Zinc in PDB 6bh7: Phosphotriesterase Variant R18+254S

The structure of Phosphotriesterase Variant R18+254S, PDB code: 6bh7 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)	29.04 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.673, 86.012, 88.676, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.8

The structure of Phosphotriesterase Variant R18+254S also contains other interesting chemical elements:

Arsenic

(As)

1 atom

The binding sites of Zinc atom in the Phosphotriesterase Variant R18+254S (pdb code 6bh7). 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 R18+254S, PDB code: 6bh7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Phosphotriesterase Variant R18+254S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Phosphotriesterase Variant R18+254S within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2401 b:15.0 occ:1.00 O A:HOH2532 2.0 19.5 1.0 NE2 A:HIS57 2.0 13.5 0.8 NE2 A:HIS57 2.1 14.7 0.2 NE2 A:HIS55 2.1 14.3 1.0 OQ2 A:KCX169 2.1 15.1 1.0 OD1 A:ASP301 2.2 15.2 1.0 NE2 A:HIS55 2.3 15.1 0.0 H11 A:MPD2403 2.9 60.9 1.0 CE1 A:HIS57 2.9 14.2 0.8 CE1 A:HIS57 3.0 14.7 0.2 CX A:KCX169 3.0 17.8 1.0 CG A:ASP301 3.0 17.4 1.0 CD2 A:HIS55 3.0 14.0 1.0 CD2 A:HIS55 3.1 15.1 0.0 CD2 A:HIS57 3.1 13.2 0.8 HE1 A:HIS57 3.1 17.1 0.8 HD2 A:HIS55 3.1 18.1 0.0 CE1 A:HIS55 3.1 16.1 1.0 HE1 A:HIS57 3.1 17.7 0.2 CD2 A:HIS57 3.1 14.6 0.2 HD2 A:HIS55 3.2 16.8 1.0 HE1 A:HIS55 3.3 19.4 1.0 OD2 A:ASP301 3.3 19.4 1.0 H32 A:MPD2403 3.3 61.2 1.0 HD2 A:HIS57 3.3 15.9 0.8 HD2 A:HIS57 3.3 17.5 0.2 OQ1 A:KCX169 3.3 18.4 1.0 CE1 A:HIS55 3.4 15.1 0.0 HG23 A:VAL101 3.5 15.5 0.0 HG23 A:VAL101 3.6 15.7 1.0 HE1 A:HIS55 3.7 18.1 0.0 ZN A:ZN2402 3.7 25.7 0.4 HG21 A:VAL101 3.8 15.5 0.0 H31 A:MPD2403 3.9 61.2 1.0 C1 A:MPD2403 3.9 50.8 1.0 HG21 A:VAL101 3.9 15.7 1.0 CG2 A:VAL101 4.0 12.9 0.0 CG2 A:VAL101 4.1 13.1 1.0 ND1 A:HIS57 4.1 13.7 0.8 C3 A:MPD2403 4.1 51.0 1.0 NZ A:KCX169 4.1 17.6 1.0 H13 A:MPD2403 4.1 60.9 1.0 ND1 A:HIS57 4.1 14.4 0.2 HG22 A:VAL101 4.1 15.7 1.0 CG A:HIS57 4.2 12.6 0.8 CG A:HIS55 4.2 13.8 1.0 ND1 A:HIS55 4.2 15.2 1.0 HG22 A:VAL101 4.2 15.5 0.0 CG A:HIS57 4.2 14.1 0.2 HZ A:KCX169 4.3 21.2 1.0 CG A:HIS55 4.3 15.0 0.0 H53 A:MPD2403 4.3 60.5 1.0 HA A:ASP301 4.3 18.1 1.0 CB A:ASP301 4.4 15.3 1.0 ND1 A:HIS55 4.4 15.1 0.0 H12 A:MPD2403 4.5 60.9 1.0 HB2 A:ASP301 4.7 18.4 1.0 C2 A:MPD2403 4.7 51.4 1.0 HD21 A:LEU106 4.8 18.2 0.8 HD1 A:HIS57 4.8 16.4 0.8 CA A:ASP301 4.9 15.1 1.0 HE1 A:TRP131 4.9 22.9 0.0 HD1 A:HIS57 4.9 17.3 0.2 HD11 A:LEU106 4.9 13.6 0.2 HD1 A:HIS55 5.0 18.2 1.0 HE1 A:TRP131 5.0 22.9 1.0

