Zinc in PDB 7uef: Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 85 K

Enzymatic activity of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 85 K

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 85 K:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 85 K, PDB code: 7uef was solved by B.V.Plapp, L.Gakhar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 1.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.28, 51.27, 92.5, 91.81, 103.05, 110.05
R / Rfree (%) 12.3 / 14.8

Other elements in 7uef:

The structure of Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 85 K also contains other interesting chemical elements:

Fluorine (F) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 85 K (pdb code 7uef). 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 Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 85 K, PDB code: 7uef:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7uef

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Zinc binding site 1 out of 4 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 85 K


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 with Nad and Pentafluorobenzyl Alcohol at 85 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:9.7
occ:1.00
 O1 A:PFB404 1.9 9.7 1.0
NE2 A:HIS67 2.1 9.6 1.0
SG A:CYS174 2.3 9.4 1.0
SG A:CYS46 2.3 9.6 1.0
C7 A:PFB404 2.9 9.6 1.0
CE1 A:HIS67 3.0 9.3 1.0
CD2 A:HIS67 3.1 9.0 1.0
C5N A:NAJ403 3.3 8.6 1.0
CB A:CYS46 3.3 9.9 1.0
CB A:CYS174 3.4 8.8 1.0
OG A:SER48 3.8 8.6 1.0
C6N A:NAJ403 3.9 7.7 1.0
C4N A:NAJ403 3.9 8.9 1.0
CB A:SER48 4.0 9.5 1.0
F6 A:PFB404 4.1 11.0 1.0
C1 A:PFB404 4.2 9.8 1.0
ND1 A:HIS67 4.2 9.3 1.0
CG A:HIS67 4.2 8.6 1.0
NH2 A:ARG369 4.6 10.2 1.0
C6 A:PFB404 4.6 11.5 1.0
CA A:CYS174 4.7 8.2 1.0
CA A:CYS46 4.8 9.3 1.0
N A:SER48 4.9 8.7 1.0
OE2 A:GLU68 4.9 10.8 1.0
CE2 A:PHE93 4.9 10.2 1.0
N1N A:NAJ403 4.9 7.5 1.0
C3N A:NAJ403 5.0 8.0 1.0

Zinc binding site 2 out of 4 in 7uef

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Zinc binding site 2 out of 4 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 85 K


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 with Nad and Pentafluorobenzyl Alcohol at 85 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:10.8
occ:1.00
 SG A:CYS111 2.3 10.1 1.0
SG A:CYS100 2.3 11.4 1.0
SG A:CYS97 2.3 11.9 1.0
SG A:CYS103 2.3 10.6 1.0
CB A:CYS111 3.3 9.6 1.0
CB A:CYS100 3.4 12.1 1.0
CB A:CYS103 3.4 10.8 1.0
CB A:CYS97 3.4 12.6 1.0
N A:CYS97 3.5 10.4 1.0
CA A:CYS111 3.7 8.9 1.0
N A:CYS100 3.9 12.9 1.0
CA A:CYS97 3.9 12.0 1.0
N A:GLY98 3.9 12.5 1.0
N A:LEU112 4.0 9.8 1.0
N A:CYS103 4.2 10.1 1.0
CA A:CYS100 4.2 12.9 1.0
C A:CYS111 4.3 9.7 1.0
C A:CYS97 4.3 12.7 1.0
CA A:CYS103 4.3 9.8 1.0
N A:LYS99 4.5 13.8 1.0
C A:GLN96 4.6 10.5 1.0
N A:LYS113 4.8 10.8 1.0
C A:CYS100 4.9 12.2 1.0
CG A:LYS113 4.9 15.9 1.0
CA A:GLN96 4.9 9.8 1.0
O A:CYS100 4.9 12.0 1.0
CA A:GLY98 5.0 13.4 1.0
O A:HOH867 5.0 26.4 1.0

