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

The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Sodium Succinate, PDB code: 7qtf 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)	48.46 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.894, 108.172, 115.033, 90, 93.87, 90
R / Rfree (%)	15.1 / 17.3

The binding sites of Sodium atom in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Sodium Succinate (pdb code 7qtf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Sodium Succinate, PDB code: 7qtf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Sodium 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 Sodium Succinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:22.4 occ:0.68 NE2 A:HIS237 2.1 23.4 1.0 O2 A:SIN302 2.1 44.5 0.9 OD1 A:ASP103 2.2 24.3 1.0 NE2 A:HIS101 2.2 23.6 1.0 HE1 A:HIS237 2.7 23.2 1.0 CE1 A:HIS237 2.7 19.3 1.0 CD2 A:HIS101 2.9 23.6 1.0 HD2 A:HIS101 2.9 28.3 1.0 C1 A:SIN302 3.0 53.3 0.9 O1 A:SIN302 3.1 51.0 0.9 CG A:ASP103 3.2 22.3 1.0 CD2 A:HIS237 3.2 20.9 1.0 CE1 A:HIS101 3.3 25.7 1.0 OD2 A:ASP103 3.6 25.3 1.0 HD2 A:HIS237 3.6 25.0 1.0 HE1 A:HIS101 3.6 30.9 1.0 ND1 A:HIS237 3.8 17.9 1.0 O A:HOH581 3.9 50.8 1.0 HZ2 A:TRP230 4.0 21.4 1.0 HD13 A:ILE97 4.1 54.0 1.0 CG A:HIS237 4.1 16.7 1.0 CG A:HIS101 4.1 18.3 1.0 HG21 A:ILE97 4.2 54.7 1.0 ND1 A:HIS101 4.3 19.6 1.0 C2 A:SIN302 4.4 40.9 0.9 HH12 A:ARG251 4.4 58.8 1.0 HH11 A:ARG251 4.5 58.8 1.0 HA A:ASP103 4.5 20.8 1.0 H32 A:SIN302 4.5 35.0 0.9 HD1 A:HIS237 4.5 21.5 1.0 CB A:ASP103 4.5 18.4 1.0 O A:HOH478 4.7 30.1 1.0 NH1 A:ARG251 4.7 49.0 1.0 CZ2 A:TRP230 4.7 17.8 1.0 H22 A:SIN302 4.8 49.0 0.9 HB3 A:ASP103 4.8 22.0 1.0 C3 A:SIN302 4.9 29.2 0.9 CA A:ASP103 4.9 17.3 1.0 CD1 A:ILE97 5.0 45.0 1.0 HG23 A:ILE97 5.0 54.7 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Sodium 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 Sodium Succinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:26.5 occ:0.58 NE2 B:HIS237 2.1 22.9 1.0 O2 B:SIN301 2.1 52.8 0.9 OD1 B:ASP103 2.3 25.2 1.0 NE2 B:HIS101 2.3 21.6 1.0 HE1 B:HIS237 2.6 24.0 1.0 CE1 B:HIS237 2.6 20.0 1.0 HD2 B:HIS101 2.9 26.9 1.0 CD2 B:HIS101 2.9 22.4 1.0 CD2 B:HIS237 3.3 18.5 1.0 CG B:ASP103 3.3 23.6 1.0 C1 B:SIN301 3.3 65.0 0.9 CE1 B:HIS101 3.4 23.1 1.0 OD2 B:ASP103 3.7 24.6 1.0 HD2 B:HIS237 3.7 22.2 1.0 HE1 B:HIS101 3.7 27.7 1.0 ND1 B:HIS237 3.8 19.3 1.0 HZ2 B:TRP230 3.9 21.9 1.0 O1 B:SIN301 3.9 42.3 0.9 HD13 B:ILE97 4.1 50.5 1.0 CG B:HIS237 4.2 14.0 1.0 CG B:HIS101 4.2 16.1 1.0 ND1 B:HIS101 4.4 18.2 1.0 H32 B:SIN301 4.4 36.5 0.9 C2 B:SIN301 4.5 41.1 0.9 HH11 B:ARG251 4.5 57.0 1.0 HD1 B:HIS237 4.5 23.1 1.0 HA B:ASP103 4.5 17.4 1.0 HG21 B:ILE97 4.5 62.6 1.0 HH12 B:ARG251 4.6 57.0 1.0 H21 B:SIN301 4.6 49.3 0.9 CB B:ASP103 4.6 15.6 1.0 O B:HOH459 4.6 25.0 1.0 CZ2 B:TRP230 4.7 18.3 1.0 H31 B:SIN301 4.8 36.5 0.9 C3 B:SIN301 4.8 30.4 0.9 NH1 B:ARG251 4.9 47.5 1.0 HB3 B:ASP103 4.9 18.8 1.0 CA B:ASP103 5.0 14.