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Zinc in PDB 1mg0: Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol

Enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol, PDB code: 1mg0 was solved by J.K.Rubach, B.V.Plapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.114, 180.310, 86.912, 90.00, 105.99, 90.00
R / Rfree (%) 17.9 / 21.4

Other elements in 1mg0:

The structure of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol also contains other interesting chemical elements:

Fluorine (F) 16 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol (pdb code 1mg0). 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 Nad+ and 2, 3-Difluorobenzyl Alcohol, PDB code: 1mg0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1mg0

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Zinc binding site 1 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol


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 Nad+ and 2, 3-Difluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:23.5
occ:1.00
 NE2 A:HIS67 2.1 10.8 1.0
O1 A:DFB378 2.2 14.1 1.0
SG A:CYS174 2.3 15.1 1.0
SG A:CYS46 2.3 13.8 1.0
CE1 A:HIS67 3.1 8.1 1.0
CD2 A:HIS67 3.1 9.7 1.0
C7 A:DFB378 3.1 15.6 0.5
C7 A:DFB378 3.1 18.2 0.5
CB A:CYS46 3.3 14.0 1.0
C5N A:NAD377 3.3 13.9 1.0
CB A:CYS174 3.4 13.6 1.0
OG A:SER48 3.9 14.4 1.0
C6N A:NAD377 4.0 12.6 1.0
C4N A:NAD377 4.0 15.0 1.0
CB A:SER48 4.1 13.6 1.0
ND1 A:HIS67 4.2 10.6 1.0
CG A:HIS67 4.2 10.8 1.0
C1 A:DFB378 4.4 18.3 0.5
C1 A:DFB378 4.4 15.7 0.5
NH2 A:ARG369 4.7 16.1 1.0
CA A:CYS46 4.8 14.3 1.0
CA A:CYS174 4.8 13.7 1.0
OE2 A:GLU68 4.8 16.8 1.0
N A:SER48 4.9 13.6 1.0
CE2 A:PHE93 4.9 8.7 1.0
C6 A:DFB378 4.9 19.3 0.5

Zinc binding site 2 out of 8 in 1mg0

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Zinc binding site 2 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol


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 Nad+ and 2, 3-Difluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:17.2
occ:1.00
 SG A:CYS103 2.3 13.7 1.0
SG A:CYS100 2.3 16.5 1.0
SG A:CYS111 2.3 13.6 1.0
SG A:CYS97 2.4 17.8 1.0
CB A:CYS111 3.2 14.4 1.0
CB A:CYS103 3.4 16.8 1.0
CB A:CYS100 3.4 18.2 1.0
CB A:CYS97 3.4 16.2 1.0
N A:CYS97 3.5 15.3 1.0
CA A:CYS111 3.7 14.0 1.0
N A:CYS100 3.8 19.2 1.0
N A:LEU112 3.9 15.1 1.0
CA A:CYS97 3.9 16.7 1.0
N A:GLY98 4.0 18.2 1.0
CA A:CYS100 4.2 17.9 1.0
C A:CYS111 4.2 14.4 1.0
N A:CYS103 4.3 16.6 1.0
C A:CYS97 4.4 17.6 1.0
CA A:CYS103 4.4 16.4 1.0
N A:LYS99 4.5 20.0 1.0
C A:GLN96 4.6 15.2 1.0
CG A:LYS113 4.7 18.4 1.0
N A:LYS113 4.8 15.3 1.0
C A:CYS100 4.9 17.8 1.0
CA A:GLN96 4.9 15.0 1.0
O A:CYS100 4.9 17.0 1.0

Zinc binding site 3 out of 8 in 1mg0

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Zinc binding site 3 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol


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 Nad+ and 2, 3-Difluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:23.9
occ:1.00
 NE2 B:HIS67 2.1 16.6 1.0
O1 B:DFB378 2.2 19.1 1.0
SG B:CYS174 2.3 15.0 1.0
SG B:CYS46 2.4 15.4 1.0
CD2 B:HIS67 3.1 17.9 1.0
C7 B:DFB378 3.1 19.1 0.5
C7 B:DFB378 3.1 18.7 0.5
CE1 B:HIS67 3.2 18.0 1.0
C5N B:NAD377 3.2 14.2 1.0
CB B:CYS46 3.3 15.7 1.0
CB B:CYS174 3.5 13.6 1.0
C6N B:NAD377 3.9 13.5 1.0
OG B:SER48 3.9 17.4 1.0
CB B:SER48 4.0 15.1 1.0
C4N B:NAD377 4.0 15.7 1.0
CG B:HIS67 4.3 15.7 1.0
ND1 B:HIS67 4.3 17.2 1.0
C1 B:DFB378 4.3 19.1 0.5
C1 B:DFB378 4.5 18.8 0.5
NH2 B:ARG369 4.7 15.2 1.0
OE2 B:GLU68 4.7 17.4 1.0
C6 B:DFB378 4.8 19.2 0.5
CA B:CYS46 4.8 15.8 1.0
N B:SER48 4.8 14.5 1.0
CA B:CYS174 4.9 14.0 1.0
N1N B:NAD377 5.0 10.7 1.0
CE2 B:PHE93 5.0 13.2 1.0

