Zinc in PDB 4xd5: Phosphotriesterase Variant R2

The structure of Phosphotriesterase Variant R2, PDB code: 4xd5 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)	44.19 / 1.85
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.704, 85.869, 88.382, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 20.4

The structure of Phosphotriesterase Variant R2 also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Phosphotriesterase Variant R2 (pdb code 4xd5). 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 R2, PDB code: 4xd5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase Variant R2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant R2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:13.8 occ:1.00 O1 A:CAC2403 2.0 9.9 0.7 NE2 A:HIS57 2.1 12.5 1.0 NE2 A:HIS55 2.1 10.8 1.0 OD1 A:ASP301 2.2 9.4 1.0 OQ2 A:KCX169 2.2 14.6 1.0 CD2 A:HIS55 3.0 10.1 1.0 CG A:ASP301 3.0 10.3 1.0 CE1 A:HIS57 3.0 10.7 1.0 CD2 A:HIS57 3.1 10.9 1.0 CX A:KCX169 3.1 17.0 1.0 CE1 A:HIS55 3.1 10.7 1.0 OD2 A:ASP301 3.3 15.4 1.0 AS A:CAC2403 3.3 26.0 0.7 OQ1 A:KCX169 3.5 14.3 1.0 ZN A:ZN2402 3.7 14.2 0.8 C2 A:CAC2403 3.8 20.5 0.7 CG2 A:VAL101 4.1 10.0 1.0 NZ A:KCX169 4.1 16.2 1.0 ND1 A:HIS57 4.2 8.6 1.0 CG A:HIS55 4.2 11.6 1.0 CE1 A:HIS230 4.2 16.2 1.0 ND1 A:HIS55 4.2 9.2 1.0 CG A:HIS57 4.2 8.8 1.0 O2 A:CAC2403 4.3 18.1 0.7 CB A:ASP301 4.4 10.5 1.0 NE2 A:HIS230 4.5 12.7 1.0 C1 A:CAC2403 4.8 26.3 0.7 CA A:ASP301 4.8 10.1 1.0 O A:HOH2650 4.9 33.7 1.0

Zinc binding site 2 out of 4 in the Phosphotriesterase Variant R2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant R2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:14.2 occ:0.77 OQ1 A:KCX169 2.0 14.3 1.0 NE2 A:HIS230 2.1 12.7 1.0 O2 A:CAC2403 2.1 18.1 0.7 ND1 A:HIS201 2.2 19.0 1.0 O1 A:CAC2403 2.7 9.9 0.7 CX A:KCX169 3.0 17.0 1.0 CE1 A:HIS230 3.0 16.2 1.0 AS A:CAC2403 3.1 26.0 0.7 CD2 A:HIS230 3.1 17.3 1.0 CE1 A:HIS201 3.1 28.6 1.0 CG A:HIS201 3.2 23.0 1.0 NH2 A:ARG254 3.2 26.5 0.3 OQ2 A:KCX169 3.3 14.6 1.0 CB A:HIS201 3.5 20.3 1.0 ZN A:ZN2401 3.7 13.8 1.0 NE1 A:TRP131 3.9 21.5 1.0 NZ A:KCX169 4.2 16.2 1.0 CE1 A:HIS55 4.2 10.7 1.0 ND1 A:HIS230 4.2 15.7 1.0 CZ A:ARG254 4.2 23.5 0.3 CG A:HIS230 4.2 20.6 1.0 NE2 A:HIS55 4.2 10.8 1.0 NE2 A:HIS201 4.3 23.7 1.0 CD2 A:HIS201 4.3 18.1 1.0 CA A:HIS201 4.4 15.8 1.0 OD2 A:ASP301 4.5 15.4 1.0 C2 A:CAC2403 4.5 20.5 0.7 C1 A:CAC2403 4.5 26.3 0.7 CD1 A:TRP131 4.6 14.8 1.0 CE A:KCX169 4.6 17.7 1.0 NE A:ARG254 4.7 20.1 0.3

Zinc binding site 3 out of 4 in the Phosphotriesterase Variant R2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant R2 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn402 b:14.9 occ:0.95 O1 G:CAC401 1.9 17.9 0.8 NE2 G:HIS57 2.1 12.5 1.0 OQ2 G:KCX169 2.1 16.1 1.0 NE2 G:HIS55 2.1 19.6 1.0 OD1 G:ASP301 2.2 15.8 1.0 CD2 G:HIS55 3.0 18.2 1.0 CE1 G:HIS57 3.0 15.3 1.0 CD2 G:HIS57 3.1 14.6 1.0 CG G:ASP301 3.1 18.4 1.0 CX G:KCX169 3.1 19.8 1.0 CE1 G:HIS55 3.2 16.1 1.0 AS G:CAC401 3.3 26.3 0.8 OD2 G:ASP301 3.4 23.6 1.0 OQ1 G:KCX169 3.7 17.1 1.0 ZN G:ZN403 3.8 18.0 0.9 C2 G:CAC401 3.9 19.7 0.8 CG2 G:VAL101 4.1 12.1 1.0 CE1 G:HIS230 4.1 19.8 1.0 NZ G:KCX169 4.1 15.8 1.0 ND1 G:HIS57 4.2 12.3 1.0 CG G:HIS55 4.2 15.1 1.0 CG G:HIS57 4.2 16.1 1.0 ND1 G:HIS55 4.2 18.0 1.0 O2 G:CAC401 4.2 22.3 0.8 NE2 G:HIS230 4.3 18.7 1.0 CB G:ASP301 4.4 13.7 1.0 C1 G:CAC401 4.8 26.7 0.8 CA G:ASP301 4.9 14.4 1.0

Zinc binding site 4 out of 4 in the Phosphotriesterase Variant R2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant R2 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn403 b:18.0 occ:0.87 OQ1 G:KCX169 2.0 17.1 1.0 ND1 G:HIS201 2.1 15.1 1.0 NE2 G:HIS230 2.1 18.7 1.0 O2 G:CAC401 2.2 22.3 0.8 O1 G:CAC401 2.8 17.9 0.8 CX G:KCX169 2.9 19.8 1.0 CD2 G:HIS230 3.0 21.6 1.0 CE1 G:HIS201 3.0 25.4 1.0 AS G:CAC401 3.1 26.3 0.8 CG G:HIS201 3.2 15.6 1.0 OQ2 G:KCX169 3.2 16.1 1.0 CE1 G:HIS230 3.2 19.8 1.0 NH2 G:ARG254 3.4 25.9 0.3 CB G:HIS201 3.5 11.8 1.0 ZN G:ZN402 3.8 14.9 0.9 NE1 G:TRP131 3.9 18.6 1.0 NZ G:KCX169 4.1 15.8 1.0 NE2 G:HIS201 4.2 21.2 1.0 CG G:HIS230 4.2 18.5 1.0 CD2 G:HIS201 4.2 22.3 1.0 ND1 G:HIS230 4.3 17.3 1.0 CE1 G:HIS55 4.3 16.1 1.0 NE2 G:HIS55 4.3 19.6 1.0 C1 G:CAC401 4.4 26.7 0.8 CZ G:ARG254 4.4 25.9 0.3 CA G:HIS201 4.4 17.0 1.0 C2 G:CAC401 4.6 19.7 0.8 CD1 G:TRP131 4.6 16.7 1.0 CE G:KCX169 4.6 17.7 1.0 OD2 G:ASP301 4.7 23.6 1.0 NE G:ARG254 4.7 22.3 0.3

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