Zinc in PDB 4xuk: Crystal Structure of Hydrolase Aboph in Beta Lactamase Superfamily

The structure of Crystal Structure of Hydrolase Aboph in Beta Lactamase Superfamily, PDB code: 4xuk was solved by J.Chen, J.H.Xu, J.H.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.84 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.812, 82.735, 99.767, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.8

The binding sites of Zinc atom in the Crystal Structure of Hydrolase Aboph in Beta Lactamase Superfamily (pdb code 4xuk). 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 Hydrolase Aboph in Beta Lactamase Superfamily, PDB code: 4xuk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Hydrolase Aboph in Beta Lactamase Superfamily


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 Hydrolase Aboph in Beta Lactamase Superfamily within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:20.0 occ:1.00 NE2 A:HIS160 2.0 26.0 1.0 OD2 A:ASP265 2.1 17.3 1.0 NE2 A:HIS312 2.2 20.2 1.0 OD2 A:ASP159 2.3 16.1 1.0 CD2 A:HIS160 2.9 16.3 1.0 CE1 A:HIS160 3.1 14.1 1.0 CG A:ASP265 3.1 19.5 1.0 ZN A:ZN402 3.1 20.0 1.0 CE1 A:HIS312 3.1 17.2 1.0 CG A:ASP159 3.2 17.7 1.0 CD2 A:HIS312 3.2 16.4 1.0 O A:HOH652 3.3 25.9 1.0 OD1 A:ASP265 3.3 15.4 1.0 OD1 A:ASP159 3.4 20.1 1.0 NE2 A:HIS155 4.1 18.9 1.0 CG A:HIS160 4.1 18.7 1.0 ND1 A:HIS160 4.1 19.2 1.0 ND1 A:HIS312 4.3 20.5 1.0 CE1 A:HIS155 4.3 16.4 1.0 CG A:HIS312 4.3 17.9 1.0 CB A:ASP265 4.4 21.5 1.0 NE2 A:HIS268 4.5 19.0 1.0 CB A:ASP159 4.5 17.9 1.0 NE2 A:HIS244 4.8 20.6 1.0 CB A:HIS157 4.9 14.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Hydrolase Aboph in Beta Lactamase Superfamily


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 Hydrolase Aboph in Beta Lactamase Superfamily within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:20.0 occ:1.00 NE2 A:HIS244 2.2 20.6 1.0 NE2 A:HIS155 2.3 18.9 1.0 ND1 A:HIS157 2.4 16.8 1.0 OD2 A:ASP265 2.4 17.3 1.0 O A:HOH652 2.9 25.9 1.0 CD2 A:HIS244 3.1 18.2 1.0 CD2 A:HIS155 3.1 14.7 1.0 ZN A:ZN401 3.1 20.0 1.0 CE1 A:HIS244 3.2 14.3 1.0 CG A:HIS157 3.3 20.4 1.0 CG A:ASP265 3.4 19.5 1.0 CE1 A:HIS155 3.4 16.4 1.0 CE1 A:HIS157 3.4 21.8 1.0 CB A:HIS157 3.4 14.6 1.0 NE2 A:HIS160 3.8 26.0 1.0 CB A:ASP265 3.8 21.5 1.0 CD2 A:HIS160 4.1 16.3 1.0 CG A:HIS244 4.3 16.3 1.0 ND1 A:HIS244 4.3 17.3 1.0 CG A:HIS155 4.3 19.1 1.0 OD1 A:ASP265 4.4 15.4 1.0 ND1 A:HIS155 4.4 17.1 1.0 OD1 A:ASP159 4.5 20.1 1.0 CD2 A:HIS157 4.5 17.3 1.0 NE2 A:HIS157 4.5 18.6 1.0 NE2 A:HIS268 4.5 19.0 1.0 CE1 A:HIS160 4.8 14.1 1.0 OD2 A:ASP159 4.8 16.1 1.0 NE2 A:HIS312 4.9 20.2 1.0 CA A:HIS157 4.9 17.5 1.0 CE1 A:HIS268 4.9 17.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Hydrolase Aboph in Beta Lactamase Superfamily


