:GLN96 4.9 15.7 1.0
CA B:GLY98 4.9 21.2 1.0
O B:CYS100 5.0 19.6 1.0
CG B:LYS113 5.0 23.0 1.0

Zinc binding site 5 out of 8 in 1p1r

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Zinc binding site 5 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide


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 with Nadh and R- N-1-Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn375

b:12.8
occ:1.00
 NE2 C:HIS67 2.1 10.3 1.0
O C:NMH378 2.2 11.9 1.0
SG C:CYS174 2.2 11.7 1.0
SG C:CYS46 2.3 11.5 1.0
C C:NMH378 2.9 13.0 1.0
CE1 C:HIS67 3.0 10.6 1.0
CD2 C:HIS67 3.1 10.6 1.0
CB C:CYS46 3.2 11.6 1.0
CB C:CYS174 3.3 11.0 1.0
C5N C:NAI377 3.5 9.9 1.0
OG C:SER48 4.0 10.5 1.0
CB C:SER48 4.1 9.5 1.0
C4N C:NAI377 4.1 10.4 1.0
C6N C:NAI377 4.1 10.8 1.0
ND1 C:HIS67 4.2 10.2 1.0
N C:NMH378 4.2 14.1 1.0
CG C:HIS67 4.2 9.7 1.0
NH2 C:ARG369 4.5 16.0 1.0
OE2 C:GLU68 4.5 14.2 1.0
CA C:CYS174 4.7 11.3 1.0
CA C:CYS46 4.7 12.1 1.0
N C:GLY175 4.9 10.7 1.0
N C:SER48 4.9 10.4 1.0
C C:CYS174 4.9 10.4 1.0
CE2 C:PHE93 4.9 10.9 1.0

Zinc binding site 6 out of 8 in 1p1r

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Zinc binding site 6 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide


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 with Nadh and R- N-1-Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn376

b:16.3
occ:1.00
 SG C:CYS103 2.3 14.9 1.0
SG C:CYS97 2.3 17.0 1.0
SG C:CYS111 2.4 14.3 1.0
SG C:CYS100 2.4 16.6 1.0
CB C:CYS103 3.3 15.6 1.0
CB C:CYS111 3.3 12.9 1.0
CB C:CYS100 3.4 17.6 1.0
CB C:CYS97 3.4 16.7 1.0
N C:CYS97 3.6 14.6 1.0
CA C:CYS111 3.8 12.8 1.0
N C:CYS100 3.8 20.2 1.0
CA C:CYS97 3.9 16.0 1.0
N C:GLY98 4.0 17.4 1.0
N C:LEU112 4.0 14.0 1.0
N C:CYS103 4.2 15.5 1.0
CA C:CYS100 4.2 19.1 1.0
C C:CYS111 4.3 13.3 1.0
C C:CYS97 4.3 16.6 1.0
CA C:CYS103 4.3 15.5 1.0
N C:LYS99 4.4 20.1 1.0
C C:GLN96 4.6 14.7 1.0
N C:LYS113 4.8 13.4 1.0
C C:CYS100 4.9 18.9 1.0
O C:HOH7408 4.9 32.0 1.0
O C:CYS100 4.9 17.5 1.0
CA C:GLN96 4.9 14.3 1.0
CG C:LYS113 4.9 18.8 1.0
CA C:GLY98 4.9 18.1 1.0
C C:LYS99 5.0 21.9 1.0

Zinc binding site 7 out of 8 in 1p1r

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Zinc binding site 7 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide


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 with Nadh and R- N-1-Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn375

b:15.6
occ:1.00
 NE2 D:HIS67 2.0 13.8 1.0
O D:NMH378 2.1 15.4 1.0
SG D:CYS46 2.2 14.1 1.0
SG D:CYS174 2.3 14.3 1.0
C D:NMH378 2.8 17.7 1.0
CE1 D:HIS67 3.0 12.9 1.0
CD2 D:HIS67 3.0 13.0 1.0
CB D:CYS46 3.2 13.9 1.0
CB D:CYS174 3.3 13.7 1.0
C5N D:NAI377 3.5 10.9 1.0
OG D:SER48 4.0 12.8 1.0
C6N D:NAI377 4.1 10.2 1.0
C4N D:NAI377 4.1 11.8 1.0
N D:NMH378 4.1 17.4 1.0
CB D:SER48 4.1 13.3 1.0
ND1 D:HIS67 4.1 11.6 1.0
CG D:HIS67 4.2 13.2 1.0
NH2 D:ARG369 4.4 18.3 1.0
OE2 D:GLU68 4.7 17.4 1.0
CA D:CYS174 4.7 13.8 1.0
CA D:CYS46 4.7 13.8 1.0
CE2 D:PHE93 4.9 14.1 1.0
N D:GLY175 4.9 13.9 1.0
N D:SER48 5.0 13.1 1.0

Zinc binding site 8 out of 8 in 1p1r

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Zinc binding site 8 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nadh and R- N-1-Methylhexylformamide


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 with Nadh and R- N-1-Methylhexylformamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn376

b:16.3
occ:1.00
 SG D:CYS103 2.3 15.8 1.0
SG D:CYS111 2.3 14.6 1.0
SG D:CYS100 2.4 15.8 1.0
SG D:CYS97 2.4 17.9 1.0
CB D:CYS111 3.3 14.2 1.0
CB D:CYS103 3.3 16.4 1.0
CB D:CYS100 3.4 17.8 1.0
CB D:CYS97 3.5 17.3 1.0
N D:CYS97 3.5 15.8 1.0
CA D:CYS111 3.7 13.4 1.0
N D:CYS100 3.9 19.3 1.0
N D:GLY98 3.9 17.4 1.0
CA D:CYS97 3.9 15.9 1.0
N D:LEU112 4.0 14.2 1.0
CA D:CYS100 4.2 18.1 1.0
N D:CYS103 4.2 15.4 1.0
C D:CYS111 4.3 13.8 1.0
CA D:CYS103 4.3 15.8 1.0
C D:CYS97 4.4 17.4 1.0
N D:LYS99 4.5 20.9 1.0
C D:GLN96 4.6 14.8 1.0
CG D:LYS113 4.8 19.6 1.0
C D:CYS100 4.8 18.0 1.0
CA D:GLN96 4.9 14.3 1.0
N D:LYS113 4.9 15.8 1.0
O D:CYS100 4.9 17.1 1.0
CA D:GLY98 4.9 18.8 1.0

Reference:

T.H.Venkataramaiah, B.V.Plapp. Formamides Mimic Aldehydes and Inhibit Liver Alcohol Dehydrogenases and Ethanol Metabolism J.Biol.Chem. V. 278 36699 2003.
ISSN: ISSN 0021-9258
PubMed: 12855684
DOI: 10.1074/JBC.M305419200
Page generated: Wed Oct 16 17:40:36 2024

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