Zinc in PDB 4xd6: Phosphotriesterase Variant E2A

The structure of Phosphotriesterase Variant E2A, PDB code: 4xd6 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)	39.28 / 1.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.739, 85.759, 88.372, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.9

The structure of Phosphotriesterase Variant E2A also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Phosphotriesterase Variant E2A (pdb code 4xd6). 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 E2A, PDB code: 4xd6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase Variant E2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant E2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:8.4 occ:1.00 NE2 A:HIS57 2.0 8.9 1.0 OD1 A:ASP301 2.1 6.1 1.0 NE2 A:HIS55 2.1 5.8 1.0 O2 A:CAC403 2.1 15.1 1.0 OQ2 A:KCX169 2.2 9.8 1.0 CD2 A:HIS55 3.0 6.1 1.0 CE1 A:HIS57 3.0 8.1 1.0 CG A:ASP301 3.0 13.2 1.0 CX A:KCX169 3.0 9.6 1.0 CD2 A:HIS57 3.0 8.1 1.0 CE1 A:HIS55 3.1 6.5 1.0 AS A:CAC403 3.3 79.7 1.0 C1 A:CAC403 3.4 33.3 1.0 OD2 A:ASP301 3.4 13.2 1.0 OQ1 A:KCX169 3.4 7.8 1.0 ZN A:ZN402 3.5 13.0 1.0 CG2 A:VAL101 4.1 6.8 1.0 NZ A:KCX169 4.1 11.7 1.0 ND1 A:HIS57 4.1 8.3 1.0 O A:HOH859 4.2 22.9 1.0 CG A:HIS57 4.2 7.0 1.0 ND1 A:HIS55 4.2 10.5 1.0 CG A:HIS55 4.2 13.0 1.0 CE1 A:HIS230 4.2 13.3 1.0 CB A:ASP301 4.3 9.0 1.0 NE2 A:HIS230 4.4 8.5 1.0 O1 A:CAC403 4.5 56.4 1.0 C2 A:CAC403 4.7 43.6 1.0 CA A:ASP301 4.8 8.6 1.0 O A:HOH679 4.9 28.8 1.0

Zinc binding site 2 out of 4 in the Phosphotriesterase Variant E2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant E2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:13.0 occ:1.00 OQ1 A:KCX169 2.0 7.8 1.0 NE2 A:HIS230 2.0 8.5 1.0 O2 A:CAC403 2.2 15.1 1.0 ND1 A:HIS201 2.2 18.5 1.0 CE1 A:HIS230 2.9 13.3 1.0 CX A:KCX169 3.0 9.6 1.0 O1 A:CAC403 3.0 56.4 1.0 CD2 A:HIS230 3.1 10.3 1.0 CE1 A:HIS201 3.1 18.3 1.0 AS A:CAC403 3.2 79.7 1.0 CG A:HIS201 3.2 13.2 1.0 OQ2 A:KCX169 3.3 9.8 1.0 O A:HOH859 3.4 22.9 1.0 ZN A:ZN401 3.5 8.4 1.0 CB A:HIS201 3.6 15.2 1.0 CE1 A:HIS55 3.9 6.5 1.0 NE2 A:HIS55 4.0 5.8 1.0 NE1 A:TRP131 4.0 15.2 1.0 ND1 A:HIS230 4.1 12.3 1.0 NZ A:KCX169 4.2 11.7 1.0 CG A:HIS230 4.2 9.2 1.0 NE2 A:HIS201 4.2 18.0 1.0 CD2 A:HIS201 4.3 15.3 1.0 OD2 A:ASP301 4.4 13.2 1.0 CA A:HIS201 4.4 11.2 1.0 CE A:KCX169 4.6 7.3 1.0 C1 A:CAC403 4.6 33.3 1.0 C2 A:CAC403 4.7 43.6 1.0 CD1 A:TRP131 4.7 11.1 1.0 OD1 A:ASP301 4.8 6.1 1.0 CG A:ASP301 4.9 13.2 1.0

Zinc binding site 3 out of 4 in the Phosphotriesterase Variant E2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant E2A within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn401 b:22.2 occ:1.00 OQ1 G:KCX169 2.0 16.7 1.0 NE2 G:HIS230 2.0 24.1 1.0 ND1 G:HIS201 2.2 25.8 1.0 O1 G:CAC402 2.2 20.0 1.0 CX G:KCX169 2.9 17.4 1.0 CD2 G:HIS230 3.0 18.0 1.0 O2 G:CAC402 3.1 72.2 1.0 CE1 G:HIS230 3.1 28.4 1.0 CE1 G:HIS201 3.1 23.3 1.0 OQ2 G:KCX169 3.2 15.1 1.0 CG G:HIS201 3.2 24.3 1.0 AS G:CAC402 3.2 63.6 1.0 ZN G:ZN403 3.5 18.6 1.0 CB G:HIS201 3.5 17.2 1.0 O G:HOH815 3.6 25.4 1.0 NE1 G:TRP131 4.0 23.4 1.0 NE2 G:HIS55 4.0 23.2 1.0 CE1 G:HIS55 4.0 15.2 1.0 NZ G:KCX169 4.1 17.5 1.0 ND1 G:HIS230 4.2 22.3 1.0 CG G:HIS230 4.2 27.3 1.0 NE2 G:HIS201 4.2 24.9 1.0 CD2 G:HIS201 4.3 23.5 1.0 C2 G:CAC402 4.4 28.4 1.0 CA G:HIS201 4.4 11.7 1.0 CE G:KCX169 4.5 12.7 1.0 CD1 G:TRP131 4.7 17.9 1.0 C1 G:CAC402 4.9 56.5 1.0 OD2 G:ASP301 4.9 27.1 1.0

Zinc binding site 4 out of 4 in the Phosphotriesterase Variant E2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant E2A within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn403 b:18.6 occ:1.00 OQ2 G:KCX169 2.1 15.1 1.0 O1 G:CAC402 2.1 20.0 1.0 NE2 G:HIS55 2.1 23.2 1.0 OD1 G:ASP301 2.2 20.5 1.0 NE2 G:HIS57 2.2 15.2 1.0 CD2 G:HIS55 3.0 21.8 1.0 CD2 G:HIS57 3.0 13.4 1.0 CX G:KCX169 3.1 17.4 1.0 CG G:ASP301 3.1 25.2 1.0 CE1 G:HIS55 3.2 15.2 1.0 CE1 G:HIS57 3.3 15.3 1.0 AS G:CAC402 3.3 63.6 1.0 OD2 G:ASP301 3.5 27.1 1.0 OQ1 G:KCX169 3.5 16.7 1.0 ZN G:ZN401 3.5 22.2 1.0 C2 G:CAC402 3.6 28.4 1.0 O G:HOH815 3.8 25.4 1.0 NZ G:KCX169 4.1 17.5 1.0 CE1 G:HIS230 4.1 28.4 1.0 CG2 G:VAL101 4.1 9.9 1.0 CG G:HIS55 4.2 19.4 1.0 CG G:HIS57 4.2 10.8 1.0 NE2 G:HIS230 4.3 24.1 1.0 ND1 G:HIS55 4.3 20.6 1.0 ND1 G:HIS57 4.3 13.6 1.0 CB G:ASP301 4.4 17.8 1.0 C1 G:CAC402 4.4 56.5 1.0 O2 G:CAC402 4.7 72.2 1.0 CA G:ASP301 5.0 17.7 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