Zinc in PDB 5wiz: Phosphotriesterase Variant S5

The structure of Phosphotriesterase Variant S5, PDB code: 5wiz was solved by C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.95 / 1.96
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.248, 85.688, 88.484, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 23.3

The structure of Phosphotriesterase Variant S5 also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Phosphotriesterase Variant S5 (pdb code 5wiz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Phosphotriesterase Variant S5, PDB code: 5wiz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase Variant S5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant S5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:20.5 occ:0.87 O1 A:CAC2404 2.0 17.4 0.7 NE2 A:HIS57 2.1 21.3 1.0 NE2 A:HIS55 2.1 23.0 1.0 OQ1 A:KCX169 2.1 26.2 1.0 OD1 A:ASP301 2.3 24.5 1.0 CE1 A:HIS57 3.0 21.5 1.0 CD2 A:HIS55 3.1 22.4 1.0 CD2 A:HIS57 3.1 21.7 1.0 CE1 A:HIS55 3.1 22.3 1.0 CX A:KCX169 3.2 24.5 1.0 CG A:ASP301 3.2 26.7 1.0 AS A:CAC2404 3.3 35.5 0.7 OD2 A:ASP301 3.5 28.5 1.0 OQ2 A:KCX169 3.6 26.4 1.0 C2 A:CAC2404 3.7 26.8 0.7 ZN A:ZN2402 3.8 27.9 0.7 CG2 A:VAL101 4.0 19.1 1.0 ND1 A:HIS57 4.2 20.9 1.0 CG A:HIS55 4.2 22.4 1.0 CE1 A:HIS230 4.2 32.1 1.0 ND1 A:HIS55 4.2 21.8 1.0 CG A:HIS57 4.2 21.8 1.0 NZ A:KCX169 4.2 22.0 1.0 O2 A:CAC2404 4.3 33.0 0.7 CB A:ASP301 4.5 26.1 1.0 NE2 A:HIS230 4.5 31.4 1.0 C1 A:CAC2404 4.8 32.9 0.7 CA A:ASP301 5.0 26.0 1.0

Zinc binding site 2 out of 4 in the Phosphotriesterase Variant S5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant S5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:27.9 occ:0.74 OQ2 A:KCX169 1.9 26.4 1.0 ND1 A:HIS201 2.1 27.4 1.0 O2 A:CAC2404 2.1 33.0 0.7 NE2 A:HIS230 2.1 31.4 1.0 O1 A:CAC2404 2.7 17.4 0.7 CE1 A:HIS201 3.0 28.7 1.0 AS A:CAC2404 3.0 35.5 0.7 CX A:KCX169 3.0 24.5 1.0 CD2 A:HIS230 3.1 31.1 1.0 CE1 A:HIS230 3.1 32.1 1.0 CG A:HIS201 3.1 28.0 1.0 OQ1 A:KCX169 3.3 26.2 1.0 CB A:HIS201 3.5 28.0 1.0 ZN A:ZN2401 3.8 20.5 0.9 NE1 A:TRP131 4.0 27.1 1.0 NE2 A:HIS201 4.1 29.5 1.0 NZ A:KCX169 4.1 22.0 1.0 CD2 A:HIS201 4.2 29.1 1.0 C1 A:CAC2404 4.2 32.9 0.7 ND1 A:HIS230 4.2 31.8 1.0 CE1 A:HIS55 4.2 22.3 1.0 CG A:HIS230 4.3 31.4 1.0 NE2 A:HIS55 4.3 23.0 1.0 C2 A:CAC2404 4.4 26.8 0.7 CA A:HIS201 4.5 27.4 1.0 CD1 A:TRP131 4.5 26.8 1.0 CE A:KCX169 4.6 22.3 1.0 OD2 A:ASP301 4.8 28.5 1.0

Zinc binding site 3 out of 4 in the Phosphotriesterase Variant S5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant S5 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2401 b:29.8 occ:0.94 O1 G:CAC2405 1.9 37.6 0.8 NE2 G:HIS57 2.0 29.3 1.0 NE2 G:HIS55 2.2 31.3 1.0 OD1 G:ASP301 2.4 36.7 1.0 OQ2 G:KCX169 2.4 30.4 1.0 CE1 G:HIS57 2.9 29.6 1.0 CD2 G:HIS57 3.0 29.9 1.0 AS G:CAC2405 3.1 63.4 0.8 CD2 G:HIS55 3.1 31.6 1.0 CE1 G:HIS55 3.2 31.4 1.0 CG G:ASP301 3.4 36.9 1.0 CX G:KCX169 3.4 30.3 1.0 C1 G:CAC2405 3.6 58.3 0.8 ZN G:ZN2402 3.7 31.9 0.8 OQ1 G:KCX169 3.7 30.8 1.0 OD2 G:ASP301 3.8 38.7 1.0 O2 G:CAC2405 3.9 16.7 0.8 ND1 G:HIS57 4.1 29.6 1.0 CG G:HIS57 4.1 29.4 1.0 CG2 G:VAL101 4.2 24.0 1.0 CE1 G:HIS230 4.2 33.2 1.0 CG G:HIS55 4.3 30.9 1.0 ND1 G:HIS55 4.3 30.9 1.0 NE2 G:HIS230 4.4 33.8 1.0 NZ G:KCX169 4.5 29.8 1.0 CB G:ASP301 4.6 34.8 1.0 C2 G:CAC2405 4.7 67.8 0.8

Zinc binding site 4 out of 4 in the Phosphotriesterase Variant S5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant S5 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2402 b:31.9 occ:0.80 OQ1 G:KCX169 2.0 30.8 1.0 NE2 G:HIS230 2.1 33.8 1.0 ND1 G:HIS201 2.2 34.1 1.0 O1 G:CAC2405 2.2 37.6 0.8 AS G:CAC2405 2.9 63.4 0.8 C2 G:CAC2405 2.9 67.8 0.8 CD2 G:HIS230 3.0 33.7 1.0 CE1 G:HIS201 3.1 35.4 1.0 CX G:KCX169 3.1 30.3 1.0 CE1 G:HIS230 3.2 33.2 1.0 CG G:HIS201 3.2 33.7 1.0 OQ2 G:KCX169 3.4 30.4 1.0 CB G:HIS201 3.5 34.3 1.0 O2 G:CAC2405 3.6 16.7 0.8 ZN G:ZN2401 3.7 29.8 0.9 NE1 G:TRP131 4.1 32.4 1.0 CE1 G:HIS55 4.1 31.4 1.0 NE2 G:HIS55 4.2 31.3 1.0 CG G:HIS230 4.2 33.7 1.0 NE2 G:HIS201 4.2 35.1 1.0 ND1 G:HIS230 4.2 34.1 1.0 CD2 G:HIS201 4.3 34.4 1.0 NZ G:KCX169 4.3 29.8 1.0 CA G:HIS201 4.4 34.9 1.0 CD1 G:TRP131 4.7 31.3 1.0 C1 G:CAC2405 4.7 58.3 0.8 CE G:KCX169 4.7 31.5 1.0 O G:HOH2504 4.9 41.5 1.0

C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki. Phosphotriesterase Variant S5 To Be Published.