Zinc in PDB 5wcq: Phosphotriesterase Variant S2

The structure of Phosphotriesterase Variant S2, PDB code: 5wcq 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)	39.20 / 1.58
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.233, 85.476, 88.215, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 19.3

The structure of Phosphotriesterase Variant S2 also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Phosphotriesterase Variant S2 (pdb code 5wcq). 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 S2, PDB code: 5wcq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase Variant S2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant S2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:14.6 occ:0.93 O2 A:CAC2403 1.9 14.5 0.9 NE2 A:HIS57 2.0 14.5 1.0 NE2 A:HIS55 2.0 14.4 1.0 OQ1 A:KCX169 2.1 17.8 1.0 OD1 A:ASP301 2.3 16.6 1.0 CE1 A:HIS57 3.0 14.4 1.0 CD2 A:HIS55 3.0 15.2 1.0 CX A:KCX169 3.0 16.6 1.0 CD2 A:HIS57 3.0 12.1 1.0 CE1 A:HIS55 3.1 16.8 1.0 CG A:ASP301 3.2 15.6 1.0 AS A:CAC2403 3.3 17.8 0.9 OD2 A:ASP301 3.4 16.5 1.0 OQ2 A:KCX169 3.6 14.4 1.0 C1 A:CAC2403 3.7 17.7 0.9 CG2 A:VAL101 4.0 11.9 1.0 ZN A:ZN2402 4.0 15.2 0.8 NZ A:KCX169 4.0 17.2 1.0 CE1 A:HIS230 4.1 19.7 1.0 O1 A:CAC2403 4.1 14.8 0.9 ND1 A:HIS57 4.1 15.5 1.0 ND1 A:HIS55 4.1 13.7 1.0 CG A:HIS55 4.2 15.1 1.0 CG A:HIS57 4.2 13.2 1.0 NE2 A:HIS230 4.4 18.0 1.0 CB A:ASP301 4.5 14.1 1.0 C2 A:CAC2403 4.8 17.1 0.9

Zinc binding site 2 out of 4 in the Phosphotriesterase Variant S2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant S2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:15.2 occ:0.85 O1 A:CAC2403 1.9 14.8 0.9 OQ2 A:KCX169 2.0 14.4 1.0 ND1 A:HIS201 2.0 17.2 1.0 NE2 A:HIS230 2.0 18.0 1.0 CE1 A:HIS201 2.9 20.8 1.0 CD2 A:HIS230 3.0 21.4 1.0 CX A:KCX169 3.0 16.6 1.0 CE1 A:HIS230 3.0 19.7 1.0 CG A:HIS201 3.1 18.2 1.0 AS A:CAC2403 3.1 17.8 0.9 O2 A:CAC2403 3.1 14.5 0.9 OQ1 A:KCX169 3.4 17.8 1.0 CB A:HIS201 3.5 17.9 1.0 NE1 A:TRP131 3.8 16.1 1.0 ZN A:ZN2401 4.0 14.6 0.9 NE2 A:HIS201 4.0 20.4 1.0 CG A:HIS230 4.1 19.9 1.0 ND1 A:HIS230 4.1 20.1 1.0 CD2 A:HIS201 4.1 18.3 1.0 NZ A:KCX169 4.2 17.2 1.0 O A:HOH2687 4.3 38.7 1.0 CA A:HIS201 4.3 17.0 1.0 CE1 A:HIS55 4.3 16.8 1.0 C2 A:CAC2403 4.4 17.1 0.9 CD1 A:TRP131 4.4 16.6 1.0 C1 A:CAC2403 4.5 17.7 0.9 NE2 A:HIS55 4.5 14.4 1.0 CE A:KCX169 4.6 18.4 1.0 OD2 A:ASP301 4.9 16.5 1.0 CE2 A:TRP131 5.0 16.6 1.0

Zinc binding site 3 out of 4 in the Phosphotriesterase Variant S2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant S2 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2401 b:17.4 occ:1.00 O2 G:CAC2403 1.9 17.5 0.9 NE2 G:HIS57 2.0 14.0 1.0 NE2 G:HIS55 2.0 18.2 1.0 OQ2 G:KCX169 2.1 16.4 1.0 OD1 G:ASP301 2.3 17.5 1.0 CE1 G:HIS57 2.9 16.9 1.0 CD2 G:HIS55 3.0 17.6 1.0 CX G:KCX169 3.0 18.7 1.0 CE1 G:HIS55 3.0 20.0 1.0 CD2 G:HIS57 3.1 18.0 1.0 CG G:ASP301 3.2 17.4 1.0 AS G:CAC2403 3.3 18.9 0.9 OD2 G:ASP301 3.4 17.9 1.0 OQ1 G:KCX169 3.5 17.0 1.0 C1 G:CAC2403 3.7 18.8 0.9 CG2 G:VAL101 3.9 15.6 1.0 ZN G:ZN2402 4.0 16.9 0.9 NZ G:KCX169 4.0 18.8 1.0 O1 G:CAC2403 4.1 17.3 0.9 CE1 G:HIS230 4.1 20.1 1.0 ND1 G:HIS57 4.1 15.9 1.0 ND1 G:HIS55 4.1 17.0 1.0 CG G:HIS55 4.1 15.8 1.0 CG G:HIS57 4.2 16.4 1.0 NE2 G:HIS230 4.4 18.7 1.0 CB G:ASP301 4.5 16.3 1.0 C2 G:CAC2403 4.8 19.8 0.9

Zinc binding site 4 out of 4 in the Phosphotriesterase Variant S2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant S2 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2402 b:16.9 occ:0.92 OQ1 G:KCX169 1.9 17.0 1.0 O1 G:CAC2403 1.9 17.3 0.9 NE2 G:HIS230 2.0 18.7 1.0 ND1 G:HIS201 2.0 15.8 1.0 CD2 G:HIS230 2.9 20.5 1.0 CE1 G:HIS201 2.9 23.3 1.0 CX G:KCX169 3.0 18.7 1.0 AS G:CAC2403 3.1 18.9 0.9 CE1 G:HIS230 3.1 20.1 1.0 CG G:HIS201 3.1 15.8 1.0 O2 G:CAC2403 3.1 17.5 0.9 OQ2 G:KCX169 3.3 16.4 1.0 CB G:HIS201 3.5 15.1 1.0 NE1 G:TRP131 3.8 18.1 1.0 ZN G:ZN2401 4.0 17.4 1.0 NE2 G:HIS201 4.1 22.6 1.0 O G:HOH2725 4.1 41.5 1.0 CG G:HIS230 4.1 17.5 1.0 ND1 G:HIS230 4.1 18.9 1.0 CD2 G:HIS201 4.2 18.3 1.0 NZ G:KCX169 4.2 18.8 1.0 C2 G:CAC2403 4.3 19.8 0.9 CA G:HIS201 4.3 16.9 1.0 CE1 G:HIS55 4.3 20.0 1.0 CD1 G:TRP131 4.4 17.8 1.0 C1 G:CAC2403 4.5 18.8 0.9 NE2 G:HIS55 4.5 18.2 1.0 CE G:KCX169 4.6 17.9 1.0 OD2 G:ASP301 4.9 17.9 1.0 CE2 G:TRP131 5.0 20.3 1.0

C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki. Phosphotriesterase Variant S2 To Be Published.