Sodium in PDB 6r1e: Structure of Dodecin From Streptomyces Coelicolor

The structure of Structure of Dodecin From Streptomyces Coelicolor, PDB code: 6r1e was solved by L.-O.Essen, B.Sander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	11.86 / 2.60
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	92.945, 92.945, 227.845, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 24.3

The structure of Structure of Dodecin From Streptomyces Coelicolor also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Structure of Dodecin From Streptomyces Coelicolor (pdb code 6r1e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Dodecin From Streptomyces Coelicolor, PDB code: 6r1e:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Dodecin From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Dodecin From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:54.2 occ:1.00 OD1 A:ASP65 3.5 56.3 1.0 N A:ASP65 3.6 59.4 1.0 CL B:CL103 4.0 76.0 1.0 O B:HOH214 4.2 45.4 1.0 CA A:ASP65 4.3 60.3 1.0 CG A:ASP65 4.5 57.4 1.0 CA A:GLU64 4.5 54.0 1.0 C A:GLU64 4.6 54.5 1.0

Sodium binding site 2 out of 4 in the Structure of Dodecin From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Dodecin From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:52.6 occ:1.00 OD1 B:ASP65 3.5 55.3 1.0 N B:ASP65 3.7 57.1 1.0 CL D:CL102 4.2 68.6 1.0 O D:HOH215 4.3 46.9 1.0 CA B:ASP65 4.4 58.9 1.0 CG B:ASP65 4.5 58.7 1.0 CA B:GLU64 4.6 51.4 1.0 C B:GLU64 4.6 52.1 1.0

Sodium binding site 3 out of 4 in the Structure of Dodecin From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Dodecin From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ C:Na104 b:52.6 occ:1.00 OD1 C:ASP65 3.5 59.5 1.0 N C:ASP65 3.7 57.5 1.0 CA C:ASP65 4.4 58.7 1.0 CG C:ASP65 4.5 57.6 1.0 CA C:GLU64 4.5 54.2 1.0 C C:GLU64 4.6 52.3 1.0

Sodium binding site 4 out of 4 in the Structure of Dodecin From Streptomyces Coelicolor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Dodecin From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ D:Na103 b:54.0 occ:1.00 OD1 D:ASP65 3.4 58.7 1.0 N D:ASP65 3.7 61.6 1.0 O A:HOH213 4.0 39.4 1.0 CL A:CL104 4.2 72.6 1.0 CA D:ASP65 4.4 61.4 1.0 CG D:ASP65 4.5 60.0 1.0 CA D:GLU64 4.5 55.0 1.0 C D:GLU64 4.6 54.4 1.0

F.Bourdeaux, P.Ludwig, K.Paithankar, B.Sander, L.O.Essen, M.Grininger, M.Mack. Comparative Biochemical and Structural Analysis of the Flavin-Binding Dodecins Fromstreptomyces Davaonensisandstreptomyces Coelicolorreveals Striking Differences with Regard to Multimerization. Microbiology (Reading, V. 165 1095 2019ENGL.).
ISSN: ESSN 1465-2080
PubMed: 31339487
DOI: 10.1099/MIC.0.000835