Zinc in PDB 5w6b: Phosphotriesterase Variant S1

The structure of Phosphotriesterase Variant S1, PDB code: 5w6b 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)	30.74 / 1.74
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.660, 85.790, 88.170, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.8

The structure of Phosphotriesterase Variant S1 also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Phosphotriesterase Variant S1 (pdb code 5w6b). 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 S1, PDB code: 5w6b:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase Variant S1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant S1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:13.2 occ:0.93 O2 A:CAC2403 1.9 14.7 0.8 NE2 A:HIS57 2.1 11.5 1.0 NE2 A:HIS55 2.1 13.6 1.0 OQ2 A:KCX169 2.1 15.1 1.0 OD1 A:ASP301 2.2 13.4 1.0 CE1 A:HIS57 3.0 11.1 1.0 CD2 A:HIS55 3.0 12.1 1.0 CX A:KCX169 3.1 14.2 1.0 CE1 A:HIS55 3.1 13.9 1.0 CD2 A:HIS57 3.1 11.9 1.0 CG A:ASP301 3.1 15.9 1.0 AS A:CAC2403 3.3 17.2 0.8 OD2 A:ASP301 3.4 15.0 1.0 OQ1 A:KCX169 3.5 14.8 1.0 C1 A:CAC2403 3.7 14.4 0.8 ZN A:ZN2402 4.0 13.6 0.8 CG2 A:VAL101 4.1 11.0 1.0 O1 A:CAC2403 4.1 15.2 0.8 NZ A:KCX169 4.1 14.5 1.0 ND1 A:HIS57 4.1 11.6 1.0 CE1 A:HIS230 4.1 15.5 1.0 CG A:HIS55 4.2 12.1 1.0 ND1 A:HIS55 4.2 12.3 1.0 CG A:HIS57 4.2 11.6 1.0 O A:HOH2661 4.3 34.1 1.0 CB A:ASP301 4.4 13.8 1.0 NE2 A:HIS230 4.5 16.6 1.0 C2 A:CAC2403 4.8 18.3 0.8 CA A:ASP301 5.0 13.9 1.0

Zinc binding site 2 out of 4 in the Phosphotriesterase Variant S1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant S1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:13.6 occ:0.77 O1 A:CAC2403 1.9 15.2 0.8 OQ1 A:KCX169 2.0 14.8 1.0 NE2 A:HIS230 2.0 16.6 1.0 ND1 A:HIS201 2.1 18.1 1.0 CD2 A:HIS230 3.0 17.6 1.0 CE1 A:HIS201 3.0 22.2 1.0 O2 A:CAC2403 3.0 14.7 0.8 CX A:KCX169 3.0 14.2 1.0 CE1 A:HIS230 3.0 15.5 1.0 CG A:HIS201 3.1 17.6 1.0 AS A:CAC2403 3.1 17.2 0.8 OQ2 A:KCX169 3.4 15.1 1.0 CB A:HIS201 3.4 17.9 1.0 NE1 A:TRP131 3.8 14.8 1.0 ZN A:ZN2401 4.0 13.2 0.9 NE2 A:HIS201 4.1 20.3 1.0 ND1 A:HIS230 4.1 17.8 1.0 CG A:HIS230 4.1 18.0 1.0 CD2 A:HIS201 4.2 17.1 1.0 NZ A:KCX169 4.2 14.5 1.0 C2 A:CAC2403 4.3 18.3 0.8 CA A:HIS201 4.4 14.6 1.0 CE1 A:HIS55 4.4 13.9 1.0 CD1 A:TRP131 4.4 14.5 1.0 C1 A:CAC2403 4.5 14.4 0.8 NE2 A:HIS55 4.5 13.6 1.0 CE A:KCX169 4.6 13.7 1.0 OD2 A:ASP301 4.8 15.0 1.0 O A:HOH2653 4.9 30.6 1.0 CE2 A:TRP131 5.0 16.0 1.0

Zinc binding site 3 out of 4 in the Phosphotriesterase Variant S1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant S1 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2401 b:22.4 occ:1.00 O2 G:CAC2403 1.9 23.7 0.9 NE2 G:HIS57 2.0 19.4 1.0 NE2 G:HIS55 2.1 21.0 1.0 OQ1 G:KCX169 2.2 20.1 1.0 OD1 G:ASP301 2.2 22.9 1.0 CE1 G:HIS57 3.0 20.0 1.0 CD2 G:HIS55 3.0 20.8 1.0 CD2 G:HIS57 3.1 18.4 1.0 CX G:KCX169 3.1 19.9 1.0 CE1 G:HIS55 3.1 27.5 1.0 CG G:ASP301 3.1 24.3 1.0 AS G:CAC2403 3.3 24.6 0.9 OD2 G:ASP301 3.4 22.0 1.0 OQ2 G:KCX169 3.5 19.1 1.0 C1 G:CAC2403 3.7 26.2 0.9 ZN G:ZN2402 3.9 23.0 0.9 CG2 G:VAL101 4.0 20.7 1.0 O1 G:CAC2403 4.1 22.7 0.9 CE1 G:HIS230 4.1 25.4 1.0 ND1 G:HIS57 4.1 20.8 1.0 NZ G:KCX169 4.1 23.8 1.0 CG G:HIS55 4.2 22.4 1.0 ND1 G:HIS55 4.2 24.2 1.0 CG G:HIS57 4.2 20.5 1.0 NE2 G:HIS230 4.4 22.4 1.0 CB G:ASP301 4.5 21.8 1.0 C2 G:CAC2403 4.8 30.7 0.9

Zinc binding site 4 out of 4 in the Phosphotriesterase Variant S1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant S1 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2402 b:23.0 occ:0.91 OQ2 G:KCX169 1.9 19.1 1.0 O1 G:CAC2403 2.0 22.7 0.9 NE2 G:HIS230 2.0 22.4 1.0 ND1 G:HIS201 2.1 24.1 1.0 CD2 G:HIS230 2.9 20.9 1.0 CE1 G:HIS201 3.0 26.8 1.0 O2 G:CAC2403 3.0 23.7 0.9 CX G:KCX169 3.0 19.9 1.0 CE1 G:HIS230 3.1 25.4 1.0 AS G:CAC2403 3.1 24.6 0.9 CG G:HIS201 3.1 25.5 1.0 OQ1 G:KCX169 3.4 20.1 1.0 CB G:HIS201 3.5 19.4 1.0 NE1 G:TRP131 3.9 22.3 1.0 ZN G:ZN2401 3.9 22.4 1.0 CG G:HIS230 4.1 21.9 1.0 NE2 G:HIS201 4.1 29.1 1.0 ND1 G:HIS230 4.1 21.9 1.0 CD2 G:HIS201 4.2 30.0 1.0 NZ G:KCX169 4.2 23.8 1.0 CE1 G:HIS55 4.3 27.5 1.0 CA G:HIS201 4.4 21.9 1.0 C2 G:CAC2403 4.4 30.7 0.9 NE2 G:HIS55 4.5 21.0 1.0 C1 G:CAC2403 4.5 26.2 0.9 CD1 G:TRP131 4.5 21.1 1.0 CE G:KCX169 4.7 23.6 1.0 OD2 G:ASP301 4.8 22.0 1.0

C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki. Phosphotriesterase Variant S1 To Be Published.