Sodium in PDB 7qtd: Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and Alpha-Ketoglutarate

The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and Alpha-Ketoglutarate, PDB code: 7qtd 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)	63.90 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.124, 108.215, 116.408, 90, 94.75, 90
R / Rfree (%)	14.1 / 16.5

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

Iron

(Fe)

4 atoms

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

Sodium binding site 1 out of 2 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Iron and Alpha-Ketoglutarate


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 Iron and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:49.3 occ:1.00 O D:HOH566 2.4 43.0 1.0 O D:HOH551 2.5 33.3 1.0 OD1 B:ASP280 2.8 29.7 1.0 O D:HOH582 2.9 30.1 1.0 HG2 D:ARG209 3.0 37.7 1.0 OD2 B:ASP280 3.2 30.0 1.0 CG B:ASP280 3.3 29.6 1.0 HA D:PHE210 3.4 15.9 1.0 HD1 D:PHE210 3.5 19.0 1.0 HE D:ARG209 3.5 86.7 1.0 HB2 D:PHE210 3.8 16.0 1.0 HE1 D:TYR206 3.9 17.1 1.0 HD3 D:ARG209 3.9 60.6 1.0 CG D:ARG209 3.9 31.4 1.0 NE D:ARG209 4.0 72.2 1.0 O B:HOH637 4.0 43.6 1.0 CA D:PHE210 4.1 13.2 1.0 CD D:ARG209 4.1 50.5 1.0 HH D:TYR206 4.2 20.6 1.0 O B:HOH425 4.3 34.2 1.0 HB3 B:ASN198 4.3 17.0 1.0 N D:PHE210 4.3 13.5 1.0 CE1 D:TYR206 4.3 14.2 1.0 CD1 D:PHE210 4.3 15.8 1.0 HB3 D:ARG209 4.4 25.9 1.0 CB D:PHE210 4.4 13.4 1.0 H D:PHE210 4.5 16.2 1.0 HG3 D:ARG209 4.5 37.7 1.0 C D:ARG209 4.6 17.1 1.0 O D:HOH486 4.6 40.2 1.0 OH D:TYR206 4.7 17.1 1.0 HD22 B:ASN198 4.7 26.9 1.0 CB D:ARG209 4.7 21.6 1.0 CZ D:TYR206 4.8 15.5 1.0 O D:ARG209 4.8 15.2 1.0 CB B:ASP280 4.8 23.9 1.0 HG D:SER213 4.8 27.6 1.0 HH21 D:ARG209 4.8 77.2 1.0 OG D:SER213 4.8 23.0 1.0 CZ D:ARG209 4.9 77.8 1.0 HB3 B:ASP280 4.9 28.7 1.0 CG D:PHE210 4.9 14.6 1.0 ND2 B:ASN198 5.0 22.4 1.0

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


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 Iron and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na305 b:49.1 occ:1.00 O A:HOH535 2.5 35.1 1.0 O A:HOH578 2.6 45.3 1.0 O A:HOH613 2.7 32.5 1.0 OD1 C:ASP280 2.8 29.1 1.0 HG2 A:ARG209 3.1 33.6 1.0 OD2 C:ASP280 3.1 31.0 1.0 CG C:ASP280 3.3 28.4 1.0 HA A:PHE210 3.4 18.4 1.0 HD1 A:PHE210 3.5 17.8 1.0 HB2 A:PHE210 3.7 15.5 1.0 HE A:ARG209 3.7 96.3 1.0 HE1 A:TYR206 3.9 19.5 1.0 CG A:ARG209 4.0 28.0 1.0 HD3 A:ARG209 4.0 66.0 1.0 CA A:PHE210 4.1 15.3 1.0 NE A:ARG209 4.1 80.2 1.0 O C:HOH637 4.2 43.5 1.0 N A:PHE210 4.2 14.4 1.0 CD A:ARG209 4.3 55.0 1.0 CB A:PHE210 4.3 12.9 1.0 HB3 C:ASN198 4.3 16.6 1.0 O C:HOH414 4.3 34.5 1.0 HB3 A:ARG209 4.3 25.2 1.0 CE1 A:TYR206 4.3 16.2 1.0 CD1 A:PHE210 4.4 14.8 1.0 H A:PHE210 4.5 17.2 1.0 O A:HOH567 4.5 46.1 1.0 C A:ARG209 4.6 15.4 1.0 HG3 A:ARG209 4.6 33.6 1.0 OH A:TYR206 4.6 18.5 1.0 CB A:ARG209 4.7 21.0 1.0 CZ A:TYR206 4.7 15.8 1.0 CB C:ASP280 4.8 25.1 1.0 HG A:SER213 4.8 30.3 1.0 O A:ARG209 4.8 15.8 1.0 OG A:SER213 4.8 25.3 1.0 CG A:PHE210 4.8 11.9 1.0 HD22 C:ASN198 4.8 24.5 1.0 HB3 C:ASP280 4.9 30.1 1.0 HH21 A:ARG209 4.9 82.6 1.0 CZ A:ARG209 4.9 82.9 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.