Zinc binding site 4 out of 8 in 1mg0

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Zinc binding site 4 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol


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 Nad+ and 2, 3-Difluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:21.0
occ:1.00
 SG B:CYS100 2.3 21.0 1.0
SG B:CYS111 2.4 15.8 1.0
SG B:CYS103 2.4 18.5 1.0
SG B:CYS97 2.4 22.0 1.0
CB B:CYS111 3.3 15.6 1.0
CB B:CYS100 3.3 22.6 1.0
CB B:CYS103 3.4 18.7 1.0
CB B:CYS97 3.5 20.4 1.0
N B:CYS97 3.6 18.9 1.0
CA B:CYS111 3.7 16.3 1.0
N B:CYS100 3.8 23.7 1.0
CA B:CYS97 3.9 21.0 1.0
N B:GLY98 3.9 22.2 1.0
N B:LEU112 4.0 17.3 1.0
CA B:CYS100 4.1 22.4 1.0
N B:CYS103 4.2 18.4 1.0
C B:CYS111 4.3 17.2 1.0
CA B:CYS103 4.3 18.4 1.0
C B:CYS97 4.4 21.6 1.0
N B:LYS99 4.5 23.6 1.0
C B:GLN96 4.6 18.0 1.0
C B:CYS100 4.8 21.9 1.0
O B:CYS100 4.8 21.2 1.0
CG B:LYS113 4.9 21.5 1.0
N B:LYS113 4.9 18.8 1.0
CA B:GLN96 4.9 17.1 1.0
CA B:GLY98 5.0 22.5 1.0

Zinc binding site 5 out of 8 in 1mg0

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Zinc binding site 5 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol


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 Nad+ and 2, 3-Difluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn375

b:24.1
occ:1.00
 NE2 C:HIS67 2.1 12.9 1.0
O1 C:DFB378 2.2 18.0 1.0
SG C:CYS174 2.3 17.3 1.0
SG C:CYS46 2.3 13.8 1.0
C7 C:DFB378 3.1 19.6 0.5
CD2 C:HIS67 3.1 13.2 1.0
C7 C:DFB378 3.1 19.2 0.5
CE1 C:HIS67 3.1 14.8 1.0
C5N C:NAD377 3.3 15.5 1.0
CB C:CYS46 3.3 14.7 1.0
CB C:CYS174 3.5 14.6 1.0
OG C:SER48 3.8 13.3 1.0
C6N C:NAD377 3.9 14.1 1.0
C4N C:NAD377 4.0 15.2 1.0
CB C:SER48 4.0 14.7 1.0
ND1 C:HIS67 4.2 13.2 1.0
CG C:HIS67 4.2 14.0 1.0
C1 C:DFB378 4.3 18.3 0.5
C1 C:DFB378 4.4 18.6 0.5
NH2 C:ARG369 4.6 16.8 1.0
C6 C:DFB378 4.8 18.2 0.5
CA C:CYS46 4.8 14.8 1.0
CA C:CYS174 4.9 14.1 1.0
CE2 C:PHE93 4.9 14.5 1.0
OE2 C:GLU68 4.9 18.4 1.0
N C:SER48 4.9 14.2 1.0
N1N C:NAD377 5.0 14.5 1.0

Zinc binding site 6 out of 8 in 1mg0

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Zinc binding site 6 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol


