Rubidium in PDB 7ld2: Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak

All present enzymatic activity of Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak:
2.3.1.9;

The structure of Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak, PDB code: 7ld2 was solved by A.C.Marshall, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.83 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.679, 79.681, 149.603, 90, 93.45, 90
R / Rfree (%)	23.4 / 27.1

The structure of Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak also contains other interesting chemical elements:

Chlorine

(Cl)

10 atoms

The binding sites of Rubidium atom in the Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak (pdb code 7ld2). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 4 binding sites of Rubidium where determined in the Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak, PDB code: 7ld2:
Jump to Rubidium binding site number: 1; 2; 3; 4;

Rubidium binding site 1 out of 4 in the Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb404 b:33.8 occ:0.74 OH A:TYR183 2.7 42.7 1.0 O A:ALA246 2.8 31.4 1.0 OH A:TYR218 3.0 42.8 1.0 O A:ALA243 3.0 37.3 1.0 O A:ILE344 3.1 44.2 1.0 O A:HOH610 3.8 12.7 1.0 O A:GLY244 3.9 36.1 1.0 CZ A:TYR218 3.9 42.5 1.0 CZ A:TYR183 3.9 39.7 1.0 CE2 A:TYR218 3.9 41.5 1.0 C A:ALA246 4.1 30.6 1.0 C A:ILE344 4.2 40.6 1.0 C A:ALA243 4.2 39.0 1.0 CE1 A:TYR183 4.3 39.2 1.0 C A:GLY244 4.4 37.6 1.0 CG2 A:ILE344 4.4 44.7 1.0 C A:SER247 4.4 29.4 1.0 CA A:GLY244 4.4 39.8 1.0 O A:SER247 4.5 31.1 1.0 N7A A:COA403 4.5 20.9 0.8 CA A:SER247 4.6 27.9 1.0 O A:HOH513 4.7 30.7 1.0 CA A:ILE344 4.7 38.9 1.0 N A:GLY248 4.8 29.0 1.0 N A:GLY244 4.8 40.3 1.0 N A:SER247 4.8 29.0 1.0 N A:ALA246 4.9 33.7 1.0

Rubidium binding site 2 out of 4 in the Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:Rb404 b:36.4 occ:0.78 OH B:TYR183 2.8 31.5 1.0 O B:ILE344 2.8 36.5 1.0 O B:ALA246 2.9 33.6 1.0 OH B:TYR218 3.2 35.3 1.0 O B:ALA243 3.2 42.8 1.0 O B:HOH613 3.7 30.0 1.0 O B:HOH520 3.7 18.1 1.0 O B:GLY244 3.8 34.8 1.0 CZ B:TYR183 3.9 30.8 1.0 CE2 B:TYR218 3.9 30.1 1.0 CZ B:TYR218 3.9 32.3 1.0 C B:ILE344 3.9 34.4 1.0 CE1 B:TYR183 4.0 31.7 1.0 CG2 B:ILE344 4.1 34.8 1.0 C B:ALA246 4.2 33.6 1.0 C B:ALA243 4.4 41.9 1.0 C B:GLY244 4.4 37.0 1.0 CA B:GLY244 4.4 39.8 1.0 CA B:ILE344 4.5 32.7 1.0 C B:SER247 4.5 33.1 1.0 O B:SER247 4.5 36.1 1.0 O B:HOH522 4.6 40.9 1.0 CA B:SER247 4.7 31.1 1.0 N7A B:COA403 4.8 71.1 1.0 N B:GLY248 4.9 31.1 1.0 N B:GLY244 4.9 41.6 1.0 N B:SER247 4.9 32.7 1.0 CB B:ILE344 4.9 32.6 1.0 N B:ALA246 5.0 35.4 1.0

Rubidium binding site 3 out of 4 in the Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak within 5.0Å range: probe atom residue distance (Å) B Occ C:Rb402 b:40.0 occ:0.64 OH C:TYR183 2.7 52.0 1.0 OH C:TYR218 2.9 58.5 1.0 O C:ALA246 3.0 53.5 1.0 O C:ILE344 3.1 55.6 1.0 O C:ALA243 3.1 49.7 1.0 CZ C:TYR218 3.8 57.4 1.0 O C:GLY244 3.8 59.4 1.0 CE2 C:TYR218 3.9 55.8 1.0 CZ C:TYR183 3.9 52.3 1.0 CE1 C:TYR183 4.2 52.2 1.0 N7A C:COA401 4.2 41.9 0.8 C C:ILE344 4.2 53.7 1.0 C C:ALA246 4.3 50.6 1.0 C C:ALA243 4.3 50.5 1.0 CG2 C:ILE344 4.4 57.1 1.0 C C:GLY244 4.4 53.9 1.0 CA C:GLY244 4.4 55.2 1.0 C C:SER247 4.6 50.1 1.0 O C:SER247 4.7 50.1 1.0 CA C:SER247 4.8 51.0 1.0 CA C:ILE344 4.8 52.9 1.0 N6A C:COA401 4.8 44.7 0.8 N C:GLY244 4.8 52.8 1.0 N C:GLY248 4.9 49.0 1.0

Rubidium binding site 4 out of 4 in the Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Zoogloea Ramigera Biosynthetic Thiolase Q183Y Mutant, Rbcl Soak within 5.0Å range: probe atom residue distance (Å) B Occ D:Rb402 b:94.3 occ:0.79 OH D:TYR183 2.8 80.4 1.0 OH D:TYR218 3.1 84.6 1.0 O D:ALA243 3.1 91.3 1.0 O D:ALA246 3.1 91.2 1.0 O D:ILE344 3.3 82.0 1.0 O D:GLY244 3.9 90.5 1.0 CZ D:TYR218 3.9 83.8 1.0 CZ D:TYR183 4.1 81.1 1.0 CE2 D:TYR218 4.1 81.7 1.0 C D:ALA243 4.3 94.0 1.0 N6A D:COA401 4.3 96.5 0.8 C D:ALA246 4.3 89.7 1.0 CA D:GLY244 4.4 95.1 1.0 C D:ILE344 4.4 79.6 1.0 C D:GLY244 4.4 92.4 1.0 CE1 D:TYR183 4.5 79.3 1.0 CG2 D:ILE344 4.5 86.9 1.0 C D:SER247 4.6 87.5 1.0 O D:SER247 4.6 89.8 1.0 N D:GLY244 4.8 95.5 1.0 CA D:SER247 4.8 87.0 1.0 N D:GLY248 4.9 83.3 1.0 CA D:ILE344 4.9 79.9 1.0

A.C.Marshall, J.B.Bruning. Engineering Potassium Activation Into Biosynthetic Thiolase. Biochem.J. V. 478 3047 2021.
ISSN: ESSN 1470-8728
PubMed: 34338286
DOI: 10.1042/BCJ20210455