Sodium in PDB 8hn2: Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum

All present enzymatic activity of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum:
7.1.1.6;

The structure of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum, PDB code: 8hn2 was solved by H.Kishimoto, R.Mutoh, H.Tanaka, G.Kurisu, H.Oh-Oka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.55 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.64, 58.695, 49.68, 90, 112.04, 90
R / Rfree (%)	20.1 / 23.6

The structure of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Sodium atom in the Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum (pdb code 8hn2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 25 binding sites of Sodium where determined in the Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum, PDB code: 8hn2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 25 in the Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:73.6 occ:1.00 O A:GLY128 2.3 69.2 1.0 CA A:CYS129 3.2 55.9 1.0 C A:GLY128 3.3 67.2 1.0 C A:CYS129 3.4 56.0 1.0 N A:LEU130 3.5 46.5 1.0 CD1 A:LEU130 3.5 58.4 1.0 CD2 B:LEU130 3.6 61.4 1.0 CB B:LEU130 3.6 45.5 1.0 N A:CYS129 3.7 70.5 1.0 O A:CYS129 4.1 48.7 1.0 CG B:LEU130 4.2 57.0 1.0 CD1 A:ILE123 4.3 51.6 1.0 CA A:LEU130 4.4 56.3 1.0 CB A:CYS129 4.5 63.2 1.0 CG A:LEU130 4.5 56.2 1.0 CB A:LEU130 4.6 54.4 1.0 CA A:GLY128 4.7 54.9 1.0 O A:HOH312 4.7 49.1 1.0 NA A:NA212 4.9 84.2 1.0 CD2 A:LEU130 4.9 55.8 1.0 CA B:LEU130 4.9 41.9 1.0 N B:LEU130 4.9 43.5 1.0

Sodium binding site 2 out of 25 in the Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:68.2 occ:1.00 N A:GLN102 3.9 42.3 1.0 NE2 B:HIS145 4.1 68.9 1.0 CD2 A:TYR101 4.3 42.0 1.0 CA A:TYR101 4.3 38.3 1.0 CB A:GLN102 4.5 49.1 1.0 CB A:TYR101 4.6 40.7 1.0 C A:TYR101 4.7 40.8 1.0 CA A:GLN102 4.8 50.2 1.0 O A:HOH327 4.8 52.2 1.0 CG A:TYR101 4.9 38.8 1.0 CD2 B:HIS145 5.0 62.6 1.0 CE1 B:HIS145 5.0 53.6 1.0

Sodium binding site 3 out of 25 in the Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:61.4 occ:1.00 O A:HOH317 2.5 54.3 1.0 O A:ILE123 2.5 51.5 1.0 OG A:SER121 2.8 50.5 1.0 CB A:SER121 3.5 41.4 1.0 CB A:ILE123 3.6 57.3 1.0 C A:ILE123 3.6 43.1 1.0 CD2 A:LEU164 3.9 45.5 1.0 CG2 A:ILE123 4.0 50.0 1.0 CA A:ILE123 4.1 44.9 1.0 CG2 A:THR125 4.1 85.8 1.0 N A:THR125 4.3 65.7 1.0 N A:ILE123 4.3 46.1 1.0 C A:CYS124 4.5 74.5 1.0 CA A:THR125 4.6 82.9 1.0 OD1 A:ASP106 4.6 70.4 1.0 CG1 A:ILE123 4.7 54.3 1.0 N A:CYS124 4.7 51.7 1.0 O A:CYS124 4.8 68.7 1.0 CA A:SER121 4.8 40.2 1.0 O A:HOH306 4.8 82.2 1.0 C A:SER121 4.9 45.2 1.0 CA A:LEU164 5.0 41.4 1.0

Sodium binding site 4 out of 25 in the Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:111.2 occ:1.00 CB A:ALA186 3.8 89.8 1.0 O A:ALA186 4.7 91.8 1.0

Sodium binding site 5 out of 25 in the Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:371.9 occ:1.00 CG1 A:ILE156 3.6 41.2 1.0 CG2 A:THR150 3.9 51.8 1.0 CD1 A:ILE156 4.1 45.0 1.0 CG2 A:ILE156 4.1 45.5 1.0 CB A:ILE156 4.3 44.4 1.0 CA A:ILE156 4.6 41.2 1.0

Sodium binding site 6 out of 25 in the Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na207 b:74.7 occ:1.00 O A:HOH314 2.7 57.4 1.0 OD2 A:ASP152 2.7 77.6 1.0 NE2 A:GLN166 3.2 64.8 1.0 CG A:ASP152 3.5 66.3 1.0 CD A:GLN166 3.7 65.0 1.0 CG A:GLN166 3.8 55.5 1.0 CG2 A:THR118 4.0 42.1 1.0 CB A:GLN166 4.0 47.5 1.0 CA A:ASP152 4.0 44.1 1.0 CB A:ASP152 4.1 46.9 1.0 CB A:THR118 4.1 40.0 1.0 O A:ALA119 4.2 34.2 1.0 CG1 A:VAL120 4.2 38.3 1.0 O A:TYR167 4.3 51.1 1.0 O A:ASP152 4.3 37.1 1.0 OD1 A:ASP152 4.3 71.2 1.0 N A:ALA119 4.5 32.9 1.0 C A:ASP152 4.5 37.1 1.0 OE1 A:GLN166 4.6 70.1 1.0 CA A:GLN166 4.7 43.3 1.0 CA A:THR118 4.8 36.3 1.0 C A:ALA119 4.9 30.8 1.0 N A:TYR167 5.0 37.5 1.0