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 Nad+ and 2, 3-Difluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn376

b:18.1
occ:1.00
 SG C:CYS103 2.3 16.2 1.0
SG C:CYS100 2.3 16.9 1.0
SG C:CYS111 2.4 14.7 1.0
SG C:CYS97 2.4 17.0 1.0
CB C:CYS111 3.2 14.4 1.0
CB C:CYS103 3.2 16.8 1.0
CB C:CYS100 3.5 19.2 1.0
CB C:CYS97 3.5 16.8 1.0
N C:CYS97 3.5 15.3 1.0
CA C:CYS111 3.7 14.5 1.0
N C:CYS100 3.9 20.1 1.0
CA C:CYS97 3.9 17.4 1.0
N C:LEU112 4.0 14.6 1.0
N C:GLY98 4.0 19.6 1.0
N C:CYS103 4.2 15.7 1.0
C C:CYS111 4.2 14.7 1.0
CA C:CYS100 4.2 18.6 1.0
CA C:CYS103 4.3 16.2 1.0
C C:CYS97 4.4 18.3 1.0
N C:LYS99 4.5 21.7 1.0
C C:GLN96 4.6 14.8 1.0
C C:CYS100 4.8 18.4 1.0
N C:LYS113 4.9 15.8 1.0
O C:CYS100 4.9 17.4 1.0
CG C:LYS113 4.9 19.7 1.0
CA C:GLN96 4.9 14.1 1.0
CA C:GLY98 5.0 20.2 1.0

Zinc binding site 7 out of 8 in 1mg0

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Zinc binding site 7 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol


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 Nad+ and 2, 3-Difluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn375

b:22.8
occ:1.00
 NE2 D:HIS67 2.1 12.8 1.0
O1 D:DFB378 2.2 18.2 1.0
SG D:CYS174 2.2 12.1 1.0
SG D:CYS46 2.3 14.4 1.0
C7 D:DFB378 3.1 18.7 0.5
CD2 D:HIS67 3.1 11.6 1.0
CE1 D:HIS67 3.1 13.1 1.0
C7 D:DFB378 3.2 20.1 0.5
C5N D:NAD377 3.3 14.2 1.0
CB D:CYS46 3.3 13.7 1.0
CB D:CYS174 3.4 10.8 1.0
C6N D:NAD377 3.9 14.9 1.0
OG D:SER48 3.9 14.6 1.0
CB D:SER48 4.0 13.7 1.0
C4N D:NAD377 4.0 14.6 1.0
ND1 D:HIS67 4.2 11.8 1.0
CG D:HIS67 4.2 12.1 1.0
C1 D:DFB378 4.4 20.7 0.5
C1 D:DFB378 4.4 18.7 0.5
NH2 D:ARG369 4.7 13.7 1.0
CA D:CYS174 4.7 11.2 1.0
OE2 D:GLU68 4.8 15.3 1.0
CA D:CYS46 4.8 14.2 1.0
C6 D:DFB378 4.8 20.5 0.5
N D:SER48 4.9 13.2 1.0
CE2 D:PHE93 4.9 10.4 1.0
N1N D:NAD377 4.9 14.8 1.0
N D:GLY175 5.0 11.8 1.0

Zinc binding site 8 out of 8 in 1mg0

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Zinc binding site 8 out of 8 in the Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and 2, 3-Difluorobenzyl Alcohol


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 Nad+ and 2, 3-Difluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn376

b:18.4
occ:1.00
 SG D:CYS103 2.2 16.1 1.0
SG D:CYS100 2.4 17.2 1.0
SG D:CYS97 2.4 17.8 1.0
SG D:CYS111 2.4 15.7 1.0
CB D:CYS111 3.2 15.7 1.0
CB D:CYS103 3.3 17.8 1.0
CB D:CYS97 3.4 17.5 1.0
CB D:CYS100 3.5 21.7 1.0
N D:CYS97 3.6 17.0 1.0
CA D:CYS111 3.8 15.8 1.0
N D:CYS100 3.8 22.6 1.0
CA D:CYS97 3.9 17.7 1.0
N D:LEU112 4.0 15.7 1.0
N D:GLY98 4.0 19.4 1.0
CA D:CYS100 4.2 21.5 1.0
N D:CYS103 4.2 17.8 1.0
C D:CYS111 4.3 15.8 1.0
CA D:CYS103 4.3 18.3 1.0
C D:CYS97 4.4 19.1 1.0
N D:LYS99 4.4 22.6 1.0
C D:GLN96 4.6 16.8 1.0
N D:LYS113 4.8 15.8 1.0
C D:CYS100 4.9 21.7 1.0
C D:LYS99 4.9 23.7 1.0
CG D:LYS113 4.9 19.1 1.0
O D:CYS100 4.9 21.4 1.0
CA D:GLN96 4.9 16.4 1.0

Reference:

J.K.Rubach, B.V.Plapp. Mobility of Fluorobenzyl Alcohols Bound to Liver Alcohol Dehydrogenases As Determined By uc(Nmr) and X-Ray Crystallographic Studies Biochemistry V. 41 15770 2002.
ISSN: ISSN 0006-2960
PubMed: 12501206
DOI: 10.1021/BI026581H
Page generated: Wed Oct 16 16:56:17 2024

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