Zinc in PDB 4xd3: Phosphotriesterase Variant E3

The structure of Phosphotriesterase Variant E3, PDB code: 4xd3 was solved by C.J.Jackson, E.Campbell, M.Kaltenbach, N.Tokuriki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.41 / 1.57
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.830, 85.882, 88.721, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.2

The structure of Phosphotriesterase Variant E3 also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Phosphotriesterase Variant E3 (pdb code 4xd3). 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 E3, PDB code: 4xd3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase Variant E3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant E3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:12.9 occ:0.68 O A:HOH2791 1.9 23.8 1.0 NE2 A:HIS57 2.1 13.2 1.0 OD1 A:ASP301 2.1 15.1 1.0 NE2 A:HIS55 2.2 16.1 1.0 OQ2 A:KCX169 2.2 18.8 1.0 CE1 A:HIS57 3.0 14.8 1.0 CG A:ASP301 3.0 16.5 1.0 CD2 A:HIS55 3.1 13.5 1.0 CX A:KCX169 3.1 23.9 1.0 CD2 A:HIS57 3.1 11.7 1.0 CE1 A:HIS55 3.2 14.3 1.0 O1 A:CAC2403 3.3 16.4 1.0 OD2 A:ASP301 3.3 20.8 1.0 OQ1 A:KCX169 3.5 19.0 1.0 O2 A:CAC2403 3.5 52.4 1.0 ZN A:ZN2402 3.6 15.3 0.5 NZ A:KCX169 4.1 19.4 1.0 AS A:CAC2403 4.1 0.1 1.0 ND1 A:HIS57 4.1 13.5 1.0 CG2 A:VAL101 4.2 15.4 1.0 CG A:HIS57 4.2 12.6 1.0 CE1 A:HIS230 4.2 18.1 1.0 CG A:HIS55 4.2 13.6 1.0 ND1 A:HIS55 4.3 17.2 1.0 CB A:ASP301 4.4 15.0 1.0 NE2 A:HIS230 4.5 19.4 1.0 O A:HOH2632 4.8 35.2 1.0 CA A:ASP301 4.8 12.7 1.0

Zinc binding site 2 out of 4 in the Phosphotriesterase Variant E3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant E3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:15.3 occ:0.53 OQ1 A:KCX169 2.0 19.0 1.0 NE2 A:HIS230 2.1 19.4 1.0 O A:HOH2791 2.2 23.8 1.0 ND1 A:HIS201 2.3 23.2 1.0 O1 A:CAC2403 3.0 16.4 1.0 CX A:KCX169 3.0 23.9 1.0 CE1 A:HIS230 3.0 18.1 1.0 CD2 A:HIS230 3.1 20.0 1.0 CE1 A:HIS201 3.2 26.9 1.0 OQ2 A:KCX169 3.3 18.8 1.0 CG A:HIS201 3.3 25.0 1.0 ZN A:ZN2401 3.6 12.9 0.7 CB A:HIS201 3.7 20.6 1.0 NE1 A:TRP131 4.0 22.8 1.0 ND1 A:HIS230 4.2 23.6 1.0 NZ A:KCX169 4.2 19.4 1.0 CG A:HIS230 4.2 21.2 1.0 CE1 A:HIS55 4.3 14.3 1.0 NE2 A:HIS55 4.3 16.1 1.0 NE2 A:HIS201 4.3 26.1 1.0 OD2 A:ASP301 4.4 20.8 1.0 CD2 A:HIS201 4.4 23.1 1.0 AS A:CAC2403 4.6 0.1 1.0 CA A:HIS201 4.6 22.1 1.0 CD1 A:TRP131 4.7 16.8 1.0 CE A:KCX169 4.7 18.2 1.0 OD1 A:ASP301 5.0 15.1 1.0

