Zinc in PDB 6fs3: Phosphotriesterase PTE_A53_1

All present enzymatic activity of Phosphotriesterase PTE_A53_1:
3.1.8.1;

The structure of Phosphotriesterase PTE_A53_1, PDB code: 6fs3 was solved by O.Dym, N.Aggarwal, S.Albeck, T.Unger, S.Hamer Rogotner, I.Silman, H.Leader, Y.Ashani, M.Goldsmith, P.Greisen, D.Tawfik, L.J.Sussman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.48 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.469, 81.460, 70.710, 90.00, 95.12, 90.00
R / Rfree (%)	16.7 / 20.1

The binding sites of Zinc atom in the Phosphotriesterase PTE_A53_1 (pdb code 6fs3). 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 PTE_A53_1, PDB code: 6fs3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase PTE_A53_1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase PTE_A53_1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:12.7 occ:1.00 O9 A:9ON404 2.0 14.3 1.0 NE2 A:HIS57 2.0 11.7 1.0 NE2 A:HIS55 2.1 16.3 1.0 O1 A:FMT401 2.1 12.4 1.0 OD1 A:ASP301 2.2 12.0 1.0 C1 A:9ON404 2.9 16.1 1.0 CD2 A:HIS55 2.9 11.7 1.0 CE1 A:HIS57 3.0 12.7 1.0 CD2 A:HIS57 3.0 10.1 1.0 CG A:ASP301 3.1 15.1 1.0 CE1 A:HIS55 3.2 14.0 1.0 C A:FMT401 3.2 13.5 1.0 OD2 A:ASP301 3.4 14.9 1.0 C2 A:9ON404 3.4 18.4 1.0 C3 A:9ON404 3.5 22.9 1.0 O2 A:FMT401 3.7 13.0 1.0 ZN A:ZN403 3.9 13.0 1.0 O8 A:9ON404 3.9 12.7 1.0 CG2 A:VAL101 4.0 12.6 1.0 C4 A:9ON404 4.1 28.8 1.0 CG A:HIS55 4.1 15.5 1.0 ND1 A:HIS57 4.1 11.6 1.0 CE1 A:HIS230 4.1 12.8 1.0 CG A:HIS57 4.2 12.6 1.0 ND1 A:HIS55 4.2 11.6 1.0 CB A:ASP301 4.3 15.8 1.0 NE2 A:HIS230 4.5 10.2 1.0 O12 A:9ON404 4.5 25.1 1.0 NZ A:LYS169 4.5 18.9 1.0 C7 A:9ON404 4.7 28.3 1.0 CA A:ASP301 4.8 15.4 1.0

Zinc binding site 2 out of 4 in the Phosphotriesterase PTE_A53_1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase PTE_A53_1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:13.0 occ:1.00 O2 A:FMT401 2.0 13.0 1.0 O8 A:9ON404 2.0 12.7 1.0 NE2 A:HIS230 2.0 10.2 1.0 ND1 A:HIS201 2.1 16.1 1.0 O9 A:9ON404 2.5 14.3 1.0 C1 A:9ON404 2.6 16.1 1.0 CE1 A:HIS201 3.0 17.9 1.0 CD2 A:HIS230 3.0 13.1 1.0 CE1 A:HIS230 3.0 12.8 1.0 C A:FMT401 3.0 13.5 1.0 CG A:HIS201 3.1 14.2 1.0 O1 A:FMT401 3.3 12.4 1.0 CB A:HIS201 3.5 13.4 1.0 ZN A:ZN402 3.9 12.7 1.0 NE1 A:TRP131 4.0 16.5 1.0 C2 A:9ON404 4.0 18.4 1.0 NE2 A:HIS201 4.1 22.5 1.0 ND1 A:HIS230 4.1 13.3 1.0 CG A:HIS230 4.1 11.8 1.0 CD2 A:HIS201 4.2 15.3 1.0 CE1 A:HIS55 4.2 14.0 1.0 NE2 A:HIS55 4.3 16.3 1.0 CA A:HIS201 4.3 12.4 1.0 O12 A:9ON404 4.4 25.1 1.0 CD1 A:TRP131 4.5 16.8 1.0 O A:HOH658 4.6 28.2 1.0 NZ A:LYS169 4.7 18.9 1.0 CE A:LYS169 4.8 13.7 1.0 OD2 A:ASP301 4.9 14.9 1.0 C7 A:9ON404 5.0 28.3 1.0

