Zinc in PDB 4pbf: Phosphotriesterase Variant REV12

The structure of Phosphotriesterase Variant REV12, PDB code: 4pbf was solved by E.Campbell, M.Kaltenbach, N.Tokuriki, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.33 / 1.90
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	123.696, 123.696, 112.132, 90.00, 90.00, 120.00
R / Rfree (%)	14.1 / 17.3

The structure of Phosphotriesterase Variant REV12 also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Phosphotriesterase Variant REV12 (pdb code 4pbf). 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 REV12, PDB code: 4pbf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase Variant REV12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant REV12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:13.0 occ:1.00 O1 A:CAC2403 1.9 12.9 1.0 NE2 A:HIS55 2.1 11.1 1.0 NE2 A:HIS57 2.1 10.6 1.0 OQ2 A:KCX169 2.2 15.8 1.0 OD1 A:ASP301 2.4 14.5 1.0 CD2 A:HIS55 3.0 11.9 1.0 CE1 A:HIS57 3.1 9.9 1.0 CD2 A:HIS57 3.1 11.5 1.0 CE1 A:HIS55 3.1 9.7 1.0 CX A:KCX169 3.1 12.7 1.0 CG A:ASP301 3.2 13.8 1.0 AS A:CAC2403 3.3 21.5 1.0 OD2 A:ASP301 3.4 13.1 1.0 OQ1 A:KCX169 3.5 12.4 1.0 O2 A:CAC2403 3.6 21.7 1.0 ZN A:ZN2402 3.8 16.3 1.0 CG2 A:VAL101 4.1 9.8 1.0 NZ A:KCX169 4.2 14.7 1.0 CE1 A:HIS230 4.2 12.5 1.0 CG A:HIS55 4.2 11.2 1.0 ND1 A:HIS57 4.2 9.6 1.0 ND1 A:HIS55 4.2 14.6 1.0 CG A:HIS57 4.2 6.2 1.0 NE2 A:HIS230 4.4 8.9 1.0 CB A:ASP301 4.5 10.8 1.0 C1 A:CAC2403 4.6 22.2 1.0 C2 A:CAC2403 4.7 17.2 1.0 O A:HOH2667 4.8 23.5 1.0 CA A:ASP301 5.0 14.7 1.0

Zinc binding site 2 out of 4 in the Phosphotriesterase Variant REV12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant REV12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:16.3 occ:1.00 NE2 A:HIS230 2.0 8.9 1.0 OQ1 A:KCX169 2.1 12.4 1.0 C1 A:CAC2403 2.3 22.2 1.0 ND1 A:HIS201 2.3 14.5 1.0 O1 A:CAC2403 2.8 12.9 1.0 CD2 A:HIS230 2.9 11.9 1.0 AS A:CAC2403 3.1 21.5 1.0 CX A:KCX169 3.1 12.7 1.0 CE1 A:HIS230 3.1 12.5 1.0 CG A:HIS201 3.2 12.8 1.0 CE1 A:HIS201 3.4 13.9 1.0 OQ2 A:KCX169 3.4 15.8 1.0 CB A:HIS201 3.4 11.3 1.0 ZN A:ZN2401 3.8 13.0 1.0 NE1 A:TRP131 3.8 13.3 1.0 CG A:HIS230 4.1 15.6 1.0 ND1 A:HIS230 4.2 11.9 1.0 CE1 A:HIS55 4.2 9.7 1.0 O2 A:CAC2403 4.2 21.7 1.0 NZ A:KCX169 4.3 14.7 1.0 CA A:HIS201 4.3 13.8 1.0 NE2 A:HIS55 4.4 11.1 1.0 CD2 A:HIS201 4.4 11.9 1.0 NE2 A:HIS201 4.5 16.4 1.0 CD1 A:TRP131 4.5 10.6 1.0 C2 A:CAC2403 4.6 17.2 1.0 OD2 A:ASP301 4.7 13.1 1.0 CE A:KCX169 4.7 9.3 1.0 CE2 A:TRP131 4.9 14.9 1.0

