Zinc in PDB 6bhl: Phosphotriesterase Variant S5DELTAL7

The structure of Phosphotriesterase Variant S5DELTAL7, PDB code: 6bhl was solved by C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.75 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.146, 85.485, 88.535, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 16.1

The structure of Phosphotriesterase Variant S5DELTAL7 also contains other interesting chemical elements:

Arsenic

(As)

2 atoms

The binding sites of Zinc atom in the Phosphotriesterase Variant S5DELTAL7 (pdb code 6bhl). 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 S5DELTAL7, PDB code: 6bhl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase Variant S5DELTAL7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant S5DELTAL7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:9.9 occ:1.00 O2 A:CAC2407 1.9 10.6 0.6 NE2 A:HIS57 2.0 9.6 0.0 NE2 A:HIS57 2.0 7.7 1.0 NE2 A:HIS55 2.1 9.0 1.0 OQ2 A:KCX169 2.1 11.2 1.0 OD1 A:ASP292 2.3 10.5 1.0 CE1 A:HIS57 3.0 8.2 1.0 CE1 A:HIS57 3.0 9.5 0.0 CD2 A:HIS55 3.0 8.4 1.0 CD2 A:HIS57 3.0 9.5 0.0 CX A:KCX169 3.1 12.4 1.0 CD2 A:HIS57 3.1 8.2 1.0 CE1 A:HIS55 3.1 9.9 1.0 HE1 A:HIS57 3.1 9.8 1.0 HE1 A:HIS57 3.2 11.4 0.0 HD2 A:HIS55 3.2 10.1 1.0 CG A:ASP292 3.2 11.7 1.0 AS A:CAC2407 3.2 13.3 0.6 HD2 A:HIS57 3.2 11.4 0.0 HE1 A:HIS55 3.3 11.9 1.0 HD2 A:HIS57 3.3 9.8 1.0 HE1 A:HIS230 3.4 17.0 1.0 OQ1 A:KCX169 3.5 12.3 1.0 OD2 A:ASP292 3.5 12.4 1.0 HG23 A:VAL101 3.5 10.6 1.0 O A:HOH2501 3.5 8.0 1.0 C1 A:CAC2407 3.5 12.7 0.6 HG23 A:VAL101 3.5 11.4 0.0 HG21 A:VAL101 3.7 11.4 0.0 ZN A:ZN2402 3.7 12.6 0.9 HG21 A:VAL101 3.8 10.6 1.0 CG2 A:VAL101 4.0 9.5 0.0 CG2 A:VAL101 4.0 8.8 1.0 O1 A:CAC2407 4.1 12.0 0.6 CE1 A:HIS230 4.1 14.2 1.0 NZ A:KCX169 4.1 12.0 1.0 ND1 A:HIS57 4.1 8.8 1.0 ND1 A:HIS57 4.1 9.4 0.0 CG A:HIS57 4.2 9.4 0.0 HG22 A:VAL101 4.2 10.6 1.0 HG22 A:VAL101 4.2 11.4 0.0 ND1 A:HIS55 4.2 9.1 1.0 CG A:HIS55 4.2 8.5 1.0 CG A:HIS57 4.2 8.4 1.0 HZ A:KCX169 4.2 14.4 1.0 NE2 A:HIS230 4.3 13.6 1.0 CB A:ASP292 4.5 10.9 1.0 HA A:ASP292 4.5 12.3 1.0 HB2 A:ASP292 4.6 13.1 1.0 HD1 A:HIS57 4.9 10.6 1.0 HD1 A:HIS57 4.9 11.3 0.0 C2 A:CAC2407 4.9 14.5 0.6 HD1 A:HIS55 5.0 10.9 1.0 HD11 A:LEU106 5.0 12.9 0.0