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Sodium 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 Sodium Succinate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:25.2 occ:0.66 NE2 C:HIS237 2.1 24.3 1.0 O3 C:SIN302 2.2 48.8 0.9 OD1 C:ASP103 2.2 24.9 1.0 NE2 C:HIS101 2.3 23.1 1.0 HE1 C:HIS237 2.6 26.5 1.0 CE1 C:HIS237 2.7 22.1 1.0 C4 C:SIN302 2.9 53.0 0.9 O4 C:SIN302 2.9 46.1 0.9 HD2 C:HIS101 3.0 27.3 1.0 CD2 C:HIS101 3.0 22.7 1.0 CG C:ASP103 3.2 20.6 1.0 CD2 C:HIS237 3.3 18.3 1.0 CE1 C:HIS101 3.5 23.7 1.0 OD2 C:ASP103 3.6 26.0 1.0 HD2 C:HIS237 3.7 22.0 1.0 HE1 C:HIS101 3.8 28.4 1.0 HZ2 C:TRP230 3.9 23.3 1.0 ND1 C:HIS237 3.9 19.8 1.0 CG C:HIS237 4.2 15.5 1.0 CG C:HIS101 4.2 18.8 1.0 HG21 C:ILE97 4.3 62.9 1.0 HH11 C:ARG251 4.4 52.3 1.0 C3 C:SIN302 4.4 38.2 0.9 HH12 C:ARG251 4.4 52.3 1.0 HD13 C:ILE97 4.4 61.5 1.0 ND1 C:HIS101 4.4 18.9 1.0 HA C:ASP103 4.5 18.6 1.0 O C:HOH485 4.5 28.3 1.0 HD1 C:HIS237 4.6 23.8 1.0 CB C:ASP103 4.6 17.5 1.0 CZ2 C:TRP230 4.6 19.4 1.0 H22 C:SIN302 4.7 36.5 0.9 NH1 C:ARG251 4.7 43.6 1.0 H32 C:SIN302 4.7 45.9 0.9 HB3 C:ASP103 4.9 21.0 1.0 C2 C:SIN302 5.0 30.4 0.9 CA C:ASP103 5.0 15.5 1.0 HG23 C:ILE97 5.0 62.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Sodium Succinate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase PLAO1 in Complex with Sodium Succinate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:21.2 occ:0.53 NE2 D:HIS237 2.1 24.0 1.0 O1 D:SIN301 2.2 61.4 1.0 NE2 D:HIS101 2.2 23.0 1.0 OD1 D:ASP103 2.3 25.0 1.0 HE1 D:HIS237 2.7 23.7 1.0 CE1 D:HIS237 2.7 19.8 1.0 CD2 D:HIS101 2.9 21.4 1.0 HD2 D:HIS101 2.9 25.7 1.0 C1 D:SIN301 3.0 75.2 1.0 O2 D:SIN301 3.1 60.2 1.0 CD2 D:HIS237 3.2 21.3 1.0 CG D:ASP103 3.3 24.4 1.0 CE1 D:HIS101 3.3 25.4 1.0 HD2 D:HIS237 3.6 25.6 1.0 HE1 D:HIS101 3.6 30.5 1.0 OD2 D:ASP103 3.7 25.0 1.0 ND1 D:HIS237 3.8 18.7 1.0 HZ2 D:TRP230 4.0 23.2 1.0 HD13 D:ILE97 4.0 60.1 1.0 CG D:HIS237 4.1 15.5 1.0 CG D:HIS101 4.1 16.9 1.0 ND1 D:HIS101 4.3 20.7 1.0 HH11 D:ARG251 4.4 62.9 1.0 HH12 D:ARG251 4.4 62.9 1.0 C2 D:SIN301 4.4 50.9 1.0 H32 D:SIN301 4.5 36.6 1.0 HA D:ASP103 4.5 19.1 1.0 HD1 D:HIS237 4.5 22.4 1.0 HG21 D:ILE97 4.6 76.0 1.0 CB D:ASP103 4.6 17.6 1.0 O D:HOH484 4.7 26.9 1.0 NH1 D:ARG251 4.7 52.4 1.0 CZ2 D:TRP230 4.7 19.3 1.0 H22 D:SIN301 4.8 61.1 1.0 HB3 D:ASP103 4.9 21.2 1.0 C3 D:SIN301 4.9 30.5 1.0 CD1 D:ILE97 4.9 50.1 1.0 HD11 D:ILE97 5.0 60.1 1.0 H31 D:SIN301 5.0 36.6 1.0 O D:HOH610 5.0 47.8 1.0 CA D:ASP103 5.0 15.9 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.