Zinc in PDB 4gy0: Round 18 Arylesterase Variant of Phosphotriesterase

All present enzymatic activity of Round 18 Arylesterase Variant of Phosphotriesterase:
3.1.8.1;

The structure of Round 18 Arylesterase Variant of Phosphotriesterase, PDB code: 4gy0 was solved by C.J.Jackson, N.Tokuriki, D.S.Tawfik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.46 / 1.85
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	86.109, 86.366, 89.192, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.1

The binding sites of Zinc atom in the Round 18 Arylesterase Variant of Phosphotriesterase (pdb code 4gy0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Round 18 Arylesterase Variant of Phosphotriesterase, PDB code: 4gy0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Round 18 Arylesterase Variant of Phosphotriesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Round 18 Arylesterase Variant of Phosphotriesterase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:28.1 occ:0.79 O A:HOH703 2.0 9.9 1.0 NE2 A:HIS57 2.1 11.5 1.0 OD1 A:ASP301 2.3 14.1 0.8 O A:HOH701 2.3 26.4 1.0 OD1 A:ASP301 2.3 14.0 0.2 ZN A:ZN403 2.4 15.7 0.7 NE2 A:HIS55 2.8 22.6 1.0 CE1 A:HIS57 2.9 14.8 1.0 CG A:ASP301 3.0 14.6 0.8 OD2 A:ASP301 3.1 13.9 0.8 CG A:ASP301 3.3 14.5 0.2 CD2 A:HIS57 3.3 9.2 1.0 CD2 A:HIS55 3.4 22.9 1.0 OD2 A:ASP301 3.6 15.2 0.2 ZN A:ZN402 3.7 23.1 0.3 CE1 A:HIS55 3.8 15.4 1.0 CG2 A:VAL101 3.9 9.4 1.0 NZ A:LYS169 4.1 14.4 0.3 ND1 A:HIS57 4.1 10.3 1.0 NE2 A:HIS230 4.3 15.8 1.0 O A:HOH724 4.3 20.9 1.0 CG A:HIS57 4.3 13.1 1.0 CB A:ASP301 4.5 10.9 0.8 CB A:ASP301 4.6 11.2 0.2 CG A:HIS55 4.6 15.3 1.0 ND1 A:HIS55 4.8 19.4 1.0 CE1 A:HIS230 4.9 18.0 1.0 CA A:ASP301 5.0 13.3 0.8

Zinc binding site 2 out of 6 in the Round 18 Arylesterase Variant of Phosphotriesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Round 18 Arylesterase Variant of Phosphotriesterase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:23.1 occ:0.33 ND1 A:HIS201 2.1 18.3 0.2 O A:HOH703 2.3 9.9 1.0 CE1 A:HIS201 2.3 15.5 0.8 O A:HOH724 2.4 20.9 1.0 CE1 A:HIS230 2.4 18.0 1.0 O A:HOH701 2.5 26.4 1.0 CG A:HIS201 2.7 18.6 0.2 NE2 A:HIS230 2.7 15.8 1.0 CE1 A:HIS201 2.7 19.5 0.2 ZN A:ZN403 2.9 15.7 0.7 NE2 A:HIS201 2.9 17.7 0.8 ND1 A:HIS201 2.9 17.0 0.8 CB A:HIS201 3.2 17.4 0.2 CD2 A:HIS201 3.5 20.8 0.2 NE2 A:HIS201 3.5 20.9 0.2 ND1 A:HIS230 3.6 16.0 1.0 CD2 A:HIS201 3.7 24.0 0.8 CG A:HIS201 3.7 16.9 0.8 ZN A:ZN401 3.7 28.1 0.8 NZ A:LYS169 3.9 14.4 0.3 NZ A:LYS169 4.0 14.6 0.7 CD2 A:HIS230 4.0 15.7 1.0 NE1 A:TRP131 4.2 20.2 1.0 OD2 A:ASP301 4.3 13.9 0.8 CA A:HIS201 4.4 17.9 0.2 NE2 A:HIS55 4.4 22.6 1.0 CG A:HIS230 4.4 15.4 1.0 CE A:LYS169 4.4 15.2 0.3 CE A:LYS169 4.5 15.3 0.7 CD1 A:TRP131 4.7 18.3 1.0 CE1 A:HIS55 4.7 15.4 1.0 OD2 A:ASP301 4.8 15.2 0.2 CB A:HIS201 4.9 17.1 0.8

