Zinc in PDB 8zj7: Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad.

Enzymatic activity of Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad.

All present enzymatic activity of Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad.:
1.1.1.262;

Protein crystallography data

The structure of Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad., PDB code: 8zj7 was solved by K.A.Kumar, D.Pahwa, P.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.00 / 2.65
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 87.303, 98.148, 168.036, 90, 90, 90
R / Rfree (%) 18.1 / 25.2

Other elements in 8zj7:

The structure of Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad. also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 1 atom
Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad. (pdb code 8zj7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad., PDB code: 8zj7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8zj7

Go back to Zinc Binding Sites List in 8zj7
Zinc binding site 1 out of 4 in the Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:94.8
occ:1.00
 HE2 B:HIS159 1.3 54.1 0.0
HE2 B:HIS255 1.9 54.4 0.0
HE2 D:HIS203 2.0 85.0 0.0
NE2 B:HIS159 2.3 51.6 1.0
O B:HOH505 2.7 56.1 1.0
HE2 B:HIS259 2.8 43.0 0.0
NE2 B:HIS255 2.8 56.6 1.0
NE2 D:HIS203 2.8 86.2 1.0
O B:HOH527 3.0 48.5 1.0
CE1 B:HIS159 3.1 51.9 1.0
HE1 B:HIS159 3.1 51.6 1.0
NE2 B:HIS259 3.3 43.2 1.0
O B:HOH536 3.3 179.9 1.0
HD2 B:HIS259 3.4 44.8 1.0
CD2 B:HIS159 3.4 48.4 1.0
HE1 D:HIS203 3.5 82.9 1.0
CE1 D:HIS203 3.5 84.4 1.0
CD2 B:HIS259 3.6 45.3 1.0
HD2 B:HIS159 3.7 48.8 1.0
CE1 B:HIS255 3.7 56.1 1.0
CD2 B:HIS255 3.7 52.9 1.0
HD2 B:HIS255 3.8 53.5 1.0
HE1 B:HIS255 3.8 55.8 1.0
CD2 D:HIS203 4.0 82.8 1.0
HD2 D:HIS203 4.2 81.7 1.0
ND1 B:HIS159 4.3 49.1 1.0
CE1 B:HIS259 4.3 43.3 1.0
CG B:HIS159 4.4 46.4 1.0
HZ3 B:LYS263 4.5 75.8 1.0
HD12 B:LEU158 4.7 48.0 1.0
HE1 B:HIS259 4.7 43.3 1.0
ND1 D:HIS203 4.7 78.1 1.0
CG B:HIS259 4.8 44.1 1.0
ND1 B:HIS255 4.9 55.2 1.0
CG B:HIS255 4.9 52.7 1.0
CG D:HIS203 5.0 76.4 1.0
HD1 B:HIS159 5.0 48.8 0.0

