Sodium in PDB 1oij: Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate

The structure of Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate, PDB code: 1oij was solved by I.Mueller, A.Kahnert, T.Pape, T.Dierks, W.Meyer-Klauke, M.A.Kertesz, I.Uson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.92 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.447, 144.876, 160.692, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 21.5

The binding sites of Sodium atom in the Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate (pdb code 1oij). 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 Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate, PDB code: 1oij:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate


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 Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1301 b:34.0 occ:0.70 OD1 A:ASP110 2.1 38.2 1.0 O5 A:AKG1302 2.2 48.1 0.7 NE2 A:HIS264 2.3 31.7 1.0 O2 A:AKG1302 2.4 53.1 0.7 NE2 A:HIS108 2.4 34.7 1.0 CE1 A:HIS264 2.9 30.9 1.0 C2 A:AKG1302 3.0 50.8 0.7 C1 A:AKG1302 3.1 53.7 0.7 CG A:ASP110 3.2 37.5 1.0 CD2 A:HIS108 3.3 32.8 1.0 CE1 A:HIS108 3.4 34.3 1.0 CD2 A:HIS264 3.5 27.6 1.0 OD2 A:ASP110 3.7 38.2 1.0 NH1 A:ARG279 4.0 68.9 1.0 O A:HOH2168 4.0 49.5 1.0 ND1 A:HIS264 4.1 32.7 1.0 O1 A:AKG1302 4.3 56.7 0.7 CG A:HIS264 4.4 28.6 1.0 C3 A:AKG1302 4.4 45.3 0.7 ND1 A:HIS108 4.5 32.5 1.0 CG A:HIS108 4.5 31.2 1.0 CB A:ASP110 4.5 31.1 1.0 C4 A:AKG1302 4.7 38.6 0.7 CA A:ASP110 4.7 31.3 1.0 CZ2 A:TRP257 4.9 29.8 1.0 CZ A:ARG279 4.9 65.4 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate


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 Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1301 b:37.5 occ:0.70 OD1 B:ASP110 2.2 38.3 1.0 O5 B:AKG1302 2.2 55.1 0.7 NE2 B:HIS264 2.4 32.5 1.0 NE2 B:HIS108 2.5 35.1 1.0 O2 B:AKG1302 2.5 51.9 0.7 CE1 B:HIS264 3.0 30.8 1.0 C2 B:AKG1302 3.1 52.0 0.7 C1 B:AKG1302 3.1 52.6 0.7 CD2 B:HIS108 3.4 32.5 1.0 CG B:ASP110 3.4 37.4 1.0 CE1 B:HIS108 3.5 34.5 1.0 CD2 B:HIS264 3.6 27.7 1.0 OD2 B:ASP110 3.9 38.3 1.0 NH1 B:ARG279 4.0 69.5 1.0 ND1 B:HIS264 4.2 32.2 1.0 O B:HOH2075 4.3 37.7 1.0 O1 B:AKG1302 4.3 56.5 0.7 C3 B:AKG1302 4.5 44.2 0.7 CG B:HIS264 4.5 28.4 1.0 CB B:ASP110 4.5 31.1 1.0 CG B:HIS108 4.5 30.9 1.0 ND1 B:HIS108 4.6 32.1 1.0 CA B:ASP110 4.8 31.4 1.0 CZ B:ARG279 4.8 64.6 1.0 C4 B:AKG1302 4.8 36.3 0.7 CZ2 B:TRP257 4.9 29.8 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate


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 Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1300 b:32.0 occ:1.00 O5 C:AKG1301 2.1 59.8 1.0 NE2 C:HIS264 2.2 31.8 1.0 OD1 C:ASP110 2.2 37.8 1.0 O2 C:AKG1301 2.4 48.6 1.0 NE2 C:HIS108 2.5 35.3 1.0 CE1 C:HIS264 2.9 30.8 1.0 C2 C:AKG1301 2.9 56.8 1.0 C1 C:AKG1301 3.0 57.2 1.0 CD2 C:HIS264 3.3 27.6 1.0 CG C:ASP110 3.4 37.2 1.0 CE1 C:HIS108 3.4 33.8 1.0 CD2 C:HIS108 3.5 32.0 1.0 OD2 C:ASP110 3.8 38.2 1.0 NH1 C:ARG279 3.8 63.0 1.0 ND1 C:HIS264 4.1 32.7 1.0 O1 C:AKG1301 4.2 63.8 1.0 C3 C:AKG1301 4.3 51.6 1.0 CG C:HIS264 4.3 28.7 1.0 ND1 C:HIS108 4.5 32.3 1.0 CZ C:ARG279 4.5 66.8 1.0 O C:HOH2070 4.6 35.8 1.0 CG C:HIS108 4.6 31.0 1.0 CB C:ASP110 4.6 30.9 1.0 C4 C:AKG1301 4.6 45.2 1.0 NH2 C:ARG279 4.6 64.0 1.0 CZ2 C:TRP257 4.8 29.1 1.0 CA C:ASP110 4.9 31.3 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate


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 Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase in Complex with Alphaketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1300 b:33.5 occ:0.80 O5 D:AKG1301 2.2 52.5 0.8 NE2 D:HIS264 2.2 32.0 1.0 OD1 D:ASP110 2.2 37.5 1.0 O2 D:AKG1301 2.3 42.3 0.8 NE2 D:HIS108 2.5 34.9 1.0 CE1 D:HIS264 2.8 31.2 1.0 C2 D:AKG1301 3.0 48.7 0.8 C1 D:AKG1301 3.0 53.1 0.8 CG D:ASP110 3.4 36.9 1.0 CD2 D:HIS264 3.4 27.0 1.0 CE1 D:HIS108 3.4 34.1 1.0 CD2 D:HIS108 3.4 32.0 1.0 OD2 D:ASP110 3.8 38.0 1.0 ND1 D:HIS264 4.0 32.4 1.0 O1 D:AKG1301 4.2 56.6 0.8 CG D:HIS264 4.3 28.2 1.0 C3 D:AKG1301 4.4 46.8 0.8 ND1 D:HIS108 4.5 32.5 1.0 CG D:HIS108 4.6 31.4 1.0 CB D:ASP110 4.6 31.4 1.0 O D:HOH2070 4.6 36.6 1.0 C4 D:AKG1301 4.8 37.0 0.8 CZ2 D:TRP257 4.8 29.1 1.0 CA D:ASP110 4.8 31.2 1.0

I.Mueller, A.Kahnert, T.Pape, G.M.Sheldrick, W.Meyer-Klaucke, T.Dierks, M.A.Kertesz, I.Uson. Crystal Structure of the Alkylsulfatase Atsk: Insights Into the Catalytic Mechanism of the Fe(II) Alpha-Ketoglutarate-Dependent Dioxygenase Superfamily Biochemistry V. 42 3075 2004.
ISSN: ISSN 0006-2960
PubMed: 15023059
DOI: 10.1021/BI035752V