Zinc binding site 3 out of 4 in the Phosphotriesterase Variant E3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant E3 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn402 b:12.8 occ:0.67 O1 G:CAC401 1.9 28.4 1.0 NE2 G:HIS57 2.1 13.0 1.0 OD1 G:ASP301 2.1 17.6 1.0 NE2 G:HIS55 2.2 16.0 1.0 OQ2 G:KCX169 2.2 23.9 1.0 CE1 G:HIS57 3.0 19.7 1.0 CG G:ASP301 3.0 18.8 1.0 CD2 G:HIS55 3.1 16.3 1.0 CD2 G:HIS57 3.1 15.6 1.0 CX G:KCX169 3.2 27.9 1.0 CE1 G:HIS55 3.2 16.6 1.0 AS G:CAC401 3.3 85.7 1.0 OD2 G:ASP301 3.4 17.3 1.0 OQ1 G:KCX169 3.6 22.1 1.0 ZN G:ZN403 3.6 17.3 0.6 C2 G:CAC401 3.7 43.2 1.0 CE1 G:HIS230 4.1 18.9 1.0 ND1 G:HIS57 4.1 14.3 1.0 NZ G:KCX169 4.2 21.6 1.0 CG G:HIS57 4.2 16.6 1.0 CG2 G:VAL101 4.2 13.7 1.0 O2 G:CAC401 4.2 49.1 1.0 CG G:HIS55 4.3 12.8 1.0 NE2 G:HIS230 4.3 22.5 1.0 ND1 G:HIS55 4.3 16.1 1.0 CB G:ASP301 4.4 11.7 1.0 C1 G:CAC401 4.7 52.9 1.0 CA G:ASP301 4.8 11.1 1.0

Zinc binding site 4 out of 4 in the Phosphotriesterase Variant E3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant E3 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn403 b:17.3 occ:0.56 OQ1 G:KCX169 2.0 22.1 1.0 NE2 G:HIS230 2.0 22.5 1.0 O2 G:CAC401 2.4 49.1 1.0 CD2 G:HIS201 2.4 24.6 1.0 O1 G:CAC401 2.6 28.4 1.0 CX G:KCX169 2.9 27.9 1.0 CD2 G:HIS230 3.0 24.1 1.0 CE1 G:HIS230 3.1 18.9 1.0 AS G:CAC401 3.1 85.7 1.0 OQ2 G:KCX169 3.2 23.9 1.0 CG G:HIS201 3.3 21.9 1.0 NE2 G:HIS201 3.5 34.9 1.0 ZN G:ZN402 3.6 12.8 0.7 CB G:HIS201 3.7 22.6 1.0 CG G:HIS230 4.1 18.7 1.0 ND1 G:HIS230 4.1 19.2 1.0 NZ G:KCX169 4.2 21.6 1.0 NE1 G:TRP131 4.2 24.0 1.0 CE1 G:HIS55 4.2 16.6 1.0 NE2 G:HIS55 4.2 16.0 1.0 OD2 G:ASP301 4.4 17.3 1.0 C1 G:CAC401 4.4 52.9 1.0 ND1 G:HIS201 4.5 35.9 1.0 CE1 G:HIS201 4.6 29.4 1.0 O G:HOH809 4.6 54.0 1.0 CA G:HIS201 4.6 22.2 1.0 C2 G:CAC401 4.7 43.2 1.0 CE G:KCX169 4.7 19.2 1.0 CD1 G:TRP131 4.8 22.5 1.0

E.Campbell, M.Kaltenbach, G.J.Correy, P.D.Carr, B.T.Porebski, E.K.Livingstone, L.Afriat-Jurnou, A.M.Buckle, M.Weik, F.Hollfelder, N.Tokuriki, C.J.Jackson. The Role of Protein Dynamics in the Evolution of New Enzyme Function. Nat.Chem.Biol. V. 12 944 2016.
ISSN: ESSN 1552-4469
PubMed: 27618189
DOI: 10.1038/NCHEMBIO.2175