Zinc in PDB 6aml: Phosphotriesterase Variant S8

The structure of Phosphotriesterase Variant S8, PDB code: 6aml 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)	42.57 / 1.46
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.134, 85.811, 88.658, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17.5

The structure of Phosphotriesterase Variant S8 also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Phosphotriesterase Variant S8 (pdb code 6aml). 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 S8, PDB code: 6aml:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase Variant S8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant S8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:22.6 occ:0.88 O2 A:CAC2403 1.9 20.9 0.8 NE2 A:HIS57 2.0 23.4 1.0 NE2 A:HIS55 2.0 21.3 1.0 OQ2 A:KCX169 2.2 25.8 1.0 OD1 A:ASP301 2.5 26.8 1.0 CE1 A:HIS57 2.9 26.0 1.0 CE1 A:HIS55 3.0 22.7 1.0 CD2 A:HIS55 3.0 23.6 1.0 CX A:KCX169 3.1 25.8 1.0 CD2 A:HIS57 3.1 23.1 1.0 AS A:CAC2403 3.2 26.9 0.8 CG A:ASP301 3.4 28.0 1.0 OQ1 A:KCX169 3.5 29.1 1.0 C1 A:CAC2403 3.6 22.4 0.8 OD2 A:ASP301 3.7 26.9 1.0 ZN A:ZN2402 3.9 24.7 0.8 CG2 A:VAL101 4.1 23.6 1.0 ND1 A:HIS57 4.1 23.9 1.0 O1 A:CAC2403 4.1 25.6 0.8 CE1 A:HIS230 4.1 31.1 1.0 ND1 A:HIS55 4.1 24.4 1.0 CG A:HIS55 4.2 24.8 1.0 NZ A:KCX169 4.2 26.1 1.0 CG A:HIS57 4.2 24.0 1.0 NE2 A:HIS230 4.4 25.2 1.0 C2 A:CAC2403 4.6 27.4 0.8 CB A:ASP301 4.8 27.0 1.0

Zinc binding site 2 out of 4 in the Phosphotriesterase Variant S8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant S8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:24.7 occ:0.83 OQ1 A:KCX169 1.9 29.1 1.0 O1 A:CAC2403 2.0 25.6 0.8 NE2 A:HIS230 2.0 25.2 1.0 ND1 A:HIS201 2.1 28.3 1.0 CD2 A:HIS230 2.9 29.9 1.0 CX A:KCX169 3.0 25.8 1.0 O2 A:CAC2403 3.0 20.9 0.8 CE1 A:HIS201 3.0 28.9 1.0 AS A:CAC2403 3.0 26.9 0.8 CE1 A:HIS230 3.1 31.1 1.0 CG A:HIS201 3.1 25.2 1.0 OQ2 A:KCX169 3.3 25.8 1.0 CB A:HIS201 3.5 28.6 1.0 NE1 A:TRP131 3.8 26.7 1.0 ZN A:ZN2401 3.9 22.6 0.9 CG A:HIS230 4.1 32.5 1.0 NE2 A:HIS201 4.1 29.5 1.0 ND1 A:HIS230 4.1 32.1 1.0 NZ A:KCX169 4.2 26.1 1.0 CD2 A:HIS201 4.2 27.5 1.0 CE1 A:HIS55 4.3 22.7 1.0 CA A:HIS201 4.3 27.8 1.0 C2 A:CAC2403 4.3 27.4 0.8 CD1 A:TRP131 4.4 27.4 1.0 C1 A:CAC2403 4.4 22.4 0.8 NE2 A:HIS55 4.5 21.3 1.0 CE A:KCX169 4.6 26.0 1.0 OD2 A:ASP301 5.0 26.9 1.0

Zinc binding site 3 out of 4 in the Phosphotriesterase Variant S8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant S8 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2401 b:17.8 occ:1.00 O2 G:CAC2403 1.9 14.2 0.8 NE2 G:HIS55 2.0 15.6 1.0 NE2 G:HIS57 2.1 16.0 0.9 OQ1 G:KCX169 2.1 17.3 1.0 OD1 G:ASP301 2.5 17.4 1.0 CE1 G:HIS57 3.0 15.3 0.9 CD2 G:HIS55 3.0 15.0 1.0 CX G:KCX169 3.0 20.0 1.0 CE1 G:HIS55 3.1 17.7 1.0 CD2 G:HIS57 3.1 16.0 0.9 AS G:CAC2403 3.3 19.3 0.8 CG G:ASP301 3.4 16.1 1.0 OQ2 G:KCX169 3.5 17.7 1.0 C1 G:CAC2403 3.6 19.8 0.8 OD2 G:ASP301 3.6 18.5 1.0 ZN G:ZN2402 4.0 18.4 0.8 CG2 G:VAL101 4.0 16.3 1.0 NZ G:KCX169 4.0 18.9 1.0 O1 G:CAC2403 4.1 16.9 0.8 ND1 G:HIS57 4.1 15.5 0.9 CE1 G:HIS230 4.1 22.0 1.0 ND1 G:HIS55 4.2 17.2 1.0 CG G:HIS55 4.2 15.4 1.0 CG G:HIS57 4.2 14.4 0.9 NE2 G:HIS230 4.4 21.7 1.0 CB G:ASP301 4.7 16.7 1.0 C2 G:CAC2403 4.8 20.4 0.8

Zinc binding site 4 out of 4 in the Phosphotriesterase Variant S8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant S8 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2402 b:18.4 occ:0.83 OQ2 G:KCX169 1.9 17.7 1.0 O1 G:CAC2403 1.9 16.9 0.8 NE2 G:HIS230 2.0 21.7 1.0 ND1 G:HIS201 2.1 20.4 1.0 CX G:KCX169 2.9 20.0 1.0 CD2 G:HIS230 3.0 20.0 1.0 CE1 G:HIS201 3.0 20.9 1.0 O2 G:CAC2403 3.1 14.2 0.8 AS G:CAC2403 3.1 19.3 0.8 CE1 G:HIS230 3.1 22.0 1.0 CG G:HIS201 3.1 19.4 1.0 OQ1 G:KCX169 3.4 17.3 1.0 CB G:HIS201 3.5 21.6 1.0 NE1 G:TRP131 3.9 20.9 1.0 ZN G:ZN2401 4.0 17.8 1.0 NE2 G:HIS201 4.1 22.4 1.0 NZ G:KCX169 4.1 18.9 1.0 CG G:HIS230 4.2 20.5 1.0 ND1 G:HIS230 4.2 20.9 1.0 CD2 G:HIS201 4.2 21.9 1.0 CE1 G:HIS55 4.3 17.7 1.0 CA G:HIS201 4.3 21.9 1.0 C2 G:CAC2403 4.4 20.4 0.8 CD1 G:TRP131 4.4 20.9 1.0 NE2 G:HIS55 4.5 15.6 1.0 C1 G:CAC2403 4.5 19.8 0.8 CE G:KCX169 4.6 18.7 1.0 OD2 G:ASP301 5.0 18.5 1.0

C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki. Phosphotriesterase Variant S8 To Be Published.