Zinc binding site 2 out of 4 in 8zj7

Go back to Zinc Binding Sites List in 8zj7
Zinc binding site 2 out of 4 in the Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:54.9
occ:1.00
 HE2 C:HIS159 1.3 55.5 0.0
HE2 C:HIS255 1.5 42.4 0.0
HE2 A:HIS203 1.9 55.4 0.0
NE2 C:HIS159 2.1 54.5 1.0
NE2 C:HIS255 2.3 44.6 1.0
NE2 A:HIS203 2.4 56.1 1.0
HE1 A:HIS203 2.5 59.8 1.0
C2 C:DHB401 2.6 65.2 1.0
H2 C:DHB401 2.6 65.1 1.0
CE1 A:HIS203 2.7 60.2 1.0
C1 C:DHB401 2.8 64.0 1.0
O1 C:DHB401 3.0 56.8 1.0
C C:DHB401 3.1 60.8 1.0
CE1 C:HIS159 3.1 56.2 1.0
CD2 C:HIS159 3.2 52.2 1.0
C3 C:DHB401 3.2 72.9 1.0
HE1 C:HIS159 3.3 55.2 1.0
CE1 C:HIS255 3.3 45.0 1.0
CD2 C:HIS255 3.3 44.2 1.0
HD2 C:HIS159 3.3 51.7 1.0
HE2 C:HIS259 3.3 41.4 0.0
HD2 C:HIS255 3.4 43.6 1.0
HE1 C:HIS255 3.5 44.4 1.0
C6 C:DHB401 3.5 72.1 1.0
CD2 A:HIS203 3.6 54.1 1.0
NE2 C:HIS259 3.7 41.9 1.0
HD2 C:HIS259 3.8 40.3 1.0
O3 C:DHB401 3.8 81.0 1.0
ND1 A:HIS203 3.9 59.4 1.0
C4 C:DHB401 3.9 73.7 1.0
CD2 C:HIS259 4.0 39.7 1.0
O2 C:DHB401 4.0 69.8 1.0
C5 C:DHB401 4.0 73.6 1.0
H6 C:DHB401 4.1 70.6 1.0
HD2 A:HIS203 4.1 53.8 1.0
ND1 C:HIS159 4.2 54.2 1.0
CG C:HIS159 4.3 49.6 1.0
CG A:HIS203 4.4 53.0 1.0
ND1 C:HIS255 4.4 44.0 1.0
HO3 C:DHB401 4.4 78.5 0.0
CG C:HIS255 4.5 42.7 1.0
HD1 A:HIS203 4.6 57.3 0.0
CE1 C:HIS259 4.7 44.3 1.0
HB3 A:PRO202 4.8 45.4 1.0
H5 C:DHB401 4.8 73.7 1.0
HD12 C:LEU158 4.8 44.9 1.0
HG C:LEU158 5.0 45.7 1.0

Zinc binding site 3 out of 4 in 8zj7

Go back to Zinc Binding Sites List in 8zj7
Zinc binding site 3 out of 4 in the Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:67.3
occ:1.00
 HE2 D:HIS159 1.3 46.5 0.0
HE2 D:HIS255 1.5 44.4 0.0
O2 D:DHB401 2.0 73.2 1.0
NE2 D:HIS159 2.1 46.9 1.0
HE2 B:HIS203 2.2 62.2 0.0
H2 D:DHB401 2.3 75.1 1.0
NE2 D:HIS255 2.4 43.9 1.0
HE1 B:HIS203 2.4 62.3 1.0
NE2 B:HIS203 2.5 64.0 1.0
CE1 B:HIS203 2.7 62.1 1.0
C D:DHB401 2.7 74.1 1.0
C2 D:DHB401 3.0 78.1 1.0
CE1 D:HIS159 3.1 50.3 1.0
CD2 D:HIS159 3.1 46.1 1.0
HE2 D:HIS259 3.2 49.5 0.0
C1 D:DHB401 3.2 77.9 1.0
HE1 D:HIS159 3.3 50.0 1.0
HD2 D:HIS159 3.3 45.3 1.0
CD2 D:HIS255 3.3 43.6 1.0
CE1 D:HIS255 3.3 46.1 1.0
HD2 D:HIS255 3.4 43.0 1.0
HE1 D:HIS255 3.5 45.5 1.0
NE2 D:HIS259 3.6 49.5 1.0
O1 D:DHB401 3.7 73.1 1.0
HD2 D:HIS259 3.7 47.1 1.0
CD2 B:HIS203 3.7 61.6 1.0
ND1 B:HIS203 3.9 61.8 1.0
CD2 D:HIS259 3.9 46.6 1.0
ND1 D:HIS159 4.2 48.6 1.0
C3 D:DHB401 4.2 78.0 1.0
CG D:HIS159 4.2 44.5 1.0
HD2 B:HIS203 4.3 61.8 1.0
CG B:HIS203 4.4 59.8 1.0
HD1 B:HIS203 4.4 57.9 0.0
ND1 D:HIS255 4.5 45.0 1.0
CG D:HIS255 4.5 41.9 1.0
C6 D:DHB401 4.6 82.0 1.0
CE1 D:HIS259 4.6 46.5 1.0
HD12 D:LEU158 4.7 44.9 1.0
O3 D:DHB401 4.7 86.6 1.0
HB3 B:PRO202 4.8 40.6 1.0
HG D:LEU158 4.9 43.3 1.0
CG D:HIS259 5.0 46.3 1.0
HE1 D:HIS259 5.0 47.3 1.0