Zinc binding site 3 out of 4 in the Phosphotriesterase PTE_A53_1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase PTE_A53_1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:15.8 occ:1.00 O8 B:9ON404 1.9 17.6 1.0 NE2 B:HIS57 2.0 18.0 1.0 O1 B:FMT401 2.1 18.1 1.0 NE2 B:HIS55 2.2 19.6 1.0 OD1 B:ASP301 2.2 15.1 1.0 C1 B:9ON404 2.8 21.7 1.0 CE1 B:HIS57 2.9 14.3 1.0 CD2 B:HIS55 3.0 19.9 1.0 CD2 B:HIS57 3.0 18.9 1.0 CG B:ASP301 3.1 19.3 1.0 CE1 B:HIS55 3.3 17.8 1.0 C B:FMT401 3.3 17.5 1.0 C2 B:9ON404 3.4 24.2 1.0 OD2 B:ASP301 3.4 18.2 1.0 C3 B:9ON404 3.5 28.8 1.0 O2 B:FMT401 3.7 16.6 1.0 ZN B:ZN403 3.9 18.0 1.0 O9 B:9ON404 3.9 22.0 1.0 CE1 B:HIS230 4.0 24.2 1.0 CG2 B:VAL101 4.0 13.9 1.0 ND1 B:HIS57 4.0 13.8 1.0 CG B:HIS57 4.1 16.6 1.0 C4 B:9ON404 4.1 33.1 1.0 CG B:HIS55 4.2 13.8 1.0 ND1 B:HIS55 4.3 16.4 1.0 NE2 B:HIS230 4.3 18.5 1.0 CB B:ASP301 4.4 14.0 1.0 O10 B:9ON404 4.4 39.4 1.0 C7 B:9ON404 4.6 36.7 1.0 NZ B:LYS169 4.7 20.3 1.0 CA B:ASP301 4.8 12.1 1.0

Zinc binding site 4 out of 4 in the Phosphotriesterase PTE_A53_1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase PTE_A53_1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:18.0 occ:1.00 O2 B:FMT401 2.0 16.6 1.0 O9 B:9ON404 2.0 22.0 1.0 NE2 B:HIS230 2.0 18.5 1.0 ND1 B:HIS201 2.1 20.0 1.0 O8 B:9ON404 2.5 17.6 1.0 C1 B:9ON404 2.6 21.7 1.0 CD2 B:HIS230 2.9 18.6 1.0 C B:FMT401 3.0 17.5 1.0 CE1 B:HIS201 3.0 20.8 1.0 CE1 B:HIS230 3.1 24.2 1.0 CG B:HIS201 3.1 17.0 1.0 O1 B:FMT401 3.3 18.1 1.0 CB B:HIS201 3.5 14.3 1.0 ZN B:ZN402 3.9 15.8 1.0 NE1 B:TRP131 3.9 18.0 1.0 C2 B:9ON404 4.0 24.2 1.0 CG B:HIS230 4.1 18.2 1.0 ND1 B:HIS230 4.1 18.6 1.0 NE2 B:HIS201 4.2 24.0 1.0 CD2 B:HIS201 4.2 22.5 1.0 CE1 B:HIS55 4.2 17.8 1.0 NE2 B:HIS55 4.3 19.6 1.0 CA B:HIS201 4.3 18.8 1.0 O10 B:9ON404 4.3 39.4 1.0 NZ B:LYS169 4.5 20.3 1.0 CD1 B:TRP131 4.5 16.6 1.0 CE B:LYS169 4.8 19.1 1.0 OD2 B:ASP301 4.9 18.2 1.0 C7 B:9ON404 5.0 36.7 1.0

O.Dym, N.Aggarwal, J.L.Sussman, I.Silman. Crystal Structures of Bacterail Phosphotriesterase Variant with High Catalytic Activity Towards Organophosphate Nerve Agents Developed By Use of Structure-Based Design and Molecular Evolution To Be Published.