Zinc in PDB 6ffw: Phosphotriesterase PTE_A53_5

All present enzymatic activity of Phosphotriesterase PTE_A53_5:
3.1.8.1;

The structure of Phosphotriesterase PTE_A53_5, PDB code: 6ffw 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 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.780, 81.510, 70.690, 90.00, 94.92, 90.00
R / Rfree (%)	16.1 / 18.5

The binding sites of Zinc atom in the Phosphotriesterase PTE_A53_5 (pdb code 6ffw). 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_5, PDB code: 6ffw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase PTE_A53_5


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_5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:11.9 occ:1.00 OAF A:D6K404 1.8 17.0 1.0 NE2 A:HIS57 2.0 9.9 1.0 NE2 A:HIS55 2.1 8.9 1.0 O1 A:FMT401 2.2 11.7 1.0 OD1 A:ASP301 2.3 10.9 1.0 CAL A:D6K404 2.9 13.4 1.0 CE1 A:HIS57 3.0 11.7 1.0 CD2 A:HIS55 3.0 9.5 1.0 CD2 A:HIS57 3.0 11.4 1.0 C A:FMT401 3.1 9.6 1.0 CG A:ASP301 3.1 13.3 1.0 CE1 A:HIS55 3.2 10.9 1.0 CAH A:D6K404 3.3 10.7 1.0 OD2 A:ASP301 3.4 12.3 1.0 O2 A:FMT401 3.6 10.2 1.0 CAI A:D6K404 3.7 15.4 1.0 ZN A:ZN403 3.8 11.9 1.0 CG2 A:VAL101 4.1 11.5 1.0 ND1 A:HIS57 4.1 10.8 1.0 O A:HOH501 4.1 44.5 1.0 CE1 A:HIS230 4.1 12.4 1.0 OAJ A:D6K404 4.1 14.9 1.0 CG A:HIS57 4.2 11.1 1.0 CG A:HIS55 4.2 10.2 1.0 ND1 A:HIS55 4.2 10.1 1.0 CAE A:D6K404 4.3 22.1 1.0 NZ A:LYS169 4.3 11.5 1.0 NE2 A:HIS230 4.4 10.7 1.0 CB A:ASP301 4.5 9.8 1.0 CAK A:D6K404 4.5 15.2 1.0 OAG A:D6K404 4.7 24.8 1.0 CAA A:D6K404 4.8 17.0 1.0 CA A:ASP301 5.0 9.4 1.0

Zinc binding site 2 out of 4 in the Phosphotriesterase PTE_A53_5


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_5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:11.9 occ:1.00 O2 A:FMT401 1.9 10.2 1.0 NE2 A:HIS230 2.0 10.7 1.0 ND1 A:HIS201 2.1 11.5 1.0 O A:HOH501 2.2 44.5 1.0 CAL A:D6K404 2.8 13.4 1.0 C A:FMT401 3.0 9.6 1.0 CD2 A:HIS230 3.0 11.3 1.0 CE1 A:HIS230 3.0 12.4 1.0 CE1 A:HIS201 3.1 14.7 1.0 OAF A:D6K404 3.1 17.0 1.0 CG A:HIS201 3.2 10.8 1.0 O1 A:FMT401 3.3 11.7 1.0 CB A:HIS201 3.5 9.5 1.0 ZN A:ZN402 3.8 11.9 1.0 OAJ A:D6K404 3.8 14.9 1.0 CAH A:D6K404 3.8 10.7 1.0 NE1 A:TRP131 4.0 16.5 1.0 ND1 A:HIS230 4.1 10.2 1.0 CG A:HIS230 4.2 8.9 1.0 NE2 A:HIS201 4.2 17.9 1.0 CE1 A:HIS55 4.2 10.9 1.0 O A:HOH563 4.3 17.8 1.0 CD2 A:HIS201 4.3 14.3 1.0 NE2 A:HIS55 4.3 8.9 1.0 CA A:HIS201 4.4 9.9 1.0 NZ A:LYS169 4.4 11.5 1.0 N A:TRS405 4.5 31.6 1.0 CD1 A:TRP131 4.5 13.9 1.0 OD2 A:ASP301 4.7 12.3 1.0 CE A:LYS169 4.7 11.7 1.0

Zinc binding site 3 out of 4 in the Phosphotriesterase PTE_A53_5


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_5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1004 b:15.7 occ:1.00 NE2 B:HIS57 2.0 12.6 1.0 NE2 B:HIS55 2.2 11.0 1.0 O2 B:FMT1003 2.2 14.0 1.0 OD1 B:ASP301 2.3 11.8 1.0 CE1 B:HIS57 2.9 13.1 1.0 CD2 B:HIS55 3.1 13.3 1.0 CD2 B:HIS57 3.1 15.2 1.0 C B:FMT1003 3.1 11.8 1.0 CE1 B:HIS55 3.2 11.5 1.0 CG B:ASP301 3.2 13.7 1.0 OD2 B:ASP301 3.5 15.8 1.0 O B:HOH1101 3.5 11.6 1.0 O1 B:FMT1003 3.6 11.8 1.0 ZN B:ZN1005 3.7 16.0 1.0 CG2 B:VAL101 4.0 12.5 1.0 CE1 B:HIS230 4.1 17.3 1.0 ND1 B:HIS57 4.1 10.7 1.0 O B:HOH1323 4.1 17.5 1.0 CG B:HIS57 4.2 12.6 1.0 CG B:HIS55 4.2 11.5 1.0 ND1 B:HIS55 4.3 12.9 1.0 NZ B:LYS169 4.4 14.8 1.0 NE2 B:HIS230 4.4 12.8 1.0 CB B:ASP301 4.5 12.0 1.0

Zinc binding site 4 out of 4 in the Phosphotriesterase PTE_A53_5


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_5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1005 b:16.0 occ:1.00 O1 B:FMT1003 2.0 11.8 1.0 NE2 B:HIS230 2.0 12.8 1.0 ND1 B:HIS201 2.1 18.0 1.0 O B:HOH1323 2.1 17.5 1.0 C B:FMT1003 3.0 11.8 1.0 CE1 B:HIS230 3.0 17.3 1.0 CE1 B:HIS201 3.0 18.3 1.0 CD2 B:HIS230 3.0 14.4 1.0 CG B:HIS201 3.1 15.2 1.0 O2 B:FMT1003 3.3 14.0 1.0 CB B:HIS201 3.5 14.0 1.0 ZN B:ZN1004 3.7 15.7 1.0 O B:HOH1101 3.7 11.6 1.0 NE1 B:TRP131 4.0 21.8 1.0 ND1 B:HIS230 4.1 14.0 1.0 NE2 B:HIS201 4.2 22.4 1.0 CG B:HIS230 4.2 11.8 1.0 O B:HOH1290 4.2 29.2 1.0 CE1 B:HIS55 4.2 11.5 1.0 CD2 B:HIS201 4.2 19.7 1.0 NE2 B:HIS55 4.3 11.0 1.0 CA B:HIS201 4.4 15.9 1.0 NZ B:LYS169 4.4 14.8 1.0 CD1 B:TRP131 4.5 20.7 1.0 CE B:LYS169 4.7 14.1 1.0 OD2 B:ASP301 4.7 15.8 1.0

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. Phosphotriesterase PTE_A53_5 To Be Published.