Zinc binding site 3 out of 6 in the Round 18 Arylesterase Variant of Phosphotriesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Round 18 Arylesterase Variant of Phosphotriesterase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn403 b:15.7 occ:0.70 NE2 A:HIS55 1.9 22.6 1.0 OD2 A:ASP301 2.0 13.9 0.8 NE2 A:HIS230 2.0 15.8 1.0 ZN A:ZN401 2.4 28.1 0.8 O A:HOH703 2.6 9.9 1.0 O A:HOH701 2.6 26.4 1.0 CE1 A:HIS55 2.8 15.4 1.0 CG A:ASP301 2.8 14.6 0.8 ZN A:ZN402 2.9 23.1 0.3 CD2 A:HIS55 3.0 22.9 1.0 CD2 A:HIS230 3.0 15.7 1.0 CE1 A:HIS230 3.0 18.0 1.0 OD2 A:ASP301 3.1 15.2 0.2 OD1 A:ASP301 3.1 14.0 0.2 OD1 A:ASP301 3.1 14.1 0.8 CG A:ASP301 3.2 14.5 0.2 ND1 A:HIS55 3.9 19.4 1.0 CG A:HIS55 4.0 15.3 1.0 ND1 A:HIS230 4.1 16.0 1.0 CG A:HIS230 4.2 15.4 1.0 CB A:ASP301 4.2 10.9 0.8 CB A:ASP301 4.2 11.2 0.2 O A:HOH724 4.4 20.9 1.0 NE2 A:HIS57 4.4 11.5 1.0 NZ A:LYS169 4.5 14.6 0.7 NH1 A:ARG254 4.5 27.3 1.0 ND1 A:HIS201 4.5 17.0 0.8 NZ A:LYS169 4.5 14.4 0.3 CE1 A:HIS201 4.7 15.5 0.8 CG A:ARG254 4.8 20.5 1.0 CD A:ARG254 4.8 20.1 1.0 ND1 A:HIS201 4.9 18.3 0.2

Zinc binding site 4 out of 6 in the Round 18 Arylesterase Variant of Phosphotriesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Round 18 Arylesterase Variant of Phosphotriesterase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:26.3 occ:0.57 O B:HOH717 1.9 14.1 1.0 OD1 B:ASP301 2.1 15.0 0.7 ZN B:ZN403 2.1 22.8 0.7 NE2 B:HIS57 2.2 15.4 1.0 NE2 B:HIS55 2.6 22.4 0.4 OD1 B:ASP301 2.6 13.9 0.3 CG B:ASP301 2.8 18.9 0.7 OD2 B:ASP301 2.9 15.8 0.7 CE1 B:HIS57 3.0 17.9 1.0 NE2 B:HIS55 3.3 18.8 0.6 CD2 B:HIS57 3.3 20.9 1.0 CG B:ASP301 3.4 17.2 0.3 CD2 B:HIS55 3.4 18.9 0.4 CE1 B:HIS55 3.5 19.0 0.4 CD2 B:HIS55 3.6 18.9 0.6 OD2 B:ASP301 3.9 25.1 0.3 CG2 B:VAL101 4.0 17.3 1.0 ZN B:ZN402 4.0 21.7 0.4 NZ B:LYS169 4.1 20.8 0.3 CE1 B:HIS230 4.2 16.4 0.5 ND1 B:HIS57 4.2 16.0 1.0 NE2 B:HIS230 4.2 16.5 0.6 CB B:ASP301 4.3 17.3 0.7 CE1 B:HIS55 4.3 21.2 0.6 CG B:HIS57 4.4 18.6 1.0 CB B:ASP301 4.4 17.5 0.3 NE2 B:HIS230 4.5 21.0 0.5 O B:HOH673 4.5 35.4 1.0 CG B:HIS55 4.5 18.4 0.4 ND1 B:HIS55 4.5 17.6 0.4 CG B:HIS55 4.8 18.7 0.6 CA B:ASP301 4.8 19.3 0.7 CA B:ASP301 4.8 19.2 0.3 CE1 B:HIS230 5.0 20.3 0.6