Zinc binding site 2 out of 4 in the Phosphotriesterase Variant S5DELTAL7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant S5DELTAL7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:12.6 occ:0.86 OQ1 A:KCX169 1.9 12.3 1.0 O1 A:CAC2407 1.9 12.0 0.6 NE2 A:HIS230 2.0 13.6 1.0 ND1 A:HIS201 2.1 13.7 1.0 O2 A:CAC2407 2.8 10.6 0.6 CE1 A:HIS201 2.9 16.7 1.0 CX A:KCX169 3.0 12.4 1.0 AS A:CAC2407 3.0 13.3 0.6 HB2 A:HIS201 3.0 15.5 1.0 CD2 A:HIS230 3.0 13.2 1.0 CE1 A:HIS230 3.0 14.2 1.0 HE1 A:HIS201 3.1 20.0 1.0 HE1 A:TRP131 3.1 15.8 1.0 CG A:HIS201 3.1 14.2 1.0 HD2 A:HIS230 3.2 15.9 1.0 HE1 A:HIS230 3.3 17.0 1.0 OQ2 A:KCX169 3.3 11.2 1.0 HE1 A:HIS55 3.5 11.9 1.0 CB A:HIS201 3.5 12.9 1.0 O A:HOH2501 3.6 8.0 1.0 ZN A:ZN2401 3.7 9.9 1.0 NE1 A:TRP131 3.9 13.2 1.0 HA A:HIS201 4.0 14.8 1.0 NE2 A:HIS201 4.1 17.5 1.0 NZ A:KCX169 4.1 12.0 1.0 CE1 A:HIS55 4.1 9.9 1.0 ND1 A:HIS230 4.1 13.9 1.0 HD1 A:TRP131 4.1 14.5 1.0 CG A:HIS230 4.2 13.1 1.0 CD2 A:HIS201 4.2 16.3 1.0 HE2 A:KCX169 4.2 15.2 1.0 NE2 A:HIS55 4.3 9.0 1.0 HB3 A:HIS201 4.3 15.5 1.0 C1 A:CAC2407 4.3 12.7 0.6 CA A:HIS201 4.3 12.3 1.0 CD1 A:TRP131 4.4 12.1 1.0 C2 A:CAC2407 4.4 14.5 0.6 CE A:KCX169 4.6 12.7 1.0 HE3 A:KCX169 4.6 15.2 1.0 HM2 A:MPD2404 4.6 48.5 1.0 OD2 A:ASP292 4.7 12.4 1.0 H12 A:MPD2404 4.8 50.2 1.0 HE2 A:HIS201 4.9 20.9 1.0 HD1 A:HIS230 4.9 16.7 1.0 HZ A:KCX169 4.9 14.4 1.0 O2 A:MPD2404 5.0 37.1 1.0

Zinc binding site 3 out of 4 in the Phosphotriesterase Variant S5DELTAL7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant S5DELTAL7 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2401 b:10.6 occ:1.00 O2 G:CAC2407 1.9 10.6 0.7 NE2 G:HIS57 2.0 9.3 1.0 NE2 G:HIS55 2.0 9.8 0.7 NE2 G:HIS55 2.1 9.5 0.3 OQ1 G:KCX169 2.1 11.6 1.0 OD1 G:ASP292 2.3 11.3 1.0 CE1 G:HIS57 2.9 9.0 1.0 CD2 G:HIS55 3.0 9.5 0.7 CD2 G:HIS55 3.0 9.5 0.3 CE1 G:HIS55 3.0 10.6 0.7 CX G:KCX169 3.1 11.7 1.0 HE1 G:HIS57 3.1 10.8 1.0 CD2 G:HIS57 3.1 8.8 1.0 CE1 G:HIS55 3.1 10.0 0.3 HD2 G:HIS55 3.1 11.4 0.7 HD2 G:HIS55 3.1 11.4 0.3 CG G:ASP292 3.2 10.8 1.0 AS G:CAC2407 3.2 12.8 0.7 HE1 G:HIS55 3.3 12.8 0.7 HE1 G:HIS55 3.3 12.0 0.3 HE1 G:HIS230 3.3 15.2 1.0 HD2 G:HIS57 3.3 10.5 1.0 OD2 G:ASP292 3.5 10.6 1.0 HG23 G:VAL101 3.5 11.2 0.7 OQ2 G:KCX169 3.5 11.3 1.0 O G:HOH2501 3.6 14.6 1.0 HG23 G:VAL101 3.6 14.8 0.3 C1 G:CAC2407 3.6 13.8 0.7 HG21 G:VAL101 3.7 14.8 0.3 ZN G:ZN2402 3.8 12.7 0.9 HG21 G:VAL101 3.9 11.2 0.7 CG2 G:VAL101 4.0 12.3 0.3 CG2 G:VAL101 4.0 9.3 0.7 CE1 G:HIS230 4.1 12.6 1.0 O1 G:CAC2407 4.1 11.6 0.7 HG22 G:VAL101 4.1 14.8 0.3 ND1 G:HIS57 4.1 8.5 1.0 NZ G:KCX169 4.1 10.5 1.0 ND1 G:HIS55 4.1 10.8 0.7 CG G:HIS55 4.1 9.9 0.7 HG22 G:VAL101 4.1 11.2 0.7 CG G:HIS55 4.2 9.8 0.3 ND1 G:HIS55 4.2 10.3 0.3 CG G:HIS57 4.2 8.6 1.0 HZ G:KCX169 4.2 12.6 1.0 NE2 G:HIS230 4.3 13.1 1.0 CB G:ASP292 4.5 9.9 1.0 HA G:ASP292 4.6 11.5 1.0 HB2 G:ASP292 4.7 11.9 1.0 C2 G:CAC2407 4.8 13.0 0.7 HD1 G:HIS57 4.9 10.2 1.0 HD1 G:HIS55 4.9 12.9 0.7 HD1 G:HIS55 5.0 12.3 0.3

