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Zinc in PDB 6owm: Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

Enzymatic activity of Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol

All present enzymatic activity of Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 6owm was solved by B.V.Plapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.62 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.470, 51.440, 92.560, 92.09, 102.95, 110.25
R / Rfree (%) 12.4 / 14.1

Other elements in 6owm:

The structure of Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and 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 F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol (pdb code 6owm). 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 F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol, PDB code: 6owm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6owm

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Zinc binding site 1 out of 4 in the Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and 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 F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:10.3
occ:0.85
 O1 A:PFB404 1.9 11.8 1.0
NE2 A:HIS67 2.0 11.7 1.0
SG A:CYS174 2.3 11.1 1.0
SG A:CYS46 2.3 11.0 0.9
C7 A:PFB404 2.9 12.7 1.0
CE1 A:HIS67 3.0 10.8 1.0
CD2 A:HIS67 3.1 10.9 1.0
CB A:CYS46 3.3 12.3 0.1
CB A:CYS46 3.3 12.0 0.9
SG A:CYS46 3.4 13.4 0.1
C5N A:NAJ403 3.4 10.6 1.0
CB A:CYS174 3.4 10.1 1.0
OG A:SER48 3.8 11.5 1.0
C6N A:NAJ403 4.0 9.5 1.0
CB A:SER48 4.0 10.8 1.0
C4N A:NAJ403 4.0 11.4 1.0
F6 A:PFB404 4.1 14.8 1.0
ND1 A:HIS67 4.2 10.8 1.0
C1 A:PFB404 4.2 13.3 1.0
CG A:HIS67 4.2 10.2 1.0
NH2 A:ARG369 4.6 12.6 1.0
C6 A:PFB404 4.6 14.0 1.0
CA A:CYS46 4.7 12.3 1.0
CA A:CYS174 4.7 9.8 1.0
CZ2 A:TRP93 4.8 11.3 1.0
N A:SER48 4.8 10.3 1.0
OE2 A:GLU68 4.9 14.3 1.0
NE1 A:TRP93 4.9 11.1 1.0
CE2 A:TRP93 5.0 10.5 1.0
N1N A:NAJ403 5.0 9.2 1.0

Zinc binding site 2 out of 4 in 6owm

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Zinc binding site 2 out of 4 in the Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and 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 F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:12.0
occ:1.00
 SG A:CYS111 2.3 11.6 1.0
SG A:CYS100 2.3 12.3 1.0
SG A:CYS97 2.4 13.5 1.0
SG A:CYS103 2.4 12.1 1.0
CB A:CYS111 3.3 11.1 1.0
CB A:CYS103 3.4 12.6 1.0
CB A:CYS97 3.4 14.5 1.0
CB A:CYS100 3.4 13.4 1.0
N A:CYS97 3.5 12.4 1.0
CA A:CYS111 3.7 10.8 1.0
N A:CYS100 3.9 14.1 1.0
CA A:CYS97 3.9 13.7 1.0
N A:LEU112 4.0 10.9 1.0
N A:GLY98 4.0 14.0 1.0
CA A:CYS100 4.2 14.9 1.0
N A:CYS103 4.2 11.7 1.0
C A:CYS97 4.3 13.8 1.0
C A:CYS111 4.3 11.0 1.0
CA A:CYS103 4.4 11.8 1.0
N A:LYS99 4.5 15.6 1.0
C A:GLN96 4.6 11.5 1.0
C A:CYS100 4.8 13.8 1.0
CG A:LYS113 4.9 16.5 1.0
N A:LYS113 4.9 11.8 1.0
O A:HOH926 4.9 26.3 1.0
O A:CYS100 4.9 13.2 1.0
CA A:GLN96 4.9 11.4 1.0

Zinc binding site 3 out of 4 in 6owm

Go back to Zinc Binding Sites List in 6owm
Zinc binding site 3 out of 4 in the Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and 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 F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:12.6
occ:0.95
 O1 B:PFB404 1.9 13.8 1.0
NE2 B:HIS67 2.0 13.4 1.0
SG B:CYS174 2.3 12.4 1.0
SG B:CYS46 2.3 12.5 0.9
C7 B:PFB404 2.9 13.7 1.0
CE1 B:HIS67 3.0 12.5 1.0
CD2 B:HIS67 3.1 11.8 1.0
CB B:CYS46 3.3 15.3 0.1
CB B:CYS46 3.3 13.2 0.9
CB B:CYS174 3.4 11.6 1.0
C5N B:NAJ403 3.4 12.1 1.0
SG B:CYS46 3.5 19.4 0.1
OG B:SER48 3.8 12.5 1.0
CB B:SER48 4.0 12.3 1.0
C6N B:NAJ403 4.0 11.2 1.0
C4N B:NAJ403 4.1 12.2 1.0
F6 B:PFB404 4.1 15.4 1.0
ND1 B:HIS67 4.2 12.1 1.0
CG B:HIS67 4.2 11.4 1.0
C1 B:PFB404 4.2 14.4 1.0
NH2 B:ARG369 4.6 14.6 1.0
C6 B:PFB404 4.6 14.1 1.0
CA B:CYS174 4.7 11.7 1.0
CA B:CYS46 4.8 13.0 1.0
N B:SER48 4.8 12.6 1.0
CZ2 B:TRP93 4.9 12.7 1.0
NE1 B:TRP93 4.9 12.3 1.0
OE2 B:GLU68 4.9 15.1 1.0
CE2 B:TRP93 5.0 12.0 1.0

Zinc binding site 4 out of 4 in 6owm

Go back to Zinc Binding Sites List in 6owm
Zinc binding site 4 out of 4 in the Horse Liver F93W Alcohol Dehydrogenase Complexed with Nad and 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 F93W Alcohol Dehydrogenase Complexed with Nad and Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:13.4
occ:1.00
 SG B:CYS111 2.3 13.0 1.0
SG B:CYS97 2.4 15.4 1.0
SG B:CYS100 2.4 13.8 1.0
SG B:CYS103 2.4 13.1 1.0
CB B:CYS111 3.3 12.5 1.0
CB B:CYS103 3.4 13.5 1.0
CB B:CYS100 3.4 14.8 1.0
CB B:CYS97 3.4 15.7 1.0
N B:CYS97 3.5 13.6 1.0
CA B:CYS111 3.7 12.1 1.0
N B:CYS100 3.9 16.2 1.0
CA B:CYS97 3.9 15.1 1.0
N B:GLY98 4.0 15.8 1.0
N B:LEU112 4.0 12.9 1.0
CA B:CYS100 4.2 15.7 1.0
N B:CYS103 4.2 12.9 1.0
C B:CYS111 4.3 12.1 1.0
C B:CYS97 4.3 15.1 1.0
CA B:CYS103 4.4 12.6 1.0
N B:LYS99 4.5 17.3 1.0
C B:GLN96 4.6 13.1 1.0
N B:LYS113 4.8 13.0 1.0
C B:CYS100 4.9 15.0 1.0
CG B:LYS113 4.9 17.7 1.0
CA B:GLN96 4.9 12.4 1.0
O B:CYS100 4.9 15.5 1.0
O B:HOH858 5.0 30.7 1.0

Reference:

B.V.Plapp, K.Kim. Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on Structure But Significantly Affect Catalysis of Hydrogen Transfer. To Be Published.
Page generated: Tue Oct 29 04:37:53 2024

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