Atomistry » Zinc » PDB 7jo3-7k36 » 7k35
Atomistry »
  Zinc »
    PDB 7jo3-7k36 »
      7k35 »

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

Go back to Zinc Binding Sites List in 7k35
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

Go back to Zinc Binding Sites List in 7k35
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

Go back to Zinc Binding Sites List in 7k35
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

Go back to Zinc Binding Sites List in 7k35
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

Go back to Zinc Binding Sites List in 7k35
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

Go back to Zinc Binding Sites List in 7k35
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

Go back to Zinc Binding Sites List in 7k35
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

Go back to Zinc Binding Sites List in 7k35
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy