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Zinc in PDB 6dxs: Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate

Enzymatic activity of Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate

All present enzymatic activity of Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate:
4.2.1.83;

Protein crystallography data

The structure of Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate, PDB code: 6dxs was solved by M.F.Mabanglo, F.M.Raushel, T.N.Hogancamp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.63 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.689, 78.253, 136.216, 90.00, 89.98, 90.00
R / Rfree (%) 20.2 / 26.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate (pdb code 6dxs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate, PDB code: 6dxs:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6dxs

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Zinc binding site 1 out of 4 in the Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:26.4
occ:1.00
 NE2 A:HIS8 2.2 18.6 1.0
O01 A:HJ7402 2.3 33.3 1.0
O05 A:HJ7402 2.3 24.5 1.0
NE2 A:HIS178 2.4 20.7 1.0
NE2 A:HIS10 2.5 23.3 1.0
CE1 A:HIS8 2.8 18.6 1.0
CD2 A:HIS10 2.9 22.0 1.0
C02 A:HJ7402 3.0 32.5 1.0
C03 A:HJ7402 3.0 28.6 1.0
CE1 A:HIS178 3.2 21.9 1.0
CD2 A:HIS8 3.4 19.2 1.0
CD2 A:HIS178 3.5 22.5 1.0
CG A:GLN284 3.7 23.9 1.0
CE1 A:HIS10 3.8 20.3 1.0
ND1 A:HIS8 4.0 20.5 1.0
CB A:ALA72 4.1 20.8 1.0
CG A:HIS10 4.2 22.7 1.0
O04 A:HJ7402 4.3 25.1 1.0
CG A:HIS8 4.3 21.5 1.0
ND1 A:HIS178 4.4 22.5 1.0
NE2 A:GLN284 4.5 26.7 1.0
CG A:HIS178 4.5 23.5 1.0
CD A:GLN284 4.5 25.1 1.0
C06 A:HJ7402 4.5 33.2 1.0
ND1 A:HIS10 4.6 20.2 1.0
NE2 A:HIS223 4.6 22.2 1.0
CB A:GLN284 4.8 19.5 1.0
CE2 A:TYR194 4.8 18.3 1.0
O10 A:HJ7402 5.0 35.3 1.0

Zinc binding site 2 out of 4 in 6dxs

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Zinc binding site 2 out of 4 in the Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:27.0
occ:1.00
 NE2 B:HIS10 2.0 17.5 1.0
NE2 B:HIS8 2.1 20.9 1.0
O05 B:HJ7402 2.2 30.9 1.0
NE2 B:HIS178 2.2 22.0 1.0
O01 B:HJ7402 2.8 37.8 1.0
CD2 B:HIS178 2.8 22.4 1.0
CE1 B:HIS8 3.0 21.8 1.0
CD2 B:HIS10 3.0 17.5 1.0
CE1 B:HIS10 3.0 17.5 1.0
C03 B:HJ7402 3.1 33.0 1.0
CD2 B:HIS8 3.2 20.3 1.0
C02 B:HJ7402 3.3 33.5 1.0
CE1 B:HIS178 3.4 21.1 1.0
CG B:GLN284 3.8 26.2 1.0
CG B:HIS178 4.1 20.9 1.0
ND1 B:HIS10 4.1 21.5 1.0
CG B:HIS10 4.1 19.2 1.0
ND1 B:HIS8 4.1 18.4 1.0
NE2 B:HIS223 4.2 18.1 1.0
O04 B:HJ7402 4.3 32.7 1.0
CG B:HIS8 4.3 19.6 1.0
ND1 B:HIS178 4.3 20.6 1.0
CB B:ALA72 4.3 25.4 1.0
CD B:GLN284 4.5 31.2 1.0
C06 B:HJ7402 4.7 30.4 1.0
CE1 B:HIS223 4.7 18.3 1.0
OE1 B:GLN284 4.8 27.9 1.0
SD B:MET176 4.9 18.6 1.0
CE2 B:TYR194 5.0 24.2 1.0

