Zinc in PDB 4xd4: Phosphotriesterase Variant E2B

The structure of Phosphotriesterase Variant E2B, PDB code: 4xd4 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)	39.31 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.560, 85.782, 88.443, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 24.3

The structure of Phosphotriesterase Variant E2B also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Phosphotriesterase Variant E2B (pdb code 4xd4). 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 E2B, PDB code: 4xd4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase Variant E2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant E2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:18.9 occ:1.00 O1 A:CAC2403 2.0 28.2 1.0 NE2 A:HIS57 2.0 13.4 1.0 OD1 A:ASP301 2.2 17.9 1.0 NE2 A:HIS55 2.2 12.9 1.0 OQ2 A:KCX169 2.2 18.4 1.0 CE1 A:HIS57 3.0 17.7 1.0 CG A:ASP301 3.0 16.9 1.0 CD2 A:HIS55 3.0 14.7 1.0 CD2 A:HIS57 3.1 11.8 1.0 CX A:KCX169 3.1 24.1 1.0 CE1 A:HIS55 3.3 14.6 1.0 OD2 A:ASP301 3.3 24.6 1.0 AS A:CAC2403 3.4 85.0 1.0 OQ1 A:KCX169 3.5 20.7 1.0 ZN A:ZN2402 3.9 31.3 1.0 C2 A:CAC2403 3.9 42.3 1.0 ND1 A:HIS57 4.1 12.9 1.0 CG2 A:VAL101 4.1 19.2 1.0 NZ A:KCX169 4.1 18.9 1.0 CG A:HIS57 4.2 12.1 1.0 CE1 A:HIS230 4.2 22.1 1.0 CG A:HIS55 4.2 11.3 1.0 ND1 A:HIS55 4.3 13.8 1.0 CB A:ASP301 4.4 17.3 1.0 NE2 A:HIS230 4.4 20.4 1.0 O2 A:CAC2403 4.4 43.8 1.0 C1 A:CAC2403 4.8 58.8 1.0 CA A:ASP301 4.9 13.6 1.0 O A:HOH2622 4.9 28.8 1.0

Zinc binding site 2 out of 4 in the Phosphotriesterase Variant E2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant E2B within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:31.3 occ:1.00 OQ1 A:KCX169 2.0 20.7 1.0 ND1 A:HIS201 2.1 21.9 1.0 NE2 A:HIS230 2.2 20.4 1.0 O2 A:CAC2403 2.6 43.8 1.0 O1 A:CAC2403 2.8 28.2 1.0 CX A:KCX169 3.0 24.1 1.0 CG A:HIS201 3.1 27.2 1.0 CE1 A:HIS201 3.1 31.9 1.0 CD2 A:HIS230 3.1 28.1 1.0 CE1 A:HIS230 3.2 22.1 1.0 OQ2 A:KCX169 3.3 18.4 1.0 AS A:CAC2403 3.3 85.0 1.0 CB A:HIS201 3.4 22.0 1.0 NE1 A:TRP131 3.8 20.6 1.0 NH2 A:ARG254 3.8 31.5 0.5 ZN A:ZN2401 3.9 18.9 1.0 NZ A:KCX169 4.2 18.9 1.0 NE2 A:HIS201 4.2 23.8 1.0 CD2 A:HIS201 4.2 30.9 1.0 CG A:HIS230 4.3 23.1 1.0 ND1 A:HIS230 4.3 25.2 1.0 CE1 A:HIS55 4.4 14.6 1.0 NE2 A:HIS55 4.4 12.9 1.0 CA A:HIS201 4.4 18.4 1.0 CD1 A:TRP131 4.5 18.7 1.0 CZ A:ARG254 4.5 27.6 0.5 CE A:KCX169 4.6 19.3 1.0 OD2 A:ASP301 4.6 24.6 1.0 C1 A:CAC2403 4.7 58.8 1.0 C2 A:CAC2403 4.8 42.3 1.0 CE2 A:TRP131 4.8 24.3 1.0 NE A:ARG254 4.9 26.1 0.5

Zinc binding site 3 out of 4 in the Phosphotriesterase Variant E2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant E2B within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn402 b:22.8 occ:1.00 O1 G:CAC401 1.9 28.5 1.0 NE2 G:HIS55 2.1 19.9 1.0 NE2 G:HIS57 2.2 15.3 1.0 OQ2 G:KCX169 2.2 26.0 1.0 OD1 G:ASP301 2.3 19.6 1.0 CD2 G:HIS55 3.0 17.6 1.0 CD2 G:HIS57 3.1 13.4 1.0 CE1 G:HIS55 3.2 19.5 1.0 CE1 G:HIS57 3.2 16.2 1.0 CX G:KCX169 3.2 25.8 1.0 CG G:ASP301 3.2 24.4 1.0 AS G:CAC401 3.3 50.3 1.0 OD2 G:ASP301 3.5 23.5 1.0 C2 G:CAC401 3.7 25.9 1.0 OQ1 G:KCX169 3.7 23.4 1.0 ZN G:ZN403 3.8 32.7 1.0 CG2 G:VAL101 4.0 14.3 1.0 CE1 G:HIS230 4.1 24.9 1.0 NZ G:KCX169 4.2 23.4 1.0 CG G:HIS55 4.2 16.1 1.0 ND1 G:HIS55 4.2 16.5 1.0 ND1 G:HIS57 4.3 15.5 1.0 CG G:HIS57 4.3 12.1 1.0 O2 G:CAC401 4.4 39.2 1.0 NE2 G:HIS230 4.4 19.9 1.0 CB G:ASP301 4.5 15.4 1.0 C1 G:CAC401 4.6 37.5 1.0 CA G:ASP301 4.9 18.7 1.0

Zinc binding site 4 out of 4 in the Phosphotriesterase Variant E2B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant E2B within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn403 b:32.7 occ:1.00 OQ1 G:KCX169 2.0 23.4 1.0 NE2 G:HIS230 2.1 19.9 1.0 O2 G:CAC401 2.2 39.2 1.0 ND1 G:HIS201 2.3 24.5 1.0 O1 G:CAC401 2.8 28.5 1.0 CX G:KCX169 3.0 25.8 1.0 CD2 G:HIS230 3.0 20.7 1.0 AS G:CAC401 3.0 50.3 1.0 CE1 G:HIS230 3.1 24.9 1.0 OQ2 G:KCX169 3.2 26.0 1.0 CE1 G:HIS201 3.2 23.3 1.0 CG G:HIS201 3.2 20.4 1.0 CB G:HIS201 3.5 20.3 1.0 ZN G:ZN402 3.8 22.8 1.0 NE1 G:TRP131 4.0 20.9 1.0 CG G:HIS230 4.2 22.7 1.0 NZ G:KCX169 4.2 23.4 1.0 ND1 G:HIS230 4.2 22.5 1.0 CE1 G:HIS55 4.3 19.5 1.0 NE2 G:HIS55 4.3 19.9 1.0 C2 G:CAC401 4.3 25.9 1.0 NE2 G:HIS201 4.4 31.6 1.0 CD2 G:HIS201 4.4 24.1 1.0 CA G:HIS201 4.4 18.6 1.0 C1 G:CAC401 4.6 37.5 1.0 CD1 G:TRP131 4.7 17.1 1.0 CE G:KCX169 4.7 23.7 1.0 OD2 G:ASP301 4.7 23.5 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