Cobalt in PDB 7qte: Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate

The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate, PDB code: 7qte was solved by P.Lukat, M.Daum, A.Bechthold, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.24 / 1.81
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	116.077, 142.91, 109.072, 90, 90, 90
R / Rfree (%)	15.3 / 17.6

The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Cobalt atom in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate (pdb code 7qte). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate, PDB code: 7qte:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate


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 the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:18.4 occ:1.00 O3 A:SIN303 2.0 21.2 1.0 NE2 A:HIS237 2.1 16.6 1.0 O A:HOH401 2.1 23.3 1.0 OD1 A:ASP103 2.1 16.6 1.0 O A:HOH576 2.1 20.5 1.0 NE2 A:HIS101 2.2 16.6 1.0 C4 A:SIN303 2.9 38.9 1.0 CE1 A:HIS237 2.9 16.6 1.0 O4 A:SIN303 3.0 40.3 1.0 HE1 A:HIS237 3.1 20.0 1.0 CD2 A:HIS101 3.1 17.4 1.0 CG A:ASP103 3.1 21.6 1.0 CD2 A:HIS237 3.1 16.4 1.0 CE1 A:HIS101 3.2 18.4 1.0 HD2 A:HIS101 3.2 20.9 1.0 HE1 A:HIS101 3.4 22.1 1.0 HD2 A:HIS237 3.4 19.7 1.0 OD2 A:ASP103 3.4 23.0 1.0 ND1 A:HIS237 4.1 17.6 1.0 HZ2 A:TRP230 4.1 24.6 1.0 O A:HOH616 4.2 43.7 1.0 CG A:HIS237 4.2 16.1 1.0 CG A:HIS101 4.2 15.3 1.0 ND1 A:HIS101 4.2 18.4 1.0 O A:HOH672 4.3 29.9 1.0 C3 A:SIN303 4.3 40.6 1.0 HA A:ASP103 4.4 18.6 1.0 CB A:ASP103 4.5 18.6 1.0 H31 A:SIN303 4.5 48.7 1.0 HB3 A:ASP103 4.8 22.3 1.0 HH12 A:ARG251 4.8 40.9 1.0 HH11 A:ARG251 4.8 40.9 1.0 HD1 A:HIS237 4.8 21.1 1.0 CA A:ASP103 4.9 15.5 1.0 H32 A:SIN303 4.9 48.7 1.0 O A:HOH468 4.9 34.3 1.0 CZ2 A:TRP230 5.0 20.4 1.0 H A:ASP103 5.0 19.0 1.0

Cobalt binding site 2 out of 3 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate


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 the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:17.5 occ:1.00 NE2 B:HIS237 2.0 16.4 1.0 O4 B:SIN303 2.1 19.3 1.0 NE2 B:HIS101 2.1 16.0 1.0 O B:HOH403 2.1 24.8 1.0 O B:HOH521 2.1 21.0 1.0 OD1 B:ASP103 2.1 17.8 1.0 CE1 B:HIS237 2.9 19.5 1.0 C4 B:SIN303 2.9 34.9 1.0 HE1 B:HIS237 3.0 23.5 1.0 CD2 B:HIS101 3.1 18.6 1.0 O3 B:SIN303 3.1 38.2 1.0 CE1 B:HIS101 3.1 18.1 1.0 CG B:ASP103 3.1 21.1 1.0 CD2 B:HIS237 3.1 18.6 1.0 HD2 B:HIS101 3.2 22.4 1.0 HE1 B:HIS101 3.3 21.8 1.0 HD2 B:HIS237 3.4 22.3 1.0 OD2 B:ASP103 3.4 20.4 1.0 ND1 B:HIS237 4.0 16.9 1.0 HZ2 B:TRP230 4.1 26.9 1.0 CG B:HIS237 4.2 14.3 1.0 ND1 B:HIS101 4.2 15.9 1.0 CG B:HIS101 4.2 14.1 1.0 O B:HOH670 4.3 32.1 1.0 C3 B:SIN303 4.4 35.6 1.0 HA B:ASP103 4.4 18.6 1.0 CB B:ASP103 4.5 16.9 1.0 H31 B:SIN303 4.6 42.7 1.0 HH12 B:ARG251 4.7 49.4 1.0 HD1 B:HIS237 4.8 20.3 1.0 HH11 B:ARG251 4.8 49.4 1.0 CA B:ASP103 4.9 15.5 1.0 HB3 B:ASP103 4.9 20.3 1.0 CZ2 B:TRP230 4.9 22.4 1.0 O B:HOH703 4.9 48.6 1.0 H32 B:SIN303 4.9 42.7 1.0 HD1 B:HIS101 5.0 19.1 1.0 O B:HOH666 5.0 17.2 1.0 O B:HOH497 5.0 37.6 1.0

Cobalt binding site 3 out of 3 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate


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 the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Cobalt and Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Co302 b:24.0 occ:0.90 O B:HOH614 2.0 32.6 1.0 O B:HOH543 2.1 33.2 1.0 NE2 B:HIS79 2.2 30.1 1.0 CD2 B:HIS79 3.0 28.2 1.0 HD2 B:HIS79 3.1 33.9 1.0 CE1 B:HIS79 3.2 30.7 1.0 HE1 B:HIS79 3.5 36.9 1.0 O B:HOH726 4.1 37.0 1.0 HG3 B:PRO84 4.2 43.0 1.0 CG B:HIS79 4.2 28.4 1.0 O B:HOH555 4.2 40.4 1.0 ND1 B:HIS79 4.3 30.7 1.0 HB3 B:PRO84 4.4 35.6 1.0 O B:HOH632 4.4 40.4 1.0 O B:HOH513 4.7 46.0 1.0 HA B:PRO84 4.8 35.1 1.0 O B:HOH520 4.9 49.0 1.0

P.Lukat, M.Daum, D.Zechel, A.Bechthold, O.Einsle. Structural Investigations on the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygense PLAO1 From Streptomyces Sp. TU6071 To Be Published.