Cobalt in PDB 3cak: X-Ray Structure of Wt Pte with Ethyl Phosphate

All present enzymatic activity of X-Ray Structure of Wt Pte with Ethyl Phosphate:
3.1.8.1;

The structure of X-Ray Structure of Wt Pte with Ethyl Phosphate, PDB code: 3cak was solved by J.Kim, P.-C.Tsai, S.C.Almo, F.M.Raushel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.49 / 1.83
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.286, 45.338, 78.913, 104.73, 93.40, 97.65
R / Rfree (%)	14 / 19.6

The binding sites of Cobalt atom in the X-Ray Structure of Wt Pte with Ethyl Phosphate (pdb code 3cak). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the X-Ray Structure of Wt Pte with Ethyl Phosphate, PDB code: 3cak:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the X-Ray Structure of Wt Pte with Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of X-Ray Structure of Wt Pte with Ethyl Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Co4 b:19.3 occ:0.90 OQ1 A:KCX169 1.9 19.0 1.0 NE2 A:HIS230 2.1 18.3 1.0 O4 A:DPF1 2.2 21.8 0.9 ND1 A:HIS201 2.2 17.0 1.0 CD2 A:HIS230 2.9 16.8 1.0 CX A:KCX169 3.0 17.6 1.0 CE1 A:HIS201 3.1 18.7 1.0 P1 A:DPF1 3.1 22.5 0.9 CG A:HIS201 3.2 16.9 1.0 O2 A:DPF1 3.2 19.9 0.9 CE1 A:HIS230 3.2 17.6 1.0 OQ2 A:KCX169 3.3 17.0 1.0 CB A:HIS201 3.5 16.2 1.0 CO A:CO5 4.0 15.4 1.0 NE1 A:TRP131 4.1 14.8 1.0 NZ A:KCX169 4.1 15.5 1.0 CG A:HIS230 4.1 16.6 1.0 ND1 A:HIS230 4.2 15.2 1.0 O3 A:DPF1 4.2 20.5 0.9 CE1 A:HIS55 4.2 13.0 1.0 NE2 A:HIS201 4.3 19.2 1.0 CD2 A:HIS201 4.3 17.1 1.0 O1 A:DPF1 4.3 22.2 0.9 CA A:HIS201 4.3 16.9 1.0 O A:HOH1012 4.4 18.7 1.0 NE2 A:HIS55 4.5 13.1 1.0 CE A:KCX169 4.6 13.0 1.0 CD1 A:TRP131 4.6 13.7 1.0 OD2 A:ASP301 4.8 11.3 1.0

Cobalt binding site 2 out of 4 in the X-Ray Structure of Wt Pte with Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of X-Ray Structure of Wt Pte with Ethyl Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Co5 b:15.4 occ:1.00 O2 A:DPF1 2.0 19.9 0.9 NE2 A:HIS57 2.0 10.6 1.0 NE2 A:HIS55 2.1 13.1 1.0 OQ2 A:KCX169 2.1 17.0 1.0 OD1 A:ASP301 2.4 12.0 1.0 CE1 A:HIS57 3.0 11.0 1.0 CD2 A:HIS55 3.1 12.8 1.0 CX A:KCX169 3.1 17.6 1.0 CD2 A:HIS57 3.1 9.6 1.0 CE1 A:HIS55 3.1 13.0 1.0 P1 A:DPF1 3.1 22.5 0.9 CG A:ASP301 3.2 11.8 1.0 OD2 A:ASP301 3.4 11.3 1.0 O3 A:DPF1 3.5 20.5 0.9 OQ1 A:KCX169 3.6 19.0 1.0 O4 A:DPF1 3.9 21.8 0.9 CO A:CO4 4.0 19.3 0.9 CG2 A:VAL101 4.0 10.6 1.0 NZ A:KCX169 4.1 15.5 1.0 ND1 A:HIS57 4.1 10.7 1.0 ND1 A:HIS55 4.2 12.3 1.0 CG A:HIS57 4.2 9.5 1.0 CG A:HIS55 4.2 13.7 1.0 C1 A:DPF1 4.2 21.1 0.9 CE1 A:HIS230 4.3 17.6 1.0 O1 A:DPF1 4.3 22.2 0.9 C2 A:DPF1 4.4 23.8 0.9 NE2 A:HIS230 4.4 18.3 1.0 CB A:ASP301 4.6 11.4 1.0 C4 A:DPF1 4.9 20.0 0.9

