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

Protein crystallography data

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

Other elements in 6r1e:

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

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

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 6r1e

Go back to Sodium Binding Sites List in 6r1e
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 6r1e

Go back to Sodium Binding Sites List in 6r1e
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 6r1e

Go back to Sodium Binding Sites List in 6r1e
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 6r1e

Go back to Sodium Binding Sites List in 6r1e
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

Reference:

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
Page generated: Tue Dec 15 12:51:30 2020

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