Zinc in PDB 8g4v: Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol

Enzymatic activity of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol

All present enzymatic activity of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol, PDB code: 8g4v was solved by B.V.Plapp, R.Subramanian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.17, 51.59, 92.77, 92.02, 102.89, 110.04
R / Rfree (%) 13.5 / 16.1

Other elements in 8g4v:

The structure of Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol also contains other interesting chemical elements:

Fluorine (F) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol (pdb code 8g4v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol, PDB code: 8g4v:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8g4v

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Zinc binding site 1 out of 4 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl 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 Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:12.9
occ:1.00
 O1 A:PFB404 1.9 12.8 1.0
NE2 A:HIS67 2.0 12.6 1.0
SG A:CYS174 2.3 12.6 1.0
SG A:CYS46 2.4 12.2 1.0
C7 A:PFB404 2.9 13.6 1.0
CE1 A:HIS67 3.0 11.3 1.0
CD2 A:HIS67 3.0 11.7 1.0
CB A:CYS46 3.3 13.2 1.0
C5N A:NAJ403 3.3 11.9 1.0
CB A:CYS174 3.4 12.1 1.0
OG A:SER48 3.9 11.9 1.0
C6N A:NAJ403 3.9 11.2 1.0
C4N A:NAJ403 3.9 12.3 1.0
F6 A:PFB404 4.1 17.2 1.0
CB A:SER48 4.1 11.7 1.0
ND1 A:HIS67 4.2 11.7 1.0
C1 A:PFB404 4.2 14.5 1.0
CG A:HIS67 4.2 10.9 1.0
NH2 A:ARG369 4.6 14.9 1.0
C6 A:PFB404 4.7 16.9 1.0
CA A:CYS174 4.8 10.4 1.0
CA A:CYS46 4.8 13.0 1.0
OE2 A:GLU68 4.8 16.3 1.0
CE2 A:PHE93 4.9 13.2 1.0
N A:SER48 4.9 10.9 1.0
N1N A:NAJ403 4.9 10.2 1.0

Zinc binding site 2 out of 4 in 8g4v

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Zinc binding site 2 out of 4 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl 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 Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:12.9
occ:1.00
 SG A:CYS111 2.3 12.6 1.0
SG A:CYS103 2.3 12.7 1.0
SG A:CYS100 2.4 13.2 1.0
SG A:CYS97 2.4 14.9 1.0
CB A:CYS111 3.3 12.8 1.0
CB A:CYS103 3.4 13.2 1.0
CB A:CYS100 3.4 14.5 1.0
CB A:CYS97 3.5 15.7 1.0
N A:CYS97 3.5 13.5 1.0
CA A:CYS111 3.7 11.5 1.0
N A:CYS100 3.9 15.6 1.0
CA A:CYS97 3.9 14.1 1.0
N A:LEU112 4.0 11.8 1.0
N A:GLY98 4.0 14.9 1.0
CA A:CYS100 4.2 14.6 1.0
N A:CYS103 4.2 12.7 1.0
C A:CYS97 4.3 15.1 1.0
C A:CYS111 4.3 11.9 1.0
CA A:CYS103 4.4 12.1 1.0
N A:LYS99 4.5 16.6 1.0
C A:GLN96 4.6 12.7 1.0
C A:CYS100 4.9 14.2 1.0
N A:LYS113 4.9 12.1 1.0
CA A:GLN96 4.9 12.4 1.0
O A:HOH814 4.9 32.9 1.0
O A:CYS100 4.9 14.5 1.0
CG A:LYS113 5.0 18.4 1.0
CA A:GLY98 5.0 16.6 1.0

Zinc binding site 3 out of 4 in 8g4v

Go back to Zinc Binding Sites List in 8g4v
Zinc binding site 3 out of 4 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl 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 Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:15.2
occ:1.00
 O1 B:PFB404 1.9 15.5 1.0
NE2 B:HIS67 2.0 14.7 1.0
SG B:CYS174 2.3 14.8 1.0
SG B:CYS46 2.3 14.7 1.0
C7 B:PFB404 2.9 17.8 1.0
CE1 B:HIS67 3.0 13.4 1.0
CD2 B:HIS67 3.0 14.2 1.0
CB B:CYS46 3.3 15.3 1.0
C5N B:NAJ403 3.4 13.8 1.0
CB B:CYS174 3.4 13.6 1.0
OG B:SER48 3.9 13.9 1.0
C6N B:NAJ403 3.9 13.2 1.0
C4N B:NAJ403 3.9 14.7 1.0
CB B:SER48 4.1 13.5 1.0
F6 B:PFB404 4.1 19.6 1.0
ND1 B:HIS67 4.1 14.4 1.0
CG B:HIS67 4.2 13.5 1.0
C1 B:PFB404 4.2 17.5 1.0
NH2 B:ARG369 4.6 17.5 1.0
C6 B:PFB404 4.7 17.6 1.0
CA B:CYS174 4.7 13.5 1.0
CA B:CYS46 4.7 15.7 1.0
OE2 B:GLU68 4.9 19.5 1.0
N B:SER48 4.9 12.6 1.0
CE2 B:PHE93 4.9 16.1 1.0
N1N B:NAJ403 4.9 12.4 1.0

Zinc binding site 4 out of 4 in 8g4v

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Zinc binding site 4 out of 4 in the Horse Liver Alcohol Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl 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 Dehydrogense His-51-Gln Form Complexed with Nad+ and 2,3,4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:15.1
occ:1.00
 SG B:CYS111 2.3 15.2 1.0
SG B:CYS100 2.3 15.5 1.0
SG B:CYS97 2.4 17.5 1.0
SG B:CYS103 2.4 14.3 1.0
CB B:CYS111 3.3 13.5 1.0
CB B:CYS103 3.4 14.9 1.0
CB B:CYS100 3.4 16.9 1.0
CB B:CYS97 3.4 18.2 1.0
N B:CYS97 3.6 15.4 1.0
CA B:CYS111 3.7 13.7 1.0
N B:CYS100 3.9 17.2 1.0
CA B:CYS97 4.0 18.4 1.0
N B:LEU112 4.0 14.6 1.0
N B:GLY98 4.0 18.1 1.0
N B:CYS103 4.2 14.5 1.0
CA B:CYS100 4.2 17.4 1.0
C B:CYS111 4.3 13.6 1.0
C B:CYS97 4.4 17.8 1.0
CA B:CYS103 4.4 14.7 1.0
N B:LYS99 4.5 20.6 1.0
C B:GLN96 4.7 13.6 1.0
N B:LYS113 4.8 15.2 1.0
C B:CYS100 4.9 16.6 1.0
O B:HOH504 5.0 32.6 1.0
O B:CYS100 5.0 16.1 1.0
CA B:GLN96 5.0 14.0 1.0

Reference:

B.V.Plapp, E.G.Kovaleva. Histidine-51 Facilitates Deprotonation of the Zinc-Bound Ligand During Catalysis By Horse Liver Alcohol Dehydrogenase To Be Published.
Page generated: Sat Apr 8 09:08:20 2023

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