Zinc in PDB 7k35: Eqadh-Nadh-4-Methylbenzyl Alcohol, P21

Enzymatic activity of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21

All present enzymatic activity of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21:
1.1.1.1;

Protein crystallography data

The structure of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21, PDB code: 7k35 was solved by B.V.Plapp, S.Ramaswamy, 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 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.220, 180.220, 86.860, 90.00, 106.12, 90.00
R / Rfree (%) 17.6 / 21

Zinc Binding Sites:

The binding sites of Zinc atom in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 (pdb code 7k35). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21, PDB code: 7k35:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7k35

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Zinc binding site 1 out of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:23.2
occ:1.00
 NE2 A:HIS67 2.1 20.8 1.0
SG A:CYS174 2.1 21.9 1.0
O1 A:VTG404 2.2 21.4 1.0
SG A:CYS46 2.3 22.1 1.0
CE1 A:HIS67 3.0 21.0 1.0
CD2 A:HIS67 3.1 20.6 1.0
C7 A:VTG404 3.2 22.4 1.0
CB A:CYS46 3.3 19.7 1.0
CB A:CYS174 3.3 16.3 1.0
C5N A:NAI403 3.5 17.8 1.0
C6N A:NAI403 3.9 18.4 1.0
OG A:SER48 4.0 22.4 1.0
C4N A:NAI403 4.0 19.6 1.0
ND1 A:HIS67 4.1 16.6 1.0
CB A:SER48 4.2 18.8 1.0
CG A:HIS67 4.2 16.6 1.0
C1 A:VTG404 4.6 20.6 1.0
OE2 A:GLU68 4.6 26.2 1.0
NH2 A:ARG369 4.6 25.4 1.0
CA A:CYS174 4.7 16.6 1.0
CA A:CYS46 4.7 19.2 1.0
CE2 A:PHE93 4.8 19.3 1.0
N A:SER48 4.9 20.0 1.0
N A:GLY175 4.9 19.8 1.0

Zinc binding site 2 out of 8 in 7k35

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Zinc binding site 2 out of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:20.6
occ:1.00
 SG A:CYS111 2.3 20.3 1.0
SG A:CYS97 2.3 22.0 1.0
SG A:CYS103 2.3 21.1 1.0
SG A:CYS100 2.3 20.8 1.0
CB A:CYS111 3.3 20.0 1.0
CB A:CYS103 3.4 19.5 1.0
CB A:CYS97 3.4 24.4 1.0
CB A:CYS100 3.4 24.8 1.0
N A:CYS97 3.6 19.8 1.0
CA A:CYS111 3.7 20.6 1.0
N A:CYS100 3.8 24.2 1.0
CA A:CYS97 3.9 20.1 1.0
N A:GLY98 4.0 21.1 1.0
N A:LEU112 4.0 18.6 1.0
CA A:CYS100 4.2 24.7 1.0
N A:CYS103 4.2 21.2 1.0
C A:CYS111 4.2 18.4 1.0
CA A:CYS103 4.3 21.6 1.0
C A:CYS97 4.4 21.6 1.0
N A:LYS99 4.5 23.0 1.0
C A:GLN96 4.6 20.0 1.0
N A:LYS113 4.8 21.4 1.0
C A:CYS100 4.8 23.0 1.0
CG A:LYS113 4.9 24.1 1.0
CA A:GLN96 5.0 19.5 1.0
O A:CYS100 5.0 23.2 1.0

Zinc binding site 3 out of 8 in 7k35

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Zinc binding site 3 out of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:23.1
occ:1.00
 NE2 B:HIS67 2.1 20.1 1.0
SG B:CYS174 2.1 22.3 1.0
O1 B:VTG404 2.2 22.9 1.0
SG B:CYS46 2.4 20.2 1.0
CE1 B:HIS67 3.0 20.0 1.0
CD2 B:HIS67 3.1 21.2 1.0
C7 B:VTG404 3.2 23.9 1.0
CB B:CYS46 3.3 21.6 1.0
CB B:CYS174 3.4 19.0 1.0
C5N B:NAI403 3.4 19.6 1.0
C4N B:NAI403 3.9 19.4 1.0
OG B:SER48 4.0 21.1 1.0
C6N B:NAI403 4.0 19.8 1.0
CB B:SER48 4.1 22.1 1.0
ND1 B:HIS67 4.2 20.3 1.0
CG B:HIS67 4.2 19.9 1.0
NH2 B:ARG369 4.6 23.9 1.0
C1 B:VTG404 4.6 22.8 1.0
OE2 B:GLU68 4.6 25.8 1.0
CA B:CYS46 4.7 22.5 1.0
CA B:CYS174 4.7 16.7 1.0
CE2 B:PHE93 4.9 21.0 1.0
N B:SER48 5.0 19.0 1.0
N B:GLY175 5.0 20.0 1.0