Zinc binding site 3 out of 4 in 6dxs

Go back to Zinc Binding Sites List in 6dxs
Zinc binding site 3 out of 4 in the Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:30.4
occ:1.00
 NE2 C:HIS8 2.0 20.9 1.0
CE1 C:HIS10 2.0 25.9 1.0
NE2 C:HIS10 2.3 25.7 1.0
NE2 C:HIS178 2.3 24.8 1.0
O05 C:HJ7402 2.7 22.7 1.0
O01 C:HJ7402 2.8 33.4 1.0
CE1 C:HIS8 2.9 22.9 1.0
CD2 C:HIS178 2.9 25.8 1.0
CD2 C:HIS8 3.1 23.1 1.0
ND1 C:HIS10 3.3 27.3 1.0
C03 C:HJ7402 3.4 25.6 1.0
CE1 C:HIS178 3.4 26.3 1.0
C02 C:HJ7402 3.5 31.2 1.0
CD2 C:HIS10 3.7 25.6 1.0
CG C:GLN284 3.9 21.9 1.0
ND1 C:HIS8 4.0 20.1 1.0
CG C:HIS178 4.1 25.3 1.0
CG C:HIS10 4.1 26.4 1.0
CG C:HIS8 4.1 23.7 1.0
ND1 C:HIS178 4.3 24.8 1.0
CB C:ALA72 4.4 26.4 1.0
O04 C:HJ7402 4.5 26.6 1.0
NE2 C:HIS223 4.5 21.1 1.0
O C:HOH505 4.7 29.5 1.0
CD C:GLN284 4.7 24.2 1.0
SD C:MET176 4.7 26.4 1.0
O C:HOH530 4.9 27.3 1.0
C06 C:HJ7402 4.9 32.9 1.0
O10 C:HJ7402 5.0 29.8 1.0
CB C:GLN284 5.0 20.8 1.0

Zinc binding site 4 out of 4 in 6dxs

Go back to Zinc Binding Sites List in 6dxs
Zinc binding site 4 out of 4 in the Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Ligj Hydratase E284Q Mutant Substrate Complex with (3Z)-2-Keto-4-Carboxy-3-Hexenedioate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:27.6
occ:1.00
 O01 D:HJ7402 1.9 28.4 1.0
NE2 D:HIS8 2.4 23.3 1.0
NE2 D:HIS178 2.4 20.2 1.0
O04 D:HJ7402 2.4 22.0 1.0
C02 D:HJ7402 2.7 31.8 1.0
C03 D:HJ7402 2.9 26.8 1.0
NE2 D:HIS10 3.0 27.5 1.0
CE1 D:HIS8 3.2 21.9 1.0
CE1 D:HIS178 3.4 20.9 1.0
CD2 D:HIS178 3.4 19.6 1.0
CD2 D:HIS10 3.5 27.9 1.0
CD2 D:HIS8 3.5 22.0 1.0
CG D:GLN284 3.8 24.7 1.0
CE1 D:HIS10 3.9 28.8 1.0
C06 D:HJ7402 4.2 31.6 1.0
O05 D:HJ7402 4.2 24.4 1.0
ND1 D:HIS8 4.4 22.8 1.0
O10 D:HJ7402 4.4 38.3 1.0
C08 D:HJ7402 4.5 37.0 1.0
CG D:HIS10 4.5 25.8 1.0
ND1 D:HIS178 4.5 18.9 1.0
NE2 D:GLN284 4.5 28.4 1.0
CB D:ALA72 4.5 26.1 1.0
CD D:GLN284 4.5 27.0 1.0
CG D:HIS8 4.5 18.0 1.0
CG D:HIS178 4.5 21.0 1.0
ND1 D:HIS10 4.7 27.0 1.0
CB D:GLN284 4.7 23.8 1.0
CE2 D:TYR194 4.7 18.8 1.0
NE2 D:HIS223 4.8 21.8 1.0
O09 D:HJ7402 4.8 39.2 1.0
O D:HOH548 4.8 23.5 1.0
C07 D:HJ7402 4.8 31.6 1.0
H061 D:HJ7402 4.8 37.9 1.0

Reference:

T.N.Hogancamp, M.F.Mabanglo, F.M.Raushel. Structure and Reaction Mechanism of the Ligj Hydratase: An Enzyme Critical For the Bacterial Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway. Biochemistry V. 57 5841 2018.
ISSN: ISSN 1520-4995
PubMed: 30207699
DOI: 10.1021/ACS.BIOCHEM.8B00713
Page generated: Mon Oct 28 19:56:21 2024

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