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Zinc in PDB 4xd2: Horse Liver Alcohol Dehydrogenase-Nadh Complex

Enzymatic activity of Horse Liver Alcohol Dehydrogenase-Nadh Complex

All present enzymatic activity of Horse Liver Alcohol Dehydrogenase-Nadh Complex:
1.1.1.1;

Protein crystallography data

The structure of Horse Liver Alcohol Dehydrogenase-Nadh Complex, PDB code: 4xd2 was solved by B.V.Plapp, S.Baskar Raj, D.J.Ferraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.158, 50.911, 92.660, 92.05, 103.05, 109.60
R / Rfree (%) 17.7 / 19.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Horse Liver Alcohol Dehydrogenase-Nadh Complex (pdb code 4xd2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Horse Liver Alcohol Dehydrogenase-Nadh Complex, PDB code: 4xd2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4xd2

Go back to Zinc Binding Sites List in 4xd2
Zinc binding site 1 out of 6 in the Horse Liver Alcohol Dehydrogenase-Nadh Complex


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-Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:13.9
occ:0.80
ZN A:ZN401 0.0 13.9 0.8
ZN A:ZN401 1.3 16.4 0.2
O A:HOH920 2.0 17.0 0.8
NE2 A:HIS67 2.1 14.6 1.0
SG A:CYS174 2.3 13.0 1.0
SG A:CYS46 2.3 14.1 1.0
CE1 A:HIS67 3.0 13.2 1.0
CD2 A:HIS67 3.1 13.1 1.0
CB A:CYS46 3.4 15.2 1.0
CB A:CYS174 3.4 12.1 1.0
C5N A:NAI403 3.4 11.7 1.0
C6N A:NAI403 3.8 11.9 1.0
OG A:SER48 3.9 13.6 1.0
C4N A:NAI403 4.0 11.9 1.0
CB A:SER48 4.1 11.2 1.0
ND1 A:HIS67 4.2 11.5 1.0
CG A:HIS67 4.2 11.4 1.0
NH2 A:ARG369 4.6 18.2 1.0
CA A:CYS174 4.7 11.0 1.0
CA A:CYS46 4.8 14.1 1.0
OE2 A:GLU68 4.8 19.1 1.0
N A:SER48 4.8 10.9 1.0
CE2 A:PHE93 4.9 13.7 1.0
N1N A:NAI403 4.9 10.4 1.0

Zinc binding site 2 out of 6 in 4xd2

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Zinc binding site 2 out of 6 in the Horse Liver Alcohol Dehydrogenase-Nadh Complex


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-Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:16.4
occ:0.20
ZN A:ZN401 0.0 16.4 0.2
ZN A:ZN401 1.3 13.9 0.8
SG A:CYS46 2.2 14.1 1.0
NE2 A:HIS67 2.2 14.6 1.0
SG A:CYS174 2.6 13.0 1.0
CB A:CYS46 2.6 15.2 1.0
CB A:CYS174 3.0 12.1 1.0
CE1 A:HIS67 3.0 13.2 1.0
CD2 A:HIS67 3.2 13.1 1.0
O A:HOH920 3.3 17.0 0.8
OE2 A:GLU68 3.7 19.1 1.0
NH2 A:ARG369 3.8 18.2 1.0
CA A:CYS46 4.1 14.1 1.0
ND1 A:HIS67 4.1 11.5 1.0
CD A:GLU68 4.2 15.9 1.0
CG A:HIS67 4.2 11.4 1.0
CB A:GLU68 4.2 12.4 1.0
C5N A:NAI403 4.3 11.7 1.0
CA A:CYS174 4.4 11.0 1.0
N A:GLY175 4.5 10.6 1.0
C6N A:NAI403 4.7 11.9 1.0
CG A:GLU68 4.7 15.4 1.0
OE1 A:GLU68 4.7 19.4 1.0
C A:CYS174 4.7 10.2 1.0
CB A:SER48 4.9 11.2 1.0
N A:CYS46 4.9 16.2 1.0
OG A:SER48 4.9 13.6 1.0
CZ A:ARG369 4.9 15.0 1.0
C A:CYS46 4.9 12.4 1.0

Zinc binding site 3 out of 6 in 4xd2

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Zinc binding site 3 out of 6 in the Horse Liver Alcohol Dehydrogenase-Nadh Complex


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-Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:12.9
occ:1.00
SG A:CYS100 2.3 13.4 1.0
SG A:CYS97 2.3 14.8 1.0
SG A:CYS111 2.3 12.4 1.0
SG A:CYS103 2.3 12.6 1.0
CB A:CYS111 3.3 12.1 1.0
CB A:CYS103 3.4 13.1 1.0
CB A:CYS100 3.4 15.3 1.0
CB A:CYS97 3.4 16.9 1.0
N A:CYS97 3.6 12.3 1.0
CA A:CYS111 3.7 10.6 1.0
N A:CYS100 3.9 16.3 1.0
N A:LEU112 3.9 12.4 1.0
CA A:CYS97 4.0 14.5 1.0
N A:GLY98 4.0 13.3 1.0
N A:CYS103 4.2 12.3 1.0
CA A:CYS100 4.2 15.7 1.0
C A:CYS111 4.3 11.7 1.0
C A:CYS97 4.4 14.2 1.0
CA A:CYS103 4.4 12.9 1.0
N A:LYS99 4.5 16.4 1.0
C A:GLN96 4.6 12.0 1.0
N A:LYS113 4.8 12.9 1.0
C A:CYS100 4.9 14.5 1.0
CG A:LYS113 4.9 19.3 1.0
O A:CYS100 4.9 15.1 1.0
CA A:GLN96 5.0 10.0 1.0
O A:HOH708 5.0 38.9 1.0
CA A:GLY98 5.0 14.5 1.0