Zinc binding site 4 out of 8 in 7k35

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Zinc binding site 4 out of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:22.7
occ:0.96
 SG B:CYS100 2.3 22.7 1.0
SG B:CYS97 2.3 24.4 1.0
SG B:CYS111 2.4 22.5 1.0
SG B:CYS103 2.4 24.0 1.0
CB B:CYS111 3.3 22.4 1.0
CB B:CYS103 3.4 22.9 1.0
CB B:CYS97 3.4 23.0 1.0
CB B:CYS100 3.5 24.6 1.0
N B:CYS97 3.6 22.6 1.0
CA B:CYS111 3.7 21.4 1.0
N B:CYS100 3.9 27.4 1.0
CA B:CYS97 3.9 23.9 1.0
N B:LEU112 4.0 20.6 1.0
N B:GLY98 4.0 23.5 1.0
CA B:CYS100 4.2 25.9 1.0
N B:CYS103 4.2 21.6 1.0
C B:CYS111 4.3 22.8 1.0
CA B:CYS103 4.4 22.8 1.0
C B:CYS97 4.4 26.2 1.0
N B:LYS99 4.5 25.6 1.0
C B:GLN96 4.6 21.2 1.0
O B:HOH761 4.8 35.0 1.0
C B:CYS100 4.8 21.4 1.0
CA B:GLN96 4.9 20.7 1.0
N B:LYS113 4.9 21.8 1.0
O B:CYS100 5.0 23.1 1.0
CA B:GLY98 5.0 24.9 1.0

Zinc binding site 5 out of 8 in 7k35

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Zinc binding site 5 out of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:23.1
occ:1.00
 NE2 C:HIS67 2.1 19.6 1.0
SG C:CYS174 2.1 20.9 1.0
O1 C:VTG404 2.2 23.3 1.0
SG C:CYS46 2.3 21.0 1.0
CE1 C:HIS67 3.0 21.6 1.0
CD2 C:HIS67 3.1 19.4 1.0
C7 C:VTG404 3.2 22.7 1.0
CB C:CYS46 3.3 19.8 1.0
CB C:CYS174 3.3 17.8 1.0
C5N C:NAI403 3.5 15.3 1.0
C6N C:NAI403 4.0 15.7 1.0
C4N C:NAI403 4.0 17.5 1.0
OG C:SER48 4.0 21.4 1.0
CB C:SER48 4.2 18.8 1.0
ND1 C:HIS67 4.2 16.8 1.0
CG C:HIS67 4.2 15.7 1.0
C1 C:VTG404 4.6 23.2 1.0
OE2 C:GLU68 4.6 22.1 1.0
NH2 C:ARG369 4.6 22.9 1.0
CA C:CYS174 4.7 18.3 1.0
CA C:CYS46 4.8 19.6 1.0
N C:GLY175 4.9 19.1 1.0
CE2 C:PHE93 4.9 19.9 1.0
N C:SER48 4.9 19.6 1.0
C C:CYS174 5.0 17.8 1.0