Zinc binding site 4 out of 4 in 8zj7

Go back to Zinc Binding Sites List in 8zj7
Zinc binding site 4 out of 4 in the Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:63.7
occ:1.00
 HE2 A:HIS159 1.2 39.9 0.0
HE2 A:HIS255 1.5 46.0 0.0
NE2 A:HIS159 2.0 38.6 1.0
HE2 C:HIS203 2.3 46.7 0.0
NE2 A:HIS255 2.4 50.1 1.0
HE1 C:HIS203 2.6 54.9 1.0
C3 A:DHB402 2.6 69.2 1.0
NE2 C:HIS203 2.7 48.8 1.0
CE1 C:HIS203 2.8 55.5 1.0
C4 A:DHB402 2.9 65.3 1.0
CE1 A:HIS159 2.9 38.4 1.0
O3 A:DHB402 3.0 77.5 1.0
C2 A:DHB402 3.0 73.9 1.0
CD2 A:HIS159 3.1 36.9 1.0
HE1 A:HIS159 3.1 39.2 1.0
HE2 A:HIS259 3.2 47.4 0.0
HO3 A:DHB402 3.2 77.9 0.0
CD2 A:HIS255 3.3 49.3 1.0
HD2 A:HIS159 3.3 37.0 1.0
HD2 A:HIS255 3.3 48.5 1.0
H2 A:DHB402 3.4 73.4 1.0
CE1 A:HIS255 3.4 51.4 1.0
O4 A:DHB402 3.5 63.8 1.0
C5 A:DHB402 3.5 72.0 1.0
C1 A:DHB402 3.6 79.3 1.0
HE1 A:HIS255 3.6 50.8 1.0
NE2 A:HIS259 3.6 53.1 1.0
C6 A:DHB402 3.8 78.2 1.0
HD2 A:HIS259 3.9 50.3 1.0
CD2 C:HIS203 3.9 46.1 1.0
CD2 A:HIS259 4.0 50.1 1.0
ND1 C:HIS203 4.0 56.8 1.0
HO4 A:DHB402 4.0 62.8 0.0
ND1 A:HIS159 4.1 37.0 1.0
H5 A:DHB402 4.1 70.9 1.0
CG A:HIS159 4.1 36.8 1.0
HD2 C:HIS203 4.4 46.3 1.0
CG A:HIS255 4.4 45.4 1.0
ND1 A:HIS255 4.5 48.8 1.0
H6 A:DHB402 4.5 77.2 1.0
HD12 A:LEU158 4.5 44.8 1.0
CG C:HIS203 4.5 47.3 1.0
CE1 A:HIS259 4.6 49.9 1.0
HD1 C:HIS203 4.6 54.6 0.0
C A:DHB402 4.6 82.4 1.0
HG A:LEU158 4.7 45.3 1.0
HB3 C:PRO202 4.8 35.1 1.0
O2 A:DHB402 4.8 85.1 1.0
HE1 A:HIS259 4.9 50.0 1.0
HD1 A:HIS159 4.9 37.2 0.0

Reference:

K.A.Kumar, D.Pahwa. Terephthalate 1,2-Cis-Dihydrodioldehydrogenase/Decarboxylase in Complex with 3,4-Dihydroxybenzoate and Nad. To Be Published.
Page generated: Thu Oct 31 14:15:19 2024

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