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Zinc in PDB 6dxq: Crystal Structure of the Ligj Hydratase Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate

Enzymatic activity of Crystal Structure of the Ligj Hydratase Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate

All present enzymatic activity of Crystal Structure of the Ligj Hydratase Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate:
4.2.1.83;

Protein crystallography data

The structure of Crystal Structure of the Ligj Hydratase Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate, PDB code: 6dxq was solved by M.F.Mabanglo, F.M.Raushel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.80 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.521, 78.301, 135.637, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Ligj Hydratase Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate (pdb code 6dxq). 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 Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate, PDB code: 6dxq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6dxq

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Zinc binding site 1 out of 4 in the Crystal Structure of the Ligj Hydratase Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate


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 Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:48.4
occ:1.00
NE2 A:HIS10 2.0 45.8 1.0
NE2 A:HIS8 2.2 47.1 1.0
O05 A:7QD402 2.2 49.8 1.0
NE2 A:HIS178 2.2 43.8 1.0
O01 A:7QD402 2.3 54.3 1.0
CE1 A:HIS10 2.9 45.7 1.0
CD2 A:HIS10 3.0 45.0 1.0
C03 A:7QD402 3.0 52.1 1.0
CD2 A:HIS178 3.0 43.7 1.0
C02 A:7QD402 3.0 53.2 1.0
CE1 A:HIS8 3.0 45.5 1.0
CD2 A:HIS8 3.2 46.8 1.0
CE1 A:HIS178 3.3 45.5 1.0
CG A:GLU284 3.8 43.5 1.0
ND1 A:HIS10 4.0 46.3 1.0
CG A:HIS10 4.0 45.0 1.0
O04 A:7QD402 4.2 53.9 1.0
ND1 A:HIS8 4.2 45.5 1.0
CG A:HIS178 4.2 43.4 1.0
CD A:GLU284 4.3 47.7 1.0
CG A:HIS8 4.3 46.1 1.0
OE2 A:GLU284 4.3 48.1 1.0
ND1 A:HIS178 4.4 44.5 1.0
CB A:ALA72 4.5 44.8 1.0
C06 A:7QD402 4.5 52.6 1.0
NE2 A:HIS223 4.5 39.5 1.0
C09 A:7QD402 4.9 56.1 1.0
H062 A:7QD402 4.9 63.2 1.0
O10 A:7QD402 4.9 55.6 1.0
H061 A:7QD402 5.0 63.2 1.0

Zinc binding site 2 out of 4 in 6dxq

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Zinc binding site 2 out of 4 in the Crystal Structure of the Ligj Hydratase Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate


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 Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:48.8
occ:1.00
O05 B:7QD402 2.1 45.8 1.0
NE2 B:HIS8 2.1 45.1 1.0
NE2 B:HIS178 2.2 43.7 1.0
NE2 B:HIS10 2.2 41.6 1.0
O01 B:7QD402 2.4 48.8 1.0
C03 B:7QD402 2.9 48.4 1.0
CE1 B:HIS8 2.9 42.7 1.0
CD2 B:HIS10 3.0 42.0 1.0
C02 B:7QD402 3.1 49.7 1.0
CE1 B:HIS178 3.1 44.5 1.0
CD2 B:HIS178 3.2 43.0 1.0
CD2 B:HIS8 3.3 44.6 1.0
CE1 B:HIS10 3.4 42.3 1.0
CG B:GLU284 3.7 36.6 1.0
O04 B:7QD402 4.1 49.2 1.0
ND1 B:HIS8 4.1 42.4 1.0
ND1 B:HIS178 4.2 42.7 1.0
CG B:HIS10 4.2 42.3 1.0
CB B:ALA72 4.2 45.7 1.0
CG B:HIS178 4.3 42.0 1.0
CD B:GLU284 4.3 39.2 1.0
CG B:HIS8 4.3 42.6 1.0
ND1 B:HIS10 4.3 42.7 1.0
NE2 B:HIS223 4.4 35.0 1.0
C06 B:7QD402 4.5 50.0 1.0
OE2 B:GLU284 4.7 38.4 1.0
OE1 B:GLU284 4.8 38.5 1.0
H062 B:7QD402 4.9 60.0 1.0
O08 B:7QD402 5.0 54.6 1.0