Zinc binding site 3 out of 4 in 7uef

Go back to Zinc Binding Sites List in 7uef
Zinc binding site 3 out of 4 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 85 K


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 with Nad and Pentafluorobenzyl Alcohol at 85 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:12.3
occ:1.00
 O1 B:PFB404 1.9 13.1 1.0
NE2 B:HIS67 2.0 12.0 1.0
SG B:CYS174 2.3 12.4 1.0
SG B:CYS46 2.3 12.2 1.0
C7 B:PFB404 2.9 11.4 1.0
CE1 B:HIS67 3.0 10.6 1.0
CD2 B:HIS67 3.1 11.5 1.0
CB B:CYS46 3.3 12.1 1.0
C5N B:NAJ403 3.4 10.2 1.0
CB B:CYS174 3.4 11.1 1.0
OG B:SER48 3.8 11.4 1.0
C6N B:NAJ403 3.9 10.9 1.0
C4N B:NAJ403 4.0 11.1 1.0
CB B:SER48 4.0 11.8 1.0
F6 B:PFB404 4.0 13.9 1.0
ND1 B:HIS67 4.2 11.6 1.0
C1 B:PFB404 4.2 13.1 1.0
CG B:HIS67 4.2 10.7 1.0
NH2 B:ARG369 4.6 13.1 1.0
C6 B:PFB404 4.6 13.4 1.0
CA B:CYS174 4.7 10.2 1.0
CA B:CYS46 4.8 11.8 1.0
N B:SER48 4.8 11.9 1.0
CE2 B:PHE93 4.9 11.4 1.0
N1N B:NAJ403 4.9 10.6 1.0
OE2 B:GLU68 4.9 13.1 1.0
C3N B:NAJ403 5.0 9.8 1.0

Zinc binding site 4 out of 4 in 7uef

Go back to Zinc Binding Sites List in 7uef
Zinc binding site 4 out of 4 in the Horse Liver Alcohol Dehydrogenase with Nad and Pentafluorobenzyl Alcohol at 85 K


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 with Nad and Pentafluorobenzyl Alcohol at 85 K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:13.8
occ:1.00
 SG B:CYS97 2.3 16.8 1.0
SG B:CYS111 2.3 13.5 1.0
SG B:CYS100 2.3 14.6 1.0
SG B:CYS103 2.4 12.9 1.0
CB B:CYS111 3.3 11.8 1.0
CB B:CYS100 3.4 16.9 1.0
CB B:CYS97 3.4 16.2 1.0
CB B:CYS103 3.4 13.8 1.0
N B:CYS97 3.5 14.0 1.0
CA B:CYS111 3.7 11.9 1.0
CA B:CYS97 3.9 15.2 1.0
N B:CYS100 3.9 16.2 1.0
N B:LEU112 3.9 12.7 1.0
N B:GLY98 3.9 15.5 1.0
CA B:CYS100 4.2 16.1 1.0
N B:CYS103 4.2 13.2 1.0
C B:CYS111 4.3 13.1 1.0
C B:CYS97 4.3 16.9 1.0
CA B:CYS103 4.4 11.9 1.0
N B:LYS99 4.5 17.1 1.0
C B:GLN96 4.6 12.7 1.0
N B:LYS113 4.8 13.8 1.0
C B:CYS100 4.8 14.6 1.0
CG B:LYS113 4.9 18.9 1.0
CA B:GLN96 4.9 11.7 1.0
O B:HOH815 5.0 32.0 1.0
O B:CYS100 5.0 14.8 1.0
CA B:GLY98 5.0 16.7 1.0

Reference:

B.V.Plapp, L.Gakhar, R.Subramanian. Dependence of Crystallographic Atomic Displacement Factors on Temperature (25-150 K) For Complexes of Horse Liver Alcohol Dehydrogenases Acta Crystallogr.,Sect.D V. D78 1221 2022.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798322008361
Page generated: Wed Oct 30 12:04:07 2024

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