Zinc binding site 2 out of 4 in the Phosphotriesterase Variant R18+254S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Phosphotriesterase Variant R18+254S within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2402 b:25.7 occ:0.40 OQ1 A:KCX169 1.9 18.4 1.0 ND1 A:HIS201 2.1 30.0 1.0 O A:HOH2532 2.3 19.5 1.0 CG A:HIS201 2.4 28.5 1.0 CE1 A:HIS201 2.7 30.6 1.0 HB3 A:HIS201 2.7 31.5 1.0 CX A:KCX169 3.0 17.8 1.0 CB A:HIS201 3.0 26.2 1.0 CD2 A:HIS201 3.1 30.0 1.0 HE1 A:HIS201 3.1 36.7 1.0 NE2 A:HIS201 3.2 30.3 1.0 O A:HOH2628 3.3 43.4 1.0 HE1 A:HIS55 3.3 19.4 1.0 HB2 A:HIS201 3.4 31.5 1.0 OQ2 A:KCX169 3.5 15.1 1.0 HE1 A:HIS55 3.6 18.1 0.0 HE1 A:TRP131 3.6 22.9 0.0 HE1 A:TRP131 3.7 22.9 1.0 ZN A:ZN2401 3.7 15.0 1.0 HD2 A:HIS201 3.8 36.0 1.0 HE2 A:HIS201 3.9 36.3 1.0 CE1 A:HIS55 4.0 16.1 1.0 HE2 A:KCX169 4.0 22.6 1.0 NE2 A:HIS55 4.1 15.1 0.0 CE1 A:HIS55 4.1 15.1 0.0 OD2 A:ASP301 4.1 19.4 1.0 H13 A:MPD2403 4.1 60.9 1.0 NZ A:KCX169 4.2 17.6 1.0 NE2 A:HIS55 4.2 14.3 1.0 CA A:HIS201 4.4 24.3 1.0 NE1 A:TRP131 4.4 19.1 0.0 NE1 A:TRP131 4.4 19.1 1.0 HD1 A:TRP131 4.4 21.4 1.0 H11 A:MPD2403 4.5 60.9 1.0 CE A:KCX169 4.5 18.8 1.0 C A:HIS201 4.6 29.1 1.0 HE3 A:KCX169 4.6 22.6 1.0 H32 A:MPD2403 4.6 61.2 1.0 HD1 A:TRP131 4.7 22.6 0.0 HM2 A:MPD2403 4.7 60.8 1.0 C1 A:MPD2403 4.8 50.8 1.0 CD1 A:TRP131 4.8 17.9 1.0 O A:HIS201 4.8 29.8 1.0 HA A:HIS201 4.9 29.1 1.0 HZ A:KCX169 4.9 21.2 1.0 CG A:ASP301 4.9 17.4 1.0 CD1 A:TRP131 5.0 18.8 0.0 OD1 A:ASP301 5.0 15.2 1.0