Cobalt binding site 3 out of 4 in the X-Ray Structure of Wt Pte with Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of X-Ray Structure of Wt Pte with Ethyl Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1 b:14.7 occ:1.00 O4 B:EFS906 1.9 16.4 0.9 OQ1 B:KCX169 2.1 14.2 1.0 NE2 B:HIS55 2.1 8.8 1.0 NE2 B:HIS57 2.1 9.8 1.0 OD1 B:ASP301 2.5 12.1 1.0 CD2 B:HIS55 3.0 10.5 1.0 CX B:KCX169 3.1 16.2 1.0 CE1 B:HIS57 3.1 10.1 1.0 CD2 B:HIS57 3.1 7.8 1.0 CE1 B:HIS55 3.1 10.8 1.0 P B:EFS906 3.1 17.6 0.9 CG B:ASP301 3.2 12.1 1.0 OD2 B:ASP301 3.4 12.7 1.0 O2 B:EFS906 3.4 16.6 0.9 OQ2 B:KCX169 3.5 16.4 1.0 O1 B:EFS906 3.9 15.5 0.9 CO B:CO2 3.9 17.4 1.0 C11 B:EFS906 4.0 17.6 0.9 CG2 B:VAL101 4.0 12.3 1.0 NZ B:KCX169 4.1 14.7 1.0 ND1 B:HIS55 4.2 11.7 1.0 CG B:HIS55 4.2 11.2 1.0 ND1 B:HIS57 4.2 10.0 1.0 CG B:HIS57 4.2 7.8 1.0 CE1 B:HIS230 4.2 15.5 1.0 O3 B:EFS906 4.3 17.5 0.9 NE2 B:HIS230 4.5 15.4 1.0 CB B:ASP301 4.5 10.4 1.0

Cobalt binding site 4 out of 4 in the X-Ray Structure of Wt Pte with Ethyl Phosphate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of X-Ray Structure of Wt Pte with Ethyl Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Co2 b:17.4 occ:1.00 OQ2 B:KCX169 1.9 16.4 1.0 O1 B:EFS906 2.0 15.5 0.9 ND1 B:HIS201 2.1 15.4 1.0 NE2 B:HIS230 2.1 15.4 1.0 CX B:KCX169 3.0 16.2 1.0 P B:EFS906 3.0 17.6 0.9 CE1 B:HIS201 3.0 16.8 1.0 O4 B:EFS906 3.0 16.4 0.9 CD2 B:HIS230 3.0 14.9 1.0 CG B:HIS201 3.1 16.6 1.0 CE1 B:HIS230 3.1 15.5 1.0 OQ1 B:KCX169 3.4 14.2 1.0 CB B:HIS201 3.5 14.4 1.0 CO B:CO1 3.9 14.7 1.0 NE1 B:TRP131 4.0 12.0 1.0 O3 B:EFS906 4.1 17.5 0.9 NZ B:KCX169 4.1 14.7 1.0 O2 B:EFS906 4.1 16.6 0.9 NE2 B:HIS201 4.1 17.3 1.0 CA B:HIS201 4.2 14.9 1.0 CG B:HIS230 4.2 14.1 1.0 CD2 B:HIS201 4.2 15.9 1.0 CE1 B:HIS55 4.2 10.8 1.0 ND1 B:HIS230 4.2 14.0 1.0 NE2 B:HIS55 4.4 8.8 1.0 O B:HOH1757 4.4 25.9 1.0 CD1 B:TRP131 4.5 12.8 1.0 CE B:KCX169 4.5 13.5 1.0 O B:HOH1514 4.8 29.7 1.0 OD2 B:ASP301 4.8 12.7 1.0

J.Kim, P.C.Tsai, S.L.Chen, F.Himo, S.C.Almo, F.M.Raushel. Structure of Diethyl Phosphate Bound to the Binuclear Metal Center of Phosphotriesterase. Biochemistry V. 47 9497 2008.
ISSN: ISSN 0006-2960
PubMed: 18702530
DOI: 10.1021/BI800971V