Zinc binding site 3 out of 4 in the Phosphotriesterase Variant REV12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant REV12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2401 b:13.0 occ:1.00 O1 B:CAC2403 1.9 11.9 1.0 NE2 B:HIS57 2.0 12.9 1.0 NE2 B:HIS55 2.2 11.5 1.0 OQ1 B:KCX169 2.3 15.0 1.0 OD1 B:ASP301 2.4 12.4 1.0 CD2 B:HIS57 3.0 10.7 1.0 CE1 B:HIS57 3.0 11.8 1.0 CD2 B:HIS55 3.0 13.3 1.0 CX B:KCX169 3.2 11.3 1.0 CG B:ASP301 3.2 12.8 1.0 AS B:CAC2403 3.3 19.9 1.0 CE1 B:HIS55 3.3 10.9 1.0 OD2 B:ASP301 3.4 17.9 1.0 OQ2 B:KCX169 3.6 12.2 1.0 O2 B:CAC2403 3.6 20.0 1.0 ZN B:ZN2402 3.9 16.8 1.0 ND1 B:HIS57 4.1 8.2 1.0 CG2 B:VAL101 4.1 9.4 1.0 CG B:HIS57 4.1 8.2 1.0 NZ B:KCX169 4.2 7.5 1.0 CE1 B:HIS230 4.2 12.5 1.0 CG B:HIS55 4.3 11.7 1.0 NE2 B:HIS230 4.3 11.5 1.0 ND1 B:HIS55 4.4 14.2 1.0 CB B:ASP301 4.5 9.8 1.0 C1 B:CAC2403 4.7 16.5 1.0 C2 B:CAC2403 4.7 16.9 1.0 O B:HOH2614 4.7 18.4 1.0 CA B:ASP301 5.0 11.1 1.0

Zinc binding site 4 out of 4 in the Phosphotriesterase Variant REV12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant REV12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2402 b:16.8 occ:1.00 OQ2 B:KCX169 2.1 12.2 1.0 NE2 B:HIS230 2.1 11.5 1.0 ND1 B:HIS201 2.3 15.6 1.0 C1 B:CAC2403 2.3 16.5 1.0 O1 B:CAC2403 2.7 11.9 1.0 CD2 B:HIS230 2.9 14.6 1.0 AS B:CAC2403 3.0 19.9 1.0 CX B:KCX169 3.1 11.3 1.0 CG B:HIS201 3.2 12.1 1.0 CE1 B:HIS230 3.2 12.5 1.0 CE1 B:HIS201 3.3 12.7 1.0 OQ1 B:KCX169 3.3 15.0 1.0 CB B:HIS201 3.4 10.9 1.0 ZN B:ZN2401 3.9 13.0 1.0 NE1 B:TRP131 3.9 10.4 1.0 CG B:HIS230 4.2 16.4 1.0 ND1 B:HIS230 4.3 12.5 1.0 NZ B:KCX169 4.3 7.5 1.0 O2 B:CAC2403 4.3 20.0 1.0 CA B:HIS201 4.3 13.1 1.0 CE1 B:HIS55 4.3 10.9 1.0 CD2 B:HIS201 4.4 17.0 1.0 NE2 B:HIS201 4.4 15.9 1.0 NE2 B:HIS55 4.4 11.5 1.0 C2 B:CAC2403 4.5 16.9 1.0 CD1 B:TRP131 4.6 9.9 1.0 OD2 B:ASP301 4.6 17.9 1.0 CE B:KCX169 4.8 11.5 1.0 CE2 B:TRP131 5.0 12.9 1.0

E.Campbell, M.Kaltenbach, N.Tokuriki, C.J.Jackson. Phosphotriesterase Variant REV12 To Be Published.