Zinc in PDB 6dwv: Crystal Structure of the Ligj Hydratase in the Apo State

All present enzymatic activity of Crystal Structure of the Ligj Hydratase in the Apo State:
4.2.1.83;

The structure of Crystal Structure of the Ligj Hydratase in the Apo State, PDB code: 6dwv 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)	26.14 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.170, 78.220, 135.690, 90.00, 90.02, 90.00
R / Rfree (%)	20.4 / 27.8

The binding sites of Zinc atom in the Crystal Structure of the Ligj Hydratase in the Apo State (pdb code 6dwv). 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 in the Apo State, PDB code: 6dwv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of the Ligj Hydratase in the Apo State


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 in the Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:34.3 occ:1.00 O B:HOH573 1.9 15.5 1.0 NE2 B:HIS178 2.4 26.2 1.0 NE2 B:HIS10 2.6 20.2 1.0 NE2 B:HIS8 2.7 18.4 1.0 CE1 B:HIS178 3.1 28.0 1.0 CD2 B:HIS10 3.2 18.6 1.0 CE1 B:HIS8 3.4 19.1 1.0 CG B:GLU284 3.5 23.0 1.0 CD2 B:HIS178 3.5 26.4 1.0 CE1 B:HIS10 3.7 15.9 1.0 CD2 B:HIS8 3.8 15.4 1.0 CD B:GLU284 3.9 25.1 1.0 NE2 B:HIS223 4.0 16.6 1.0 CB B:ALA72 4.1 36.2 1.0 OE1 B:GLU284 4.3 25.8 1.0 ND1 B:HIS178 4.3 27.1 1.0 OE2 B:GLU284 4.4 15.9 1.0 CE2 B:TYR194 4.4 24.5 1.0 CG B:HIS10 4.4 18.9 1.0 ND1 B:HIS8 4.5 18.8 1.0 CG B:HIS178 4.6 23.9 1.0 ND1 B:HIS10 4.7 18.4 1.0 CG B:HIS8 4.8 19.7 1.0 O C:HOH566 4.8 24.4 1.0 CD2 B:TYR194 4.8 23.5 1.0 CE1 B:HIS223 4.8 15.4 1.0 CB B:GLU284 4.8 15.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of the Ligj Hydratase in the Apo State


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 in the Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:33.8 occ:1.00 NE2 A:HIS10 1.9 36.5 1.0 NE2 A:HIS178 1.9 47.0 1.0 NE2 A:HIS8 2.2 31.2 1.0 CE1 A:HIS10 2.7 38.3 1.0 CE1 A:HIS178 2.9 48.8 1.0 O A:HOH559 2.9 43.9 1.0 CD2 A:HIS178 2.9 46.7 1.0 CD2 A:HIS10 3.0 37.8 1.0 CE1 A:HIS8 3.1 33.0 1.0 CD2 A:HIS8 3.2 36.2 1.0 ND1 A:HIS10 3.8 39.1 1.0 ND1 A:HIS178 4.0 46.7 1.0 CG A:HIS10 4.0 35.5 1.0 CG A:HIS178 4.0 45.2 1.0 ND1 A:HIS8 4.2 34.1 1.0 CG A:HIS8 4.3 36.6 1.0 CB A:ALA72 4.3 44.3 1.0 CG A:GLU284 4.4 38.1 1.0 SD A:MET176 4.6 33.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of the Ligj Hydratase in the Apo State


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 in the Apo State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:40.5 occ:1.00 NE2 C:HIS8 2.0 20.0 1.0 O C:HOH565 2.0 30.1 1.0 NE2 C:HIS178 2.4 22.4 1.0 CE1 C:HIS8 2.6 16.5 1.0 NE2 C:HIS10 2.7 23.8 1.0 CD2 C:HIS8 3.2 16.8 1.0 CD2 C:HIS178 3.3 21.3 1.0 CE1 C:HIS178 3.4 20.1 1.0 CD2 C:HIS10 3.4 22.8 1.0 CG C:GLU284 3.7 17.0 1.0 CE1 C:HIS10 3.7 19.3 1.0 ND1 C:HIS8 3.8 20.8 1.0 NE2 C:HIS223 4.0 16.4 1.0 CG C:HIS8 4.1 16.5 1.0 CD C:GLU284 4.2 46.7 1.0 CE1 C:HIS223 4.5 16.3 1.0 ND1 C:HIS178 4.5 21.1 1.0 CG C:HIS178 4.5 23.2 1.0 O C:HOH511 4.5 22.7 1.0 OE2 C:GLU284 4.6 48.9 1.0 OE1 C:GLU284 4.7 44.7 1.0 CG C:HIS10 4.7 22.5 1.0 CE2 C:TYR194 4.7 22.5 1.0 CB C:ALA72 4.7 40.5 1.0 ND1 C:HIS10 4.8 23.3 1.0 CB C:GLU284 5.0 16.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of the Ligj Hydratase in the Apo State


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 in the Apo State within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:25.1 occ:1.00 NE2 D:HIS10 1.9 39.4 1.0 NE2 D:HIS8 2.0 37.9 1.0 NE2 D:HIS178 2.1 54.5 1.0 CE1 D:HIS8 2.8 39.0 1.0 CE1 D:HIS10 2.8 42.9 1.0 CD2 D:HIS178 3.0 59.0 1.0 CD2 D:HIS8 3.0 41.2 1.0 CD2 D:HIS10 3.0 43.1 1.0 CE1 D:HIS178 3.1 59.9 1.0 O D:HOH568 3.5 35.0 1.0 ND1 D:HIS8 3.9 40.9 1.0 ND1 D:HIS10 4.0 41.8 1.0 CG D:HIS8 4.0 40.3 1.0 CG D:GLU284 4.0 47.1 1.0 CG D:HIS10 4.1 41.1 1.0 CG D:HIS178 4.1 52.8 1.0 ND1 D:HIS178 4.2 58.0 1.0 SD D:MET176 4.4 32.5 1.0 CB D:ALA72 4.7 50.4 1.0 CD D:GLU284 4.7 42.9 1.0 NE2 D:HIS223 4.8 28.6 1.0 OE2 D:GLU284 4.9 37.0 1.0

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