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Zinc in PDB 4ng5: V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol

Enzymatic activity of V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol

All present enzymatic activity of V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol:
1.1.1.1;

Protein crystallography data

The structure of V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol, PDB code: 4ng5 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) 17.91 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.520, 51.560, 92.550, 91.80, 103.05, 110.30
R / Rfree (%) 12 / 13.7

Other elements in 4ng5:

The structure of V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol (pdb code 4ng5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol, PDB code: 4ng5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4ng5

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Zinc binding site 1 out of 4 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn375

b:11.9
occ:0.60
 O1 A:PFB378 1.9 14.2 0.8
NE2 A:HIS67 2.1 15.8 1.0
SG A:CYS174 2.3 14.3 1.0
SG A:CYS46 2.3 14.1 0.8
O A:HOH995 2.8 16.2 0.4
C7 A:PFB378 2.9 14.5 0.8
CE1 A:HIS67 3.1 14.1 1.0
CD2 A:HIS67 3.1 13.8 1.0
CB A:CYS174 3.4 13.1 1.0
CB A:CYS46 3.5 16.2 0.8
C5N A:NAJ377 3.5 11.8 1.0
CB A:CYS46 3.6 15.7 0.2
SG A:CYS46 3.7 17.0 0.2
OG A:SER48 3.8 13.8 1.0
C4N A:NAJ377 3.9 13.3 1.0
CB A:SER48 4.0 12.7 1.0
F6 A:PFB378 4.0 16.0 0.8
C6N A:NAJ377 4.2 11.1 1.0
C1 A:PFB378 4.2 13.8 0.8
O A:HOH994 4.2 14.5 0.6
ND1 A:HIS67 4.2 12.6 1.0
CG A:HIS67 4.3 12.1 1.0
C6 A:PFB378 4.6 14.9 0.8
CE2 A:PHE93 4.7 12.1 1.0
CA A:CYS174 4.8 10.8 1.0
N A:SER48 4.9 11.8 1.0
NH2 A:ARG369 4.9 14.2 0.6
CZ A:PHE93 4.9 12.6 1.0
C3N A:NAJ377 5.0 11.0 1.0
CA A:CYS46 5.0 16.4 0.8

Zinc binding site 2 out of 4 in 4ng5

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Zinc binding site 2 out of 4 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn376

b:12.3
occ:1.00
 SG A:CYS111 2.3 11.8 1.0
SG A:CYS100 2.3 12.8 1.0
SG A:CYS97 2.3 13.7 1.0
SG A:CYS103 2.4 12.1 1.0
CB A:CYS111 3.3 11.4 1.0
CB A:CYS100 3.4 13.9 1.0
CB A:CYS103 3.4 11.8 1.0
CB A:CYS97 3.4 13.6 1.0
N A:CYS97 3.5 12.7 1.0
CA A:CYS111 3.8 11.1 1.0
N A:CYS100 3.9 15.3 1.0
CA A:CYS97 3.9 13.6 1.0
N A:GLY98 4.0 13.5 1.0
N A:LEU112 4.0 11.8 1.0
N A:CYS103 4.2 11.8 1.0
CA A:CYS100 4.2 14.3 1.0
C A:CYS97 4.3 14.3 1.0
C A:CYS111 4.3 11.2 1.0
CA A:CYS103 4.4 12.4 1.0
N A:LYS99 4.5 16.1 1.0
C A:GLN96 4.6 12.4 1.0
C A:CYS100 4.8 13.8 1.0
N A:LYS113 4.9 12.3 1.0
CG A:LYS113 4.9 17.2 1.0
CA A:GLN96 4.9 11.9 1.0
O A:CYS100 4.9 14.3 1.0
O A:HOH552 5.0 29.3 1.0
CA A:GLY98 5.0 15.4 1.0

