Sodium in PDB 8dvh: Crystal Structure of Atp-Dependent Lon Protease From Bacillus Subtillis (Bslonba)

All present enzymatic activity of Crystal Structure of Atp-Dependent Lon Protease From Bacillus Subtillis (Bslonba):
3.4.21.53;

The structure of Crystal Structure of Atp-Dependent Lon Protease From Bacillus Subtillis (Bslonba), PDB code: 8dvh was solved by B.Sekula, M.Li, A.Gustchina, A.Wlodawer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.85 / 1.90
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	89.892, 89.892, 83.95, 90, 90, 120
R / Rfree (%)	19.4 / 23.7

The binding sites of Sodium atom in the Crystal Structure of Atp-Dependent Lon Protease From Bacillus Subtillis (Bslonba) (pdb code 8dvh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Atp-Dependent Lon Protease From Bacillus Subtillis (Bslonba), PDB code: 8dvh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Atp-Dependent Lon Protease From Bacillus Subtillis (Bslonba)


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 Atp-Dependent Lon Protease From Bacillus Subtillis (Bslonba) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:39.7 occ:1.00 O A:LEU358 2.5 29.3 1.0 OG1 A:THR470 2.7 30.9 1.0 O A:HOH746 2.7 29.2 1.0 OG A:SER445 2.7 34.8 1.0 O A:SER445 3.2 29.6 1.0 CB A:SER445 3.5 32.3 1.0 CB A:THR470 3.5 31.5 1.0 C A:SER445 3.5 30.1 1.0 C A:LEU358 3.6 29.1 1.0 B26 A:BO2601 3.8 27.6 1.0 CA A:THR470 3.8 30.6 1.0 NZ A:LYS488 3.9 33.2 1.0 C21 A:BO2601 3.9 29.1 1.0 N A:LEU358 3.9 28.7 1.0 CE A:LYS488 3.9 32.7 1.0 N A:ALA446 4.0 28.9 1.0 CA A:SER445 4.1 30.8 1.0 O28 A:BO2601 4.1 32.1 1.0 CA A:LEU358 4.2 29.0 1.0 C22 A:BO2601 4.2 27.9 1.0 CB A:LEU358 4.3 29.4 1.0 O A:MET469 4.3 30.9 1.0 CA A:ALA446 4.4 29.1 1.0 C25 A:BO2601 4.6 31.6 1.0 CD A:LYS488 4.6 33.1 1.0 O A:HOH747 4.7 36.8 1.0 N A:ALA359 4.7 29.9 1.0 N A:GLY471 4.7 29.8 1.0 C A:THR470 4.8 31.1 1.0 CB A:ALA446 4.9 29.3 1.0 CG2 A:THR470 4.9 32.7 1.0 N A:THR470 4.9 30.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Atp-Dependent Lon Protease From Bacillus Subtillis (Bslonba)


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 Atp-Dependent Lon Protease From Bacillus Subtillis (Bslonba) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:39.8 occ:1.00 O B:LEU358 2.5 35.9 1.0 O B:HOH730 2.6 31.7 1.0 OG B:SER445 2.8 35.7 1.0 OG1 B:THR470 2.8 35.0 1.0 O B:SER445 3.1 30.7 1.0 C B:SER445 3.4 30.0 1.0 CB B:SER445 3.4 32.7 1.0 CB B:THR470 3.5 34.7 1.0 C B:LEU358 3.6 35.8 1.0 B26 B:BO2601 3.8 31.9 1.0 NZ B:LYS488 3.8 36.9 1.0 CA B:THR470 3.8 34.4 1.0 N B:ALA446 3.9 29.4 1.0 C21 B:BO2601 3.9 32.3 1.0 N B:LEU358 4.0 35.9 1.0 CE B:LYS488 4.0 37.3 1.0 CA B:SER445 4.0 30.3 1.0 O28 B:BO2601 4.1 33.1 1.0 CA B:LEU358 4.2 36.3 1.0 C22 B:BO2601 4.2 33.0 1.0 CA B:ALA446 4.3 29.8 1.0 O B:MET469 4.3 35.0 1.0 CB B:LEU358 4.3 36.9 1.0 O B:HOH733 4.4 41.6 1.0 C25 B:BO2601 4.7 33.9 1.0 N B:GLY471 4.7 33.1 1.0 CD B:LYS488 4.7 37.8 1.0 N B:ALA359 4.7 36.6 1.0 C B:THR470 4.8 34.8 1.0 CG2 B:THR470 4.8 35.5 1.0 CB B:ALA446 4.9 30.3 1.0 N B:THR470 4.9 35.0 1.0

A.Gustchina, M.Li, A.G.Andrianova, A.M.Kudzhaev, G.T.Lountos, B.Sekula, S.Cherry, J.E.Tropea, I.V.Smirnov, A.Wlodawer, T.V.Rotanova. Unique Structural Fold of Lonba Protease From Bacillus Subtilis, A Member of A Newly Identified Subfamily of Lon Proteases. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 36232729
DOI: 10.3390/IJMS231911425