Zinc binding site 4 out of 6 in 4xd2

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Zinc binding site 4 out of 6 in the Horse Liver Alcohol Dehydrogenase-Nadh Complex


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-Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:17.6
occ:0.80
ZN B:ZN401 0.0 17.6 0.8
ZN B:ZN401 1.4 20.0 0.2
NE2 B:HIS67 2.0 18.4 1.0
O B:HOH862 2.1 22.8 0.8
SG B:CYS174 2.2 16.9 1.0
SG B:CYS46 2.3 17.6 1.0
CE1 B:HIS67 3.0 15.3 1.0
CD2 B:HIS67 3.1 16.8 1.0
CB B:CYS174 3.3 16.1 1.0
CB B:CYS46 3.4 18.5 1.0
C5N B:NAI403 3.5 13.8 1.0
C6N B:NAI403 3.9 15.1 1.0
OG B:SER48 4.0 16.9 1.0
C4N B:NAI403 4.1 14.8 1.0
CB B:SER48 4.1 14.8 1.0
ND1 B:HIS67 4.1 15.9 1.0
CG B:HIS67 4.2 14.8 1.0
NH2 B:ARG369 4.6 23.8 1.0
CA B:CYS174 4.7 13.3 1.0
OE2 B:GLU68 4.8 26.6 1.0
CA B:CYS46 4.8 18.9 1.0
N B:SER48 4.9 14.8 1.0
CE2 B:PHE93 4.9 17.5 1.0
N1N B:NAI403 5.0 14.1 1.0
N B:GLY175 5.0 13.6 1.0
C B:CYS174 5.0 13.6 1.0

Zinc binding site 5 out of 6 in 4xd2

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Zinc binding site 5 out of 6 in the Horse Liver Alcohol Dehydrogenase-Nadh Complex


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-Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:20.0
occ:0.20
ZN B:ZN401 0.0 20.0 0.2
ZN B:ZN401 1.4 17.6 0.8
SG B:CYS46 2.2 17.6 1.0
NE2 B:HIS67 2.3 18.4 1.0
SG B:CYS174 2.5 16.9 1.0
CB B:CYS46 2.6 18.5 1.0
CB B:CYS174 2.9 16.1 1.0
CE1 B:HIS67 3.0 15.3 1.0
CD2 B:HIS67 3.2 16.8 1.0
O B:HOH862 3.4 22.8 0.8
OE2 B:GLU68 3.6 26.6 1.0
NH2 B:ARG369 3.8 23.8 1.0
ND1 B:HIS67 4.1 15.9 1.0
CD B:GLU68 4.1 21.5 1.0
CA B:CYS46 4.1 18.9 1.0
CB B:GLU68 4.1 17.1 1.0
CG B:HIS67 4.2 14.8 1.0
CA B:CYS174 4.4 13.3 1.0
C5N B:NAI403 4.4 13.8 1.0
N B:GLY175 4.5 13.6 1.0
CG B:GLU68 4.6 19.6 1.0
OE1 B:GLU68 4.7 24.2 1.0
C B:CYS174 4.7 13.6 1.0
C6N B:NAI403 4.8 15.1 1.0
CZ B:ARG369 4.8 18.9 1.0
N B:CYS46 4.8 18.4 1.0
O B:HOH573 4.9 16.6 1.0
CB B:SER48 4.9 14.8 1.0
OD2 B:ASP49 4.9 18.8 1.0
C B:CYS46 4.9 17.5 1.0

Zinc binding site 6 out of 6 in 4xd2

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Zinc binding site 6 out of 6 in the Horse Liver Alcohol Dehydrogenase-Nadh Complex


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-Nadh Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:17.4
occ:1.00
SG B:CYS111 2.3 16.3 1.0
SG B:CYS97 2.3 20.3 1.0
SG B:CYS100 2.3 17.5 1.0
SG B:CYS103 2.4 16.0 1.0
CB B:CYS111 3.3 15.8 1.0
CB B:CYS100 3.4 19.4 1.0
CB B:CYS97 3.4 19.2 1.0
CB B:CYS103 3.4 16.2 1.0
N B:CYS97 3.5 16.9 1.0
CA B:CYS111 3.8 15.4 1.0
CA B:CYS97 3.9 17.6 1.0
N B:LEU112 3.9 16.3 1.0
N B:CYS100 4.0 18.2 1.0
N B:GLY98 4.0 18.4 1.0
N B:CYS103 4.2 15.4 1.0
CA B:CYS100 4.2 21.0 1.0
C B:CYS111 4.3 16.1 1.0
C B:CYS97 4.3 19.4 1.0
CA B:CYS103 4.4 15.8 1.0
N B:LYS99 4.6 19.9 1.0
C B:GLN96 4.6 14.4 1.0
N B:LYS113 4.8 17.0 1.0
C B:CYS100 4.9 18.8 1.0
CG B:LYS113 4.9 25.3 1.0
CA B:GLN96 4.9 14.2 1.0
O B:CYS100 5.0 18.4 1.0

Reference:

B.V.Plapp, S.Baskar Raj, D.J.Ferraro. Structure of Horse Liver Alcohol Dehydrogenase Complexed with Nadh To Be Published.
Page generated: Wed Dec 16 05:54:12 2020

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