Cobalt in PDB 4wvx: Crystal Structure of A Phosphotriesterase-Like Lactonase Gkap in Native Form

The structure of Crystal Structure of A Phosphotriesterase-Like Lactonase Gkap in Native Form, PDB code: 4wvx was solved by J.An, Y.Zhang, G.Y.Yang, Y.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.398, 89.380, 89.915, 90.00, 99.33, 90.00
R / Rfree (%)	16.6 / 19.2

The binding sites of Cobalt atom in the Crystal Structure of A Phosphotriesterase-Like Lactonase Gkap in Native Form (pdb code 4wvx). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of A Phosphotriesterase-Like Lactonase Gkap in Native Form, PDB code: 4wvx:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of A Phosphotriesterase-Like Lactonase Gkap in Native Form


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of A Phosphotriesterase-Like Lactonase Gkap in Native Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:11.6 occ:1.00 O A:HOH672 2.0 30.0 1.0 NE2 A:HIS25 2.2 8.5 1.0 OQ2 A:KCX145 2.2 7.7 1.0 OD1 A:ASP266 2.2 7.0 1.0 NE2 A:HIS23 2.2 7.5 1.0 CE1 A:HIS25 3.0 8.3 1.0 CD2 A:HIS23 3.1 7.4 1.0 CX A:KCX145 3.1 7.9 1.0 CG A:ASP266 3.1 7.3 1.0 CD2 A:HIS25 3.2 8.2 1.0 CE1 A:HIS23 3.3 7.5 1.0 OQ1 A:KCX145 3.4 7.9 1.0 OD2 A:ASP266 3.4 7.8 1.0 CO A:CO402 3.5 13.8 1.0 ND1 A:HIS25 4.2 8.2 1.0 NZ A:KCX145 4.2 7.8 1.0 CG A:HIS23 4.3 7.4 1.0 CE1 A:HIS206 4.3 9.1 1.0 CG A:HIS25 4.3 8.0 1.0 ND1 A:HIS23 4.3 7.4 1.0 NE2 A:HIS206 4.4 8.9 1.0 O2 A:EDO403 4.4 40.9 1.0 CB A:ASP266 4.5 7.2 1.0 CG A:PRO69 4.7 8.8 1.0 CA A:ASP266 4.9 7.2 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of A Phosphotriesterase-Like Lactonase Gkap in Native Form


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of A Phosphotriesterase-Like Lactonase Gkap in Native Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:13.8 occ:1.00 O A:HOH672 2.0 30.0 1.0 OQ1 A:KCX145 2.1 7.9 1.0 NE2 A:HIS206 2.2 8.9 1.0 ND1 A:HIS178 2.2 7.6 1.0 CX A:KCX145 3.1 7.9 1.0 CD2 A:HIS206 3.1 9.1 1.0 CE1 A:HIS178 3.2 7.6 1.0 CG A:HIS178 3.2 7.8 1.0 CE1 A:HIS206 3.2 9.1 1.0 OQ2 A:KCX145 3.4 7.7 1.0 CB A:HIS178 3.5 8.0 1.0 CO A:CO401 3.5 11.6 1.0 NH2 A:ARG230 3.5 19.0 1.0 CE1 A:TYR99 3.9 17.4 1.0 OH A:TYR99 4.0 22.1 1.0 OD2 A:ASP266 4.2 7.8 1.0 NZ A:KCX145 4.3 7.8 1.0 NE2 A:HIS178 4.3 7.8 1.0 NE2 A:HIS23 4.3 7.5 1.0 CG A:HIS206 4.3 9.3 1.0 ND1 A:HIS206 4.3 9.3 1.0 CD2 A:HIS178 4.3 7.7 1.0 CE1 A:HIS23 4.3 7.5 1.0 CA A:HIS178 4.4 8.5 1.0 CZ A:TYR99 4.4 18.4 1.0 CZ A:ARG230 4.4 18.2 1.0 CE A:KCX145 4.7 7.8 1.0 NE A:ARG230 4.8 15.5 1.0 OD1 A:ASP266 4.8 7.0 1.0 CG A:ASP266 4.9 7.3 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of A Phosphotriesterase-Like Lactonase Gkap in Native Form


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of A Phosphotriesterase-Like Lactonase Gkap in Native Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:11.2 occ:1.00 O B:HOH606 1.9 14.2 1.0 OQ1 B:KCX145 2.1 8.6 1.0 NE2 B:HIS25 2.2 7.9 1.0 OD1 B:ASP266 2.2 7.6 1.0 NE2 B:HIS23 2.2 7.7 1.0 CX B:KCX145 3.1 9.0 1.0 CD2 B:HIS23 3.1 7.7 1.0 CE1 B:HIS25 3.1 8.0 1.0 CG B:ASP266 3.1 7.8 1.0 CD2 B:HIS25 3.2 7.8 1.0 CE1 B:HIS23 3.3 7.6 1.0 OQ2 B:KCX145 3.3 8.9 1.0 OD2 B:ASP266 3.4 8.1 1.0 CO B:CO402 3.4 13.7 1.0 NZ B:KCX145 4.2 8.8 1.0 ND1 B:HIS25 4.2 7.9 1.0 CE1 B:HIS206 4.3 7.6 1.0 CG B:HIS23 4.3 7.7 1.0 CG B:HIS25 4.3 7.8 1.0 ND1 B:HIS23 4.3 7.6 1.0 NE2 B:HIS206 4.4 7.7 1.0 CB B:ASP266 4.5 7.8 1.0 CG B:PRO69 4.5 8.9 1.0 CA B:ASP266 4.9 8.0 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of A Phosphotriesterase-Like Lactonase Gkap in Native Form


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of A Phosphotriesterase-Like Lactonase Gkap in Native Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Co402 b:13.7 occ:1.00 OQ2 B:KCX145 2.0 8.9 1.0 O B:HOH606 2.1 14.2 1.0 NE2 B:HIS206 2.2 7.7 1.0 ND1 B:HIS178 2.3 7.3 1.0 CX B:KCX145 3.0 9.0 1.0 CD2 B:HIS206 3.2 7.7 1.0 CE1 B:HIS206 3.2 7.6 1.0 CG B:HIS178 3.2 7.3 1.0 CE1 B:HIS178 3.2 7.3 1.0 OQ1 B:KCX145 3.4 8.6 1.0 CO B:CO401 3.4 11.2 1.0 CB B:HIS178 3.4 7.3 1.0 NH2 B:ARG230 3.6 14.2 1.0 CE1 B:TYR99 4.0 15.8 1.0 OD2 B:ASP266 4.2 8.1 1.0 NZ B:KCX145 4.2 8.8 1.0 NE2 B:HIS23 4.2 7.7 1.0 OH B:TYR99 4.3 19.7 1.0 ND1 B:HIS206 4.3 7.6 1.0 CE1 B:HIS23 4.3 7.6 1.0 CG B:HIS206 4.3 7.6 1.0 CA B:HIS178 4.3 7.5 1.0 NE2 B:HIS178 4.4 7.4 1.0 CD2 B:HIS178 4.4 7.2 1.0 CZ B:ARG230 4.4 13.6 1.0 CZ B:TYR99 4.6 16.4 1.0 CE B:KCX145 4.6 8.9 1.0 OD1 B:ASP266 4.7 7.6 1.0 NE B:ARG230 4.8 12.6 1.0 CG B:ASP266 4.8 7.8 1.0

J.An, Y.Zhang, G.Y.Yang, Y.Feng. Engineering A Thermostable Lactonase For Enhanced Phosphotriesterase Activity Against Organophosphate Pesticides To Be Published.