Zinc binding site 5 out of 6 in the Round 18 Arylesterase Variant of Phosphotriesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Round 18 Arylesterase Variant of Phosphotriesterase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:21.7 occ:0.36 CE1 B:HIS201 1.8 22.1 0.8 NE2 B:HIS201 2.1 19.5 0.8 CE1 B:HIS230 2.2 20.3 0.6 ND1 B:HIS201 2.3 21.4 0.8 NE2 B:HIS230 2.4 21.0 0.5 NE2 B:HIS230 2.5 16.5 0.6 O B:HOH717 2.6 14.1 1.0 CD2 B:HIS201 2.7 21.4 0.8 NE2 B:HIS201 2.8 20.3 0.2 CG B:HIS201 2.8 22.1 0.8 CE1 B:HIS201 2.8 22.7 0.2 ND1 B:HIS201 2.9 21.4 0.2 CD2 B:HIS201 2.9 23.0 0.2 CG B:HIS201 3.0 22.2 0.2 ZN B:ZN403 3.1 22.8 0.7 CD2 B:HIS230 3.2 18.8 0.5 CE1 B:HIS230 3.3 16.4 0.5 ND1 B:HIS230 3.4 14.3 0.6 NZ B:LYS169 3.4 20.7 0.7 CD2 B:HIS230 3.7 22.2 0.6 NZ B:LYS169 3.7 20.8 0.3 CB B:HIS201 3.9 22.1 0.2 ZN B:ZN401 4.0 26.3 0.6 CB B:HIS201 4.1 22.4 0.8 CG B:HIS230 4.1 16.9 0.6 CE B:LYS169 4.1 18.4 0.3 CE B:LYS169 4.1 20.3 0.7 CG B:HIS230 4.2 16.6 0.5 ND1 B:HIS230 4.2 18.6 0.5 NE1 B:TRP131 4.2 26.1 1.0 NE2 B:HIS55 4.4 18.8 0.6 CE1 B:HIS55 4.4 19.0 0.4 NE2 B:HIS55 4.5 22.4 0.4 OD2 B:ASP301 4.6 15.8 0.7 CD1 B:TRP131 4.7 26.5 1.0

Zinc binding site 6 out of 6 in the Round 18 Arylesterase Variant of Phosphotriesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Round 18 Arylesterase Variant of Phosphotriesterase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:22.8 occ:0.74 NE2 B:HIS55 1.8 22.4 0.4 OD2 B:ASP301 2.1 15.8 0.7 ZN B:ZN401 2.1 26.3 0.6 CE1 B:HIS230 2.1 16.4 0.5 NE2 B:HIS230 2.2 16.5 0.6 NE2 B:HIS55 2.3 18.8 0.6 CE1 B:HIS55 2.5 19.0 0.4 O B:HOH717 2.5 14.1 1.0 NE2 B:HIS230 2.7 21.0 0.5 CG B:ASP301 2.7 18.9 0.7 OD1 B:ASP301 2.8 15.0 0.7 CD2 B:HIS55 2.9 18.9 0.6 ZN B:ZN402 3.1 21.7 0.4 CD2 B:HIS55 3.1 18.9 0.4 CD2 B:HIS230 3.1 22.2 0.6 CE1 B:HIS230 3.2 20.3 0.6 ND1 B:HIS230 3.3 18.6 0.5 CG B:ASP301 3.4 17.2 0.3 OD1 B:ASP301 3.4 13.9 0.3 CE1 B:HIS55 3.5 21.2 0.6 OD2 B:ASP301 3.5 25.1 0.3 ND1 B:HIS55 3.7 17.6 0.4 CD2 B:HIS230 3.9 18.8 0.5 CG B:HIS55 4.0 18.4 0.4 CB B:ASP301 4.0 17.3 0.7 CB B:ASP301 4.1 17.5 0.3 CG B:HIS55 4.2 18.7 0.6 CG B:HIS230 4.2 16.6 0.5 NE2 B:HIS57 4.3 15.4 1.0 CG B:HIS230 4.3 16.9 0.6 ND1 B:HIS230 4.3 14.3 0.6 NZ B:LYS169 4.4 20.8 0.3 ND1 B:HIS55 4.4 15.1 0.6 ND1 B:HIS201 4.5 21.4 0.8 NZ B:LYS169 4.6 20.7 0.7 CE1 B:HIS201 4.6 22.1 0.8 NE B:ARG254 4.6 29.2 1.0 CD B:ARG254 4.8 21.6 1.0 CG B:ARG254 4.9 19.6 1.0 CG2 B:VAL101 5.0 17.3 1.0 OD1 B:ASP253 5.0 26.4 1.0

N.Tokuriki, C.J.Jackson, L.Afriat-Jurnou, K.T.Wyganowski, R.Tang, D.S.Tawfik. Diminishing Returns and Tradeoffs Constrain the Laboratory Optimization of An Enzyme Nat Commun V. 3 1257 2012.
ISSN: ESSN 2041-1723
PubMed: 23212386
DOI: 10.1038/NCOMMS2246