Sodium 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:

Cobalt

(Co)

3 atoms

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3;

Sodium 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 Sodium with other atoms in the Na 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 B:Na304 b:24.5 occ:1.00 OD2 B:ASP280 2.6 28.0 1.0 O B:ASN198 2.7 13.0 1.0 O B:HOH482 2.8 25.6 1.0 HB2 B:ASP280 2.8 23.3 1.0 HB2 B:ASP201 3.0 15.3 1.0 HB2 B:ALA202 3.1 17.3 1.0 HB3 B:ASN198 3.4 17.4 1.0 HA B:ASN198 3.5 15.7 1.0 CG B:ASP280 3.5 26.2 1.0 H B:ALA202 3.5 16.9 1.0 CB B:ASP280 3.6 19.5 1.0 C B:ASN198 3.6 15.1 1.0 HB3 B:ASP201 3.8 15.3 1.0 CB B:ASP201 3.8 12.8 1.0 HD22 B:ASN198 3.9 24.8 1.0 H B:ASP280 3.9 23.1 1.0 N B:ALA202 3.9 14.1 1.0 CA B:ASN198 3.9 13.1 1.0 CB B:ALA202 4.0 14.4 1.0 HB3 B:ASP280 4.1 23.3 1.0 CB B:ASN198 4.1 14.5 1.0 HA B:ALA202 4.3 14.9 1.0 CA B:ALA202 4.3 12.4 1.0 HB3 B:ALA202 4.4 17.3 1.0 C B:ASP201 4.6 13.0 1.0 N B:ASP280 4.6 19.3 1.0 HB1 B:ALA202 4.6 17.3 1.0 ND2 B:ASN198 4.6 20.7 1.0 OD2 B:ASP201 4.7 16.6 1.0 CZ3 B:TRP281 4.7 23.8 1.0 OD1 B:ASP280 4.7 27.4 1.0 CA B:ASP280 4.7 19.3 1.0 CA B:ASP201 4.8 14.8 1.0 HZ3 B:TRP281 4.8 28.6 1.0 N B:GLU199 4.8 12.3 1.0 CG B:ASP201 4.8 18.6 1.0 CE3 B:TRP281 4.8 35.4 1.0 HB2 B:ASN198 4.8 17.4 1.0 HA B:GLU199 4.9 16.4 1.0 CH2 B:TRP281 4.9 26.6 1.0 H B:ASP201 4.9 18.5 1.0 CG B:ASN198 5.0 18.1 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na305 b:47.9 occ:1.00 O B:HOH713 2.5 46.3 1.0 O B:HOH720 2.6 53.4 1.0 O B:HOH697 2.6 47.3 1.0 O B:ARG66 2.9 27.3 1.0 HB3 B:ARG66 3.2 31.5 1.0 O B:GLY69 3.3 26.4 1.0 HG2 B:ARG66 3.4 38.2 1.0 HA B:ARG66 3.5 33.2 1.0 C B:GLY69 3.5 24.3 1.0 HA2 B:GLY69 3.7 31.9 1.0 C B:ARG66 3.8 24.8 1.0 CB B:ARG66 3.8 26.3 1.0 HA B:GLU70 3.9 27.2 1.0 CA B:ARG66 3.9 27.7 1.0 CA B:GLY69 4.0 26.6 1.0 H B:GLY69 4.1 31.8 1.0 CG B:ARG66 4.1 31.8 1.0 N B:GLU70 4.1 22.6 1.0 O B:HOH668 4.2 54.1 1.0 N B:GLY69 4.4 26.4 1.0 HD3 B:ARG66 4.5 38.3 1.0 CA B:GLU70 4.5 22.7 1.0 H B:GLU70 4.7 27.1 1.0 HB2 B:ARG66 4.7 31.5 1.0 O B:HOH681 4.8 42.5 1.0 HG3 B:ARG66 4.8 38.2 1.0 CD B:ARG66 4.9 31.9 1.0 O B:HOH769 4.9 49.4 1.0 O B:HOH601 4.9 29.4 1.0 HA3 B:GLY69 4.9 31.9 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na306 b:54.2 occ:1.00 O B:HOH707 2.5 27.0 1.0 HB B:THR258 2.6 30.9 1.0 O B:THR258 2.9 18.2 1.0 HG B:SER260 3.0 33.4 1.0 OD2 A:ASP32 3.1 41.3 1.0 O A:HOH697 3.1 37.0 1.0 O B:HOH672 3.1 37.0 1.0 HB3 A:ASP32 3.3 33.8 1.0 OG B:SER260 3.4 27.8 1.0 CB B:THR258 3.6 25.7 1.0 CG A:ASP32 3.8 40.4 1.0 HB2 B:SER260 3.9 23.8 1.0 HG22 B:THR258 3.9 34.8 1.0 C B:THR258 3.9 19.1 1.0 H B:THR258 4.0 24.4 1.0 CB A:ASP32 4.0 28.1 1.0 O B:HOH454 4.1 17.7 1.0 CG2 B:THR258 4.2 29.0 1.0 HB3 B:PRO175 4.2 22.4 1.0 CA B:THR258 4.2 18.9 1.0 CB B:SER260 4.2 19.8 1.0 HB2 A:ASP32 4.3 33.8 1.0 O A:HOH543 4.3 23.6 1.0 HG21 B:THR258 4.3 34.8 1.0 HG3 B:PRO175 4.4 28.5 1.0 N B:THR258 4.5 20.3 1.0 OG1 B:THR258 4.5 23.9 1.0 HG1 B:THR258 4.6 28.7 1.0 OD1 A:ASP32 4.8 32.8 1.0 O B:HOH427 4.8 38.9 1.0 O B:HOH449 4.8 31.5 1.0 HB3 B:SER260 4.8 23.8 1.0 HH21 B:ARG172 4.8 19.9 1.0 H B:SER260 5.0 18.2 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.