Zinc binding site 3 out of 4 in 4ng5

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Zinc binding site 3 out of 4 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn375

b:13.7
occ:0.60
 O1 B:PFB378 2.0 16.4 0.8
NE2 B:HIS67 2.1 16.7 1.0
SG B:CYS174 2.3 16.9 1.0
SG B:CYS46 2.3 16.1 0.8
O B:HOH995 2.8 15.0 0.3
C7 B:PFB378 2.9 15.0 0.8
CE1 B:HIS67 3.1 15.8 1.0
CD2 B:HIS67 3.1 15.6 1.0
CB B:CYS174 3.4 15.2 1.0
CB B:CYS46 3.4 19.3 0.8
CB B:CYS46 3.5 19.7 0.2
C5N B:NAJ377 3.6 14.0 1.0
SG B:CYS46 3.8 19.7 0.2
OG B:SER48 3.8 15.3 1.0
C4N B:NAJ377 4.0 15.6 1.0
CB B:SER48 4.0 14.8 1.0
F6 B:PFB378 4.0 17.5 0.8
C1 B:PFB378 4.2 15.5 0.8
ND1 B:HIS67 4.2 14.3 1.0
C6N B:NAJ377 4.2 13.8 1.0
O B:HOH994 4.3 15.9 0.6
CG B:HIS67 4.3 13.5 1.0
C6 B:PFB378 4.6 15.9 0.8
CA B:CYS174 4.7 12.8 1.0
CE2 B:PHE93 4.8 13.8 1.0
NH2 B:ARG369 4.9 16.7 0.6
N B:SER48 4.9 15.0 1.0
CA B:CYS46 4.9 18.7 1.0
CZ B:PHE93 5.0 14.6 1.0
C3N B:NAJ377 5.0 12.2 1.0

Zinc binding site 4 out of 4 in 4ng5

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Zinc binding site 4 out of 4 in the V203A Horse Liver Alcohol Dehydrogenase E 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 V203A Horse Liver Alcohol Dehydrogenase E Complexed with Nad+ and 2,3, 4,5,6-Pentafluorobenzyl Alcohol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn376

b:14.2
occ:1.00
 SG B:CYS111 2.3 13.7 1.0
SG B:CYS103 2.3 13.6 1.0
SG B:CYS100 2.4 14.7 1.0
SG B:CYS97 2.4 16.8 1.0
CB B:CYS111 3.3 13.2 1.0
CB B:CYS97 3.4 16.0 1.0
CB B:CYS103 3.4 13.4 1.0
CB B:CYS100 3.4 15.9 1.0
N B:CYS97 3.5 14.2 1.0
CA B:CYS111 3.7 12.4 1.0
N B:CYS100 3.9 17.3 1.0
CA B:CYS97 3.9 16.1 1.0
N B:LEU112 4.0 13.2 1.0
N B:GLY98 4.0 15.7 1.0
CA B:CYS100 4.2 17.0 1.0
N B:CYS103 4.2 13.3 1.0
C B:CYS111 4.3 12.8 1.0
C B:CYS97 4.3 17.4 1.0
CA B:CYS103 4.4 13.2 1.0
N B:LYS99 4.5 17.9 1.0
C B:GLN96 4.7 13.8 1.0
N B:LYS113 4.8 14.0 1.0
C B:CYS100 4.8 15.7 1.0
CG B:LYS113 4.9 18.6 1.0
O B:CYS100 4.9 15.9 1.0
CA B:GLN96 5.0 13.4 1.0
O B:HOH482 5.0 30.6 1.0

Reference:

A.Yahashiri, J.K.Rubach, B.V.Plapp. Effects of Cavities at the Nicotinamide Binding Site of Liver Alcohol Dehydrogenase on Structure, Dynamics and Catalysis. Biochemistry V. 53 881 2014.
ISSN: ISSN 0006-2960
PubMed: 24437493
DOI: 10.1021/BI401583F
Page generated: Wed Dec 16 05:37:04 2020

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