Sodium binding site 7 out of 25 in the Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na208 b:70.3 occ:1.00 N A:VAL169 3.4 37.5 1.0 O A:HOH326 3.5 81.1 1.0 O A:VAL169 3.5 43.4 1.0 CA A:LYS168 3.7 47.6 1.0 C A:LYS168 4.1 44.6 1.0 CB A:LYS168 4.1 51.7 1.0 O A:HOH313 4.2 66.8 1.0 CG A:LYS168 4.2 53.6 1.0 O A:HOH314 4.3 57.4 1.0 C A:VAL169 4.4 45.9 1.0 CA A:VAL169 4.4 41.0 1.0 CG1 A:VAL169 4.4 45.6 1.0 O A:HOH334 4.5 76.9 1.0 O A:TYR167 4.6 51.1 1.0 N A:LYS168 4.9 43.4 1.0 O A:LEU117 4.9 46.8 1.0 CB A:VAL169 5.0 40.4 1.0

Sodium binding site 8 out of 25 in the Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na209 b:79.9 occ:1.00 OG A:SER179 2.7 56.2 1.0 O A:HOH334 2.8 76.9 1.0 O A:VAL177 3.1 48.0 1.0 O A:LYS168 3.6 48.8 1.0 N A:VAL169 3.6 37.5 1.0 C A:LYS168 3.7 44.6 1.0 CG A:LYS170 3.7 64.0 1.0 CB A:SER179 3.7 49.2 1.0 CA A:VAL169 3.8 41.0 1.0 N A:SER179 3.8 49.7 1.0 C A:VAL177 3.9 49.2 1.0 CB A:LYS168 3.9 51.7 1.0 N A:LYS170 4.0 48.5 1.0 C A:VAL169 4.1 45.9 1.0 CE A:LYS170 4.1 77.9 1.0 C A:VAL178 4.1 41.9 1.0 CG1 A:VAL177 4.2 49.5 1.0 CA A:VAL178 4.3 45.4 1.0 CA A:SER179 4.4 47.2 1.0 N A:VAL178 4.4 39.1 1.0 CA A:LYS168 4.5 47.6 1.0 CD A:LYS170 4.5 72.8 1.0 CB A:LYS170 4.5 57.4 1.0 NZ A:LYS170 4.6 83.1 1.0 CB A:VAL177 4.7 47.3 1.0 O A:VAL178 4.7 48.4 1.0 CE A:LYS168 4.8 72.4 1.0 O A:VAL169 4.8 43.4 1.0 CA A:LYS170 4.9 54.9 1.0 CA A:VAL177 5.0 46.6 1.0

Sodium binding site 9 out of 25 in the Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na210 b:76.3 occ:1.00 O A:LEU164 2.8 50.4 1.0 O A:ASP152 2.9 37.1 1.0 CG A:GLN166 3.2 55.5 1.0 C A:GLY153 3.6 33.0 1.0 O A:GLY153 3.7 40.9 1.0 CB A:PRO163 3.7 58.5 1.0 CD A:GLN166 3.7 65.0 1.0 CA A:GLY153 3.8 33.9 1.0 C A:LEU164 3.9 47.6 1.0 N A:LYS154 4.0 35.0 1.0 NE2 A:GLN166 4.0 64.8 1.0 CG A:LYS154 4.0 53.0 1.0 C A:ASP152 4.0 37.1 1.0 N A:LEU164 4.1 41.5 1.0 CG A:PRO163 4.3 62.8 1.0 N A:GLY153 4.4 37.9 1.0 OE1 A:GLN166 4.4 70.1 1.0 O A:HOH324 4.4 60.1 1.0 CA A:LYS154 4.4 40.5 1.0 C A:PRO163 4.5 53.5 1.0 CB A:GLN166 4.6 47.5 1.0 CA A:PRO163 4.6 56.6 1.0 N A:GLN166 4.6 38.7 1.0 CA A:LEU164 4.6 41.4 1.0 C A:LYS165 4.8 44.3 1.0 CB A:LYS154 4.8 48.7 1.0 N A:LYS165 4.9 57.2 1.0 CA A:LYS165 4.9 52.2 1.0 CG1 A:VAL120 5.0 38.3 1.0 CA A:GLN166 5.0 43.3 1.0

Sodium binding site 10 out of 25 in the Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Selenomethionine-Labelled Soluble Domain of Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na211 b:90.0 occ:1.00 N A:ALA136 4.1 58.1 1.0 N A:GLU135 4.1 40.3 1.0 CB A:GLU135 4.2 47.9 1.0 CB A:ALA136 4.4 64.4 1.0 CA A:GLU135 4.6 44.8 1.0 O A:HOH303 4.6 44.0 1.0 OD1 A:ASP134 4.6 62.2 1.0 CA A:ALA136 4.9 64.3 1.0 C A:GLU135 4.9 48.4 1.0 C A:ASP134 5.0 43.8 1.0

H.Kishimoto, C.Azai, T.Yamamoto, R.Mutoh, T.Nakaniwa, H.Tanaka, Y.Miyanoiri, G.Kurisu, H.Oh-Oka. Soluble Domains of Cytochrome C-556 and Rieske Iron-Sulfur Protein From Chlorobaculum Tepidum: Crystal Structures and Interaction Analysis. Curr Res Struct Biol V. 5 00101 2023.
ISSN: ESSN 2665-928X
PubMed: 37180033
DOI: 10.1016/J.CRSTBI.2023.100101