Zinc binding site 6 out of 8 in 7k35

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Zinc binding site 6 out of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:23.0
occ:1.00
 SG C:CYS97 2.3 24.2 1.0
SG C:CYS111 2.3 22.1 1.0
SG C:CYS100 2.3 23.1 1.0
SG C:CYS103 2.4 23.2 1.0
CB C:CYS111 3.3 21.0 1.0
CB C:CYS97 3.4 24.2 1.0
CB C:CYS103 3.4 20.9 1.0
CB C:CYS100 3.4 27.3 1.0
N C:CYS97 3.6 22.0 1.0
CA C:CYS111 3.7 22.3 1.0
N C:CYS100 3.8 25.8 1.0
CA C:CYS97 3.9 22.5 1.0
N C:LEU112 4.0 21.7 1.0
N C:GLY98 4.0 23.3 1.0
CA C:CYS100 4.2 26.2 1.0
N C:CYS103 4.2 21.8 1.0
C C:CYS111 4.2 22.2 1.0
CA C:CYS103 4.3 22.5 1.0
C C:CYS97 4.3 25.1 1.0
N C:LYS99 4.5 27.6 1.0
O C:HOH782 4.6 41.6 1.0
C C:GLN96 4.7 21.3 1.0
N C:LYS113 4.9 21.3 1.0
C C:CYS100 4.9 24.8 1.0
CG C:LYS113 4.9 28.7 1.0
O C:CYS100 5.0 25.8 1.0
CA C:GLN96 5.0 23.3 1.0
C C:LYS99 5.0 29.1 1.0

Zinc binding site 7 out of 8 in 7k35

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Zinc binding site 7 out of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:23.5
occ:1.00
 NE2 D:HIS67 2.1 19.4 1.0
O1 D:VTG404 2.1 22.0 1.0
SG D:CYS174 2.2 22.0 1.0
SG D:CYS46 2.3 19.9 1.0
CD2 D:HIS67 3.0 21.1 1.0
CE1 D:HIS67 3.1 19.3 1.0
C7 D:VTG404 3.2 25.2 1.0
CB D:CYS46 3.3 20.8 1.0
CB D:CYS174 3.4 18.4 1.0
C5N D:NAI403 3.4 20.2 1.0
C4N D:NAI403 3.9 20.0 1.0
C6N D:NAI403 4.0 19.1 1.0
OG D:SER48 4.0 20.7 1.0
CB D:SER48 4.2 21.7 1.0
ND1 D:HIS67 4.2 18.4 1.0
CG D:HIS67 4.2 21.0 1.0
NH2 D:ARG369 4.5 23.9 1.0
C1 D:VTG404 4.6 21.4 1.0
CA D:CYS174 4.7 17.7 1.0
CA D:CYS46 4.7 21.0 1.0
CE2 D:PHE93 4.8 23.0 1.0
OE2 D:GLU68 4.8 25.9 1.0
N D:SER48 5.0 20.2 1.0
N D:GLY175 5.0 19.8 1.0

Zinc binding site 8 out of 8 in 7k35

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Zinc binding site 8 out of 8 in the Eqadh-Nadh-4-Methylbenzyl Alcohol, P21


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Eqadh-Nadh-4-Methylbenzyl Alcohol, P21 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:21.4
occ:1.00
 SG D:CYS103 2.3 23.9 1.0
SG D:CYS111 2.3 20.6 1.0
SG D:CYS100 2.3 21.0 1.0
SG D:CYS97 2.4 22.6 1.0
CB D:CYS111 3.3 20.2 1.0
CB D:CYS103 3.4 23.6 1.0
CB D:CYS100 3.4 22.7 1.0
CB D:CYS97 3.5 23.7 1.0
N D:CYS97 3.6 20.7 1.0
CA D:CYS111 3.7 17.6 1.0
N D:CYS100 3.9 23.7 1.0
CA D:CYS97 3.9 20.8 1.0
N D:GLY98 4.0 22.1 1.0
N D:LEU112 4.0 18.2 1.0
CA D:CYS100 4.2 23.2 1.0
N D:CYS103 4.2 20.4 1.0
C D:CYS111 4.3 17.8 1.0
CA D:CYS103 4.4 23.7 1.0
C D:CYS97 4.4 23.3 1.0
N D:LYS99 4.5 22.2 1.0
C D:GLN96 4.7 19.8 1.0
C D:CYS100 4.8 21.5 1.0
N D:LYS113 4.9 22.3 1.0
O D:HOH739 4.9 36.1 1.0
O D:CYS100 4.9 21.9 1.0
CA D:GLN96 4.9 20.2 1.0
CA D:GLY98 5.0 23.4 1.0
CG D:LYS113 5.0 25.4 1.0

Reference:

B.V.Plapp, S.Ramaswamy. Alternative Binding Modes in Abortive Nadh and Alcohol Complexes of Horse Liver Alcohol Dehydrogenase To Be Published.
Page generated: Tue Oct 29 21:13:50 2024

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