Zinc binding site 3 out of 4 in 6dxq

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Zinc binding site 3 out of 4 in the Crystal Structure of the Ligj Hydratase Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate


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 Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:47.0
occ:1.00
O05 C:7QD402 2.1 46.4 1.0
NE2 C:HIS8 2.2 43.2 1.0
NE2 C:HIS178 2.2 44.2 1.0
NE2 C:HIS10 2.2 40.5 1.0
O01 C:7QD402 2.4 47.6 1.0
C03 C:7QD402 2.9 46.7 1.0
CE1 C:HIS178 3.0 46.2 1.0
CD2 C:HIS10 3.0 42.4 1.0
CE1 C:HIS8 3.0 43.7 1.0
C02 C:7QD402 3.0 48.8 1.0
CD2 C:HIS8 3.2 43.3 1.0
CE1 C:HIS10 3.3 38.9 1.0
CD2 C:HIS178 3.3 45.1 1.0
CG C:GLU284 3.6 42.1 1.0
ND1 C:HIS178 4.2 45.6 1.0
O04 C:7QD402 4.2 43.5 1.0
ND1 C:HIS8 4.2 41.2 1.0
CG C:HIS10 4.2 42.0 1.0
CG C:HIS8 4.3 42.2 1.0
CD C:GLU284 4.3 43.3 1.0
CB C:ALA72 4.3 44.1 1.0
ND1 C:HIS10 4.3 41.1 1.0
CG C:HIS178 4.4 45.0 1.0
NE2 C:HIS223 4.5 42.6 1.0
C06 C:7QD402 4.5 50.0 1.0
OE2 C:GLU284 4.7 39.4 1.0
H062 C:7QD402 4.8 60.0 1.0
CB C:GLU284 4.9 43.2 1.0
OE1 C:GLU284 4.9 45.8 1.0
CE1 C:HIS223 5.0 43.1 1.0

Zinc binding site 4 out of 4 in 6dxq

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Zinc binding site 4 out of 4 in the Crystal Structure of the Ligj Hydratase Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate


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 Product Complex with 4- Carboxy-4-Hydroxy-2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:51.6
occ:1.00
NE2 D:HIS10 2.1 46.0 1.0
NE2 D:HIS178 2.1 41.5 1.0
NE2 D:HIS8 2.2 42.4 1.0
O01 D:7QD402 2.2 50.8 1.0
O04 D:7QD402 2.4 46.0 1.0
CE1 D:HIS8 2.9 41.3 1.0
C02 D:7QD402 3.0 50.2 1.0
CE1 D:HIS10 3.0 45.7 1.0
CD2 D:HIS178 3.0 40.4 1.0
C03 D:7QD402 3.0 48.8 1.0
CD2 D:HIS10 3.1 45.9 1.0
CE1 D:HIS178 3.2 40.9 1.0
CD2 D:HIS8 3.3 41.6 1.0
CG D:GLU284 3.8 43.6 1.0
OE2 D:GLU284 4.1 46.6 1.0
ND1 D:HIS10 4.1 46.4 1.0
ND1 D:HIS8 4.1 39.3 1.0
CD D:GLU284 4.1 46.0 1.0
CG D:HIS10 4.2 45.2 1.0
O05 D:7QD402 4.2 48.5 1.0
CG D:HIS178 4.2 40.4 1.0
ND1 D:HIS178 4.3 40.2 1.0
CG D:HIS8 4.3 40.1 1.0
CB D:ALA72 4.3 45.0 1.0
C06 D:7QD402 4.4 49.5 1.0
NE2 D:HIS223 4.5 45.2 1.0
H061 D:7QD402 4.9 59.4 1.0
H062 D:7QD402 4.9 59.4 1.0
OE1 D:GLU284 4.9 45.7 1.0
C09 D:7QD402 5.0 52.3 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: Wed Dec 16 11:41:32 2020

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