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

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

Resolution Low / High (Å)	20.00 / 1.89
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.242, 145.344, 159.457, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 19.1

The binding sites of Sodium atom in the Crystal Structure of the Alkylsulfatase Atsk, A Non-Heme Fe(II) Alphaketoglutarate Dependent Dioxygenase (pdb code 1oih). 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, PDB code: 1oih:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1301 b:31.8 occ:0.70 NE2 A:HIS264 2.2 27.1 1.0 OD1 A:ASP110 2.2 30.3 1.0 NE2 A:HIS108 2.3 28.2 1.0 CE1 A:HIS264 2.9 25.0 1.0 CE1 A:HIS108 3.2 30.9 1.0 CD2 A:HIS108 3.3 31.4 1.0 CG A:ASP110 3.4 29.8 1.0 CD2 A:HIS264 3.4 25.1 1.0 OD2 A:ASP110 3.8 28.4 1.0 ND1 A:HIS264 4.1 25.9 1.0 ND1 A:HIS108 4.4 27.7 1.0 CG A:HIS264 4.4 23.8 1.0 CG A:HIS108 4.5 23.3 1.0 CB A:ASP110 4.6 23.1 1.0 NH2 A:ARG279 4.7 52.1 1.0 CA A:ASP110 4.9 21.1 1.0 CZ2 A:TRP257 4.9 22.9 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1301 b:30.0 occ:0.70 NE2 B:HIS264 2.3 34.2 1.0 OD1 B:ASP110 2.4 31.2 1.0 NE2 B:HIS108 2.5 43.8 1.0 CE1 B:HIS264 2.8 31.1 1.0 CD2 B:HIS108 3.4 52.8 1.0 CE1 B:HIS108 3.4 60.3 1.0 CD2 B:HIS264 3.4 33.1 1.0 CG B:ASP110 3.5 33.5 1.0 OD2 B:ASP110 3.9 33.0 1.0 ND1 B:HIS264 4.0 30.2 1.0 CG B:HIS264 4.3 23.8 1.0 ND1 B:HIS108 4.4 60.7 1.0 CG B:HIS108 4.4 35.2 1.0 O B:HOH2108 4.6 30.0 1.0 CB B:ASP110 4.7 23.3 1.0 CZ2 B:TRP257 4.9 24.7 1.0 NH2 B:ARG279 4.9 46.9 1.0 CA B:ASP110 4.9 21.2 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1300 b:38.4 occ:0.50 NE2 C:HIS108 2.6 29.2 1.0 OD1 C:ASP110 2.8 40.3 1.0 NE2 C:HIS264 3.1 31.4 1.0 CE1 C:HIS108 3.5 32.5 1.0 CD2 C:HIS108 3.7 26.8 1.0 CE1 C:HIS264 3.8 26.2 1.0 CG C:ASP110 4.0 34.1 1.0 CD2 C:HIS264 4.2 24.0 1.0 O C:HOH2060 4.2 28.1 1.0 OD2 C:ASP110 4.5 37.1 1.0 ND1 C:HIS108 4.7 27.7 1.0 CG C:HIS108 4.8 26.9 1.0 O C:HOH2105 4.9 43.4 1.0 ND1 C:HIS264 5.0 27.0 1.0 CB C:ASP110 5.0 27.8 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


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1300 b:38.9 occ:0.70 OD1 D:ASP110 2.3 34.5 1.0 NE2 D:HIS108 2.4 36.3 1.0 NE2 D:HIS264 2.6 37.9 1.0 CE1 D:HIS108 3.3 36.0 1.0 CD2 D:HIS108 3.4 35.3 1.0 CE1 D:HIS264 3.4 34.3 1.0 CG D:ASP110 3.4 33.4 1.0 CD2 D:HIS264 3.8 29.9 1.0 OD2 D:ASP110 4.0 33.5 1.0 NH2 D:ARG279 4.1 68.1 1.0 O D:HOH2049 4.1 33.2 1.0 ND1 D:HIS108 4.5 34.0 1.0 CG D:HIS108 4.5 31.5 1.0 CB D:ASP110 4.5 27.8 1.0 ND1 D:HIS264 4.6 35.2 1.0 CA D:ASP110 4.8 28.8 1.0 CG D:HIS264 4.8 28.6 1.0

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