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 Hydrolase Aboph in Beta Lactamase Superfamily within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:20.0 occ:1.00 NE2 B:HIS160 1.9 21.6 1.0 OD2 B:ASP265 2.2 14.4 1.0 NE2 B:HIS312 2.2 22.0 1.0 OD2 B:ASP159 2.4 21.2 1.0 CD2 B:HIS160 2.8 20.3 1.0 CG B:ASP265 3.0 21.6 1.0 CE1 B:HIS160 3.1 18.8 1.0 CD2 B:HIS312 3.1 18.5 1.0 CG B:ASP159 3.1 21.6 1.0 OD1 B:ASP265 3.2 15.8 1.0 ZN B:ZN402 3.2 20.0 1.0 O B:HOH659 3.2 28.8 1.0 OD1 B:ASP159 3.3 20.5 1.0 CE1 B:HIS312 3.3 20.0 1.0 CE1 B:HIS155 3.9 20.9 1.0 NE2 B:HIS155 3.9 24.4 1.0 CG B:HIS160 4.0 24.1 1.0 ND1 B:HIS160 4.1 24.4 1.0 CG B:HIS312 4.3 18.6 1.0 ND1 B:HIS312 4.4 22.0 1.0 CB B:ASP265 4.5 20.7 1.0 CB B:ASP159 4.5 18.8 1.0 NE2 B:HIS268 4.6 18.6 1.0 NE2 B:HIS244 4.8 27.8 1.0 CB B:HIS157 4.9 20.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Hydrolase Aboph in Beta Lactamase Superfamily


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 Hydrolase Aboph in Beta Lactamase Superfamily within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:20.0 occ:1.00 CE1 B:HIS155 2.0 20.9 1.0 NE2 B:HIS244 2.1 27.8 1.0 ND1 B:HIS157 2.2 21.1 1.0 OD2 B:ASP265 2.5 14.4 1.0 ND1 B:HIS155 2.9 22.0 1.0 O B:HOH659 2.9 28.8 1.0 CD2 B:HIS244 3.0 17.9 1.0 NE2 B:HIS155 3.1 24.4 1.0 CE1 B:HIS244 3.1 20.4 1.0 CG B:HIS157 3.1 23.1 1.0 CE1 B:HIS157 3.2 23.1 1.0 ZN B:ZN401 3.2 20.0 1.0 CB B:HIS157 3.4 20.3 1.0 CG B:ASP265 3.4 21.6 1.0 CB B:ASP265 3.9 20.7 1.0 NE2 B:HIS160 3.9 21.6 1.0 CD2 B:HIS160 4.0 20.3 1.0 CG B:HIS155 4.1 22.4 1.0 CD2 B:HIS155 4.2 17.4 1.0 CG B:HIS244 4.2 21.9 1.0 ND1 B:HIS244 4.2 25.3 1.0 CD2 B:HIS157 4.3 21.9 1.0 NE2 B:HIS157 4.3 17.7 1.0 OD1 B:ASP265 4.4 15.8 1.0 OD1 B:ASP159 4.4 20.5 1.0 NE2 B:HIS268 4.7 18.6 1.0 CA B:HIS157 4.9 20.3 1.0 CE1 B:HIS160 4.9 18.8 1.0 O B:HOH688 5.0 33.6 1.0

J.Chen, X.J.Lu, Q.Chen, J.Pan, J.H.Zhou, J.H.Xu. Marked Enhancement of Acinetobacter Sp. Organophosphorus Hydrolase Activity By A Single Residue Substitution ILE211ALA Bioresour Bioprocess 2015.
ISSN: ESSN 2197-4365
DOI: 10.1186/S40643-015-0067-3