Zinc binding site 4 out of 4 in the Phosphotriesterase Variant S5DELTAL7


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant S5DELTAL7 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2402 b:12.7 occ:0.87 O1 G:CAC2407 2.0 11.6 0.7 OQ2 G:KCX169 2.0 11.3 1.0 NE2 G:HIS230 2.0 13.1 1.0 ND1 G:HIS201 2.1 13.5 1.0 O2 G:CAC2407 2.8 10.6 0.7 CE1 G:HIS201 2.9 15.6 1.0 CD2 G:HIS230 3.0 14.3 1.0 HB2 G:HIS201 3.0 15.5 1.0 CX G:KCX169 3.0 11.7 1.0 AS G:CAC2407 3.0 12.8 0.7 HE1 G:HIS201 3.1 18.8 1.0 HE1 G:TRP131 3.1 15.8 1.0 CE1 G:HIS230 3.1 12.6 1.0 HE1 G:TRP131 3.1 16.2 0.0 HD2 G:HIS230 3.1 17.2 1.0 CG G:HIS201 3.1 13.3 1.0 HE1 G:HIS230 3.3 15.2 1.0 OQ1 G:KCX169 3.3 11.6 1.0 CB G:HIS201 3.5 12.9 1.0 HE1 G:HIS55 3.6 12.8 0.7 HE1 G:HIS55 3.6 12.0 0.3 O G:HOH2501 3.7 14.6 1.0 ZN G:ZN2401 3.8 10.6 1.0 NE1 G:TRP131 3.9 13.2 1.0 HA G:HIS201 3.9 14.0 1.0 NE1 G:TRP131 3.9 13.5 0.0 NE2 G:HIS201 4.1 17.6 1.0 CG G:HIS230 4.1 13.8 1.0 ND1 G:HIS230 4.2 14.1 1.0 NZ G:KCX169 4.2 10.5 1.0 CE1 G:HIS55 4.2 10.6 0.7 CD2 G:HIS201 4.2 14.9 1.0 CE1 G:HIS55 4.2 10.0 0.3 HE2 G:KCX169 4.2 12.4 1.0 HD1 G:TRP131 4.2 14.7 1.0 CA G:HIS201 4.3 11.6 1.0 HB3 G:HIS201 4.3 15.5 1.0 NE2 G:HIS55 4.3 9.8 0.7 NE2 G:HIS55 4.4 9.5 0.3 C2 G:CAC2407 4.4 13.0 0.7 C1 G:CAC2407 4.4 13.8 0.7 CD1 G:TRP131 4.5 12.2 1.0 HD1 G:TRP131 4.5 15.9 0.0 CE G:KCX169 4.6 10.3 1.0 CD1 G:TRP131 4.6 13.2 0.0 HE3 G:KCX169 4.7 12.4 1.0 OD2 G:ASP292 4.8 10.6 1.0 HE2 G:HIS201 4.9 21.1 1.0 HZ2 G:TRP131 4.9 16.6 0.0 HD1 G:HIS230 5.0 16.9 1.0 HZ G:KCX169 5.0 12.6 1.0 CE2 G:TRP131 5.0 13.6 0.0

C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki. Phosphotriesterase Variant S5DELTAL7 To Be Published.