Zinc in PDB 6fei: Phosphotriesterase PTE_A53_1

The structure of Phosphotriesterase PTE_A53_1, PDB code: 6fei 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)	39.18 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.230, 81.249, 70.666, 90.00, 94.80, 90.00
R / Rfree (%)	15.5 / 18.5

The binding sites of Zinc atom in the Phosphotriesterase PTE_A53_1 (pdb code 6fei). 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: 6fei:
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:20.2 occ:1.00 OAF A:D6K404 2.0 27.2 1.0 NE2 A:HIS57 2.0 16.3 1.0 O1 A:FMT401 2.1 19.6 1.0 NE2 A:HIS55 2.1 18.5 1.0 OD1 A:ASP301 2.3 18.9 1.0 CE1 A:HIS57 3.0 17.0 1.0 CD2 A:HIS55 3.0 17.9 1.0 CAL A:D6K404 3.0 22.2 1.0 CD2 A:HIS57 3.0 18.6 1.0 C A:FMT401 3.1 17.9 1.0 CG A:ASP301 3.1 18.8 1.0 CE1 A:HIS55 3.2 20.2 1.0 CAH A:D6K404 3.3 21.7 1.0 OD2 A:ASP301 3.4 19.9 1.0 O2 A:FMT401 3.5 17.3 1.0 CAI A:D6K404 3.8 31.7 1.0 ZN A:ZN403 3.8 20.6 1.0 CG2 A:VAL101 4.1 17.8 1.0 CE1 A:HIS230 4.1 19.4 1.0 ND1 A:HIS57 4.1 17.2 1.0 CG A:HIS57 4.2 16.9 1.0 CG A:HIS55 4.2 17.5 1.0 ND1 A:HIS55 4.2 16.0 1.0 OAJ A:D6K404 4.2 27.3 1.0 NE2 A:HIS230 4.4 19.0 1.0 NZ A:LYS169 4.4 22.5 1.0 CB A:ASP301 4.4 19.1 1.0 CAE A:D6K404 4.5 29.6 1.0 CAK A:D6K404 4.6 28.8 1.0 CAA A:D6K404 4.8 26.8 1.0 OAG A:D6K404 4.8 38.5 1.0 CA A:ASP301 4.9 17.0 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:20.6 occ:1.00 O2 A:FMT401 2.0 17.3 1.0 NE2 A:HIS230 2.0 19.0 1.0 ND1 A:HIS201 2.1 24.2 1.0 CAL A:D6K404 2.8 22.2 1.0 CD2 A:HIS230 3.0 18.4 1.0 CE1 A:HIS230 3.0 19.4 1.0 CE1 A:HIS201 3.0 26.9 1.0 C A:FMT401 3.0 17.9 1.0 OAF A:D6K404 3.1 27.2 1.0 CG A:HIS201 3.1 21.0 1.0 O1 A:FMT401 3.4 19.6 1.0 CB A:HIS201 3.5 18.6 1.0 OAJ A:D6K404 3.8 27.3 1.0 CAH A:D6K404 3.8 21.7 1.0 ZN A:ZN402 3.8 20.2 1.0 NE1 A:TRP131 3.9 24.3 1.0 ND1 A:HIS230 4.1 18.8 1.0 CG A:HIS230 4.1 18.3 1.0 NE2 A:HIS201 4.2 26.1 1.0 CD2 A:HIS201 4.2 23.2 1.0 CE1 A:HIS55 4.2 20.2 1.0 NE2 A:HIS55 4.3 18.5 1.0 O A:HOH542 4.3 30.6 1.0 CA A:HIS201 4.4 18.0 1.0 NZ A:LYS169 4.5 22.5 1.0 CD1 A:TRP131 4.5 21.9 1.0 OD2 A:ASP301 4.7 19.9 1.0 CE A:LYS169 4.8 18.4 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:23.6 occ:1.00 NE2 B:HIS57 2.0 21.0 1.0 O B:HOH629 2.1 25.7 1.0 O1 B:FMT401 2.1 22.3 1.0 NE2 B:HIS55 2.2 18.7 1.0 OD1 B:ASP301 2.2 22.4 1.0 CE1 B:HIS57 3.0 21.3 1.0 CD2 B:HIS55 3.0 19.8 1.0 CD2 B:HIS57 3.0 20.7 1.0 CG B:ASP301 3.1 24.1 1.0 C B:FMT401 3.2 24.4 1.0 CE1 B:HIS55 3.2 22.0 1.0 OD2 B:ASP301 3.4 22.9 1.0 O2 B:FMT401 3.6 21.4 1.0 ZN B:ZN403 3.8 24.9 1.0 O B:HOH701 4.0 29.8 1.0 CE1 B:HIS230 4.1 24.6 1.0 ND1 B:HIS57 4.1 19.4 1.0 CG2 B:VAL101 4.1 19.8 1.0 CG B:HIS57 4.1 18.7 1.0 CG B:HIS55 4.2 19.5 1.0 ND1 B:HIS55 4.3 20.0 1.0 NE2 B:HIS230 4.3 21.7 1.0 CB B:ASP301 4.4 19.9 1.0 NZ B:LYS169 4.5 25.7 1.0 CA B:ASP301 4.9 19.2 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:24.9 occ:1.00 O2 B:FMT401 2.0 21.4 1.0 NE2 B:HIS230 2.0 21.7 1.0 ND1 B:HIS201 2.1 27.2 1.0 O B:HOH701 2.2 29.8 1.0 O B:HOH629 2.5 25.7 1.0 CE1 B:HIS201 2.9 27.0 1.0 CD2 B:HIS230 3.0 23.1 1.0 C B:FMT401 3.0 24.4 1.0 CE1 B:HIS230 3.0 24.6 1.0 CG B:HIS201 3.1 24.9 1.0 O1 B:FMT401 3.3 22.3 1.0 CB B:HIS201 3.5 22.3 1.0 ZN B:ZN402 3.8 23.6 1.0 NE1 B:TRP131 3.9 24.6 1.0 NE2 B:HIS201 4.1 30.3 1.0 ND1 B:HIS230 4.1 23.8 1.0 CG B:HIS230 4.1 20.7 1.0 CD2 B:HIS201 4.2 27.3 1.0 CE1 B:HIS55 4.3 22.0 1.0 NE2 B:HIS55 4.3 18.7 1.0 CA B:HIS201 4.4 22.3 1.0 NZ B:LYS169 4.5 25.7 1.0 CD1 B:TRP131 4.5 22.3 1.0 OD2 B:ASP301 4.8 22.9 1.0 CE B:LYS169 4.8 22.6 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.