Zinc binding site 3 out of 4 in the Phosphotriesterase Variant R18+254S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Phosphotriesterase Variant R18+254S within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2401 b:18.3 occ:1.00 O2 G:CAC2403 1.8 18.5 0.8 NE2 G:HIS57 2.0 18.1 1.0 NE2 G:HIS55 2.1 18.8 1.0 OQ2 G:KCX169 2.1 19.0 1.0 OD1 G:ASP301 2.3 20.4 1.0 CE1 G:HIS57 2.9 17.4 1.0 CD2 G:HIS55 3.0 19.2 1.0 CX G:KCX169 3.0 18.7 1.0 HE1 G:HIS57 3.1 20.9 1.0 CE1 G:HIS55 3.1 19.7 1.0 CD2 G:HIS57 3.1 18.7 1.0 HD2 G:HIS55 3.1 23.0 1.0 CG G:ASP301 3.1 21.5 1.0 AS G:CAC2403 3.2 19.0 0.8 HE1 G:HIS55 3.3 23.7 1.0 HD2 G:HIS57 3.3 22.4 1.0 OD2 G:ASP301 3.4 22.1 1.0 HG23 G:VAL101 3.4 22.4 1.0 OQ1 G:KCX169 3.4 18.8 1.0 HE1 G:HIS230 3.5 25.2 1.0 C1 G:CAC2403 3.7 19.4 0.8 HG21 G:VAL101 3.9 22.4 1.0 ZN G:ZN2402 3.9 18.4 0.8 CG2 G:VAL101 4.0 18.7 1.0 O1 G:CAC2403 4.0 16.7 0.8 HG22 G:VAL101 4.1 22.4 1.0 ND1 G:HIS57 4.1 17.7 1.0 NZ G:KCX169 4.1 18.7 1.0 CG G:HIS55 4.1 18.8 1.0 ND1 G:HIS55 4.2 19.6 1.0 CG G:HIS57 4.2 18.6 1.0 CE1 G:HIS230 4.2 21.0 1.0 HZ G:KCX169 4.3 22.5 1.0 NE2 G:HIS230 4.5 21.0 1.0 CB G:ASP301 4.5 20.9 1.0 HA G:ASP301 4.5 24.8 1.0 HD21 G:LEU106 4.6 24.3 0.8 HB2 G:ASP301 4.6 25.1 1.0 C2 G:CAC2403 4.8 19.6 0.8 HD1 G:HIS57 4.8 21.2 1.0 HD11 G:LEU106 4.9 14.8 0.2 HD1 G:HIS55 5.0 23.6 1.0

Zinc binding site 4 out of 4 in the Phosphotriesterase Variant R18+254S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Phosphotriesterase Variant R18+254S within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn2402 b:18.4 occ:0.83 OQ1 G:KCX169 1.9 18.8 1.0 O1 G:CAC2403 1.9 16.7 0.8 NE2 G:HIS230 2.0 21.0 1.0 ND1 G:HIS201 2.1 19.6 1.0 CD2 G:HIS230 2.9 21.4 1.0 CE1 G:HIS201 3.0 21.2 1.0 HB2 G:HIS201 3.0 24.9 1.0 CX G:KCX169 3.0 18.7 1.0 HD2 G:HIS230 3.1 25.6 1.0 O2 G:CAC2403 3.1 18.5 0.8 CE1 G:HIS230 3.1 21.0 1.0 AS G:CAC2403 3.1 19.0 0.8 HE1 G:HIS201 3.1 25.4 1.0 CG G:HIS201 3.1 20.6 1.0 HE1 G:TRP131 3.1 23.5 1.0 HE1 G:HIS230 3.3 25.2 1.0 OQ2 G:KCX169 3.4 19.0 1.0 CB G:HIS201 3.5 20.7 1.0 HE1 G:HIS55 3.6 23.7 1.0 NE1 G:TRP131 3.9 19.6 1.0 HA G:HIS201 3.9 25.1 1.0 ZN G:ZN2401 3.9 18.3 1.0 O G:HOH2642 4.0 28.2 1.0 NE2 G:HIS201 4.1 23.1 1.0 CG G:HIS230 4.1 21.0 1.0 ND1 G:HIS230 4.1 21.1 1.0 NZ G:KCX169 4.2 18.7 1.0 CD2 G:HIS201 4.2 22.6 1.0 HD1 G:TRP131 4.2 23.2 1.0 CE1 G:HIS55 4.2 19.7 1.0 HE2 G:KCX169 4.2 22.5 1.0 C2 G:CAC2403 4.3 19.6 0.8 HB3 G:HIS201 4.3 24.9 1.0 CA G:HIS201 4.3 21.0 1.0 NE2 G:HIS55 4.4 18.8 1.0 CD1 G:TRP131 4.5 19.3 1.0 HE3 G:KCX169 4.6 22.5 1.0 CE G:KCX169 4.6 18.8 1.0 C1 G:CAC2403 4.6 19.4 0.8 OD2 G:ASP301 4.8 22.1 1.0 HE2 G:HIS201 4.9 27.7 1.0 HD1 G:HIS230 4.9 25.3 1.0 HZ G:KCX169 5.0 22.5 1.0

C.M.Miton, E.C.Campbell, C.J.Jackson, N.Tokuriki. Phosphotriesterase Variant R18+254S To Be Published.