Sodium in PDB 4cyb: Dpsc From Streptomyces Coelicolor

The structure of Dpsc From Streptomyces Coelicolor, PDB code: 4cyb was solved by P.D.Townsend, M.D.Hitchings, R.Del Sol, E.Pohl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	153.12 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	92.220, 153.120, 170.280, 90.00, 90.00, 90.00
R / Rfree (%)	15.913 / 19.428

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

Iron

(Fe)

12 atoms

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

Sodium binding site 1 out of 4 in the Dpsc 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 Dpsc From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1300 b:27.8 occ:1.00 O H:HOH2090 2.0 35.3 1.0 O C:HOH2149 2.3 33.4 1.0 O C:HOH2151 2.3 43.3 1.0 O H:HOH2091 2.3 42.9 1.0 O F:HOH2084 2.3 35.6 1.0 O F:HOH2086 2.5 42.3 1.0 OG H:SER175 3.0 30.4 0.5 CB F:SER175 4.0 27.4 1.0 CB H:SER175 4.0 24.9 0.5 CB H:SER175 4.0 28.8 0.5 CB C:SER175 4.1 29.2 1.0 OG F:SER175 4.1 39.1 1.0 OG C:SER175 4.3 34.4 1.0 OG H:SER175 4.3 20.5 0.5 OD1 H:ASP171 4.5 29.8 1.0 OD1 F:ASP171 4.6 31.7 1.0 OD1 C:ASP171 4.6 31.3 1.0 OD2 H:ASP171 4.7 33.5 1.0 OD2 F:ASP171 4.8 33.0 1.0 OD2 C:ASP171 4.8 28.6 1.0

Sodium binding site 2 out of 4 in the Dpsc 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 Dpsc From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ J:Na1300 b:28.2 occ:1.00 O G:HOH2058 2.2 37.5 1.0 O J:HOH2113 2.3 40.3 1.0 O J:HOH2112 2.3 47.1 1.0 O G:HOH2059 2.4 39.6 1.0 O J:HOH2111 2.4 27.9 1.0 O G:HOH2057 2.6 29.6 1.0 O G:HOH2029 4.1 40.2 1.0 CA G:GLY93 4.1 18.7 1.0 O G:HOH2020 4.2 44.2 1.0 O G:HOH2019 4.3 25.5 1.0 O G:HOH2065 4.4 37.7 1.0 N G:GLY93 4.6 19.5 1.0 O G:ASP89 4.7 21.6 1.0 OD2 G:ASP89 4.8 27.7 1.0 OD1 G:ASP89 4.8 29.9 1.0 O G:HOH2041 4.9 23.1 1.0 CG G:ASP89 5.0 29.5 1.0

Sodium binding site 3 out of 4 in the Dpsc 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 Dpsc From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ K:Na1300 b:23.8 occ:1.00 O D:HOH2114 2.1 34.7 1.0 O B:HOH2112 2.2 40.8 1.0 O B:HOH2116 2.3 30.7 1.0 O K:HOH2140 2.4 41.1 1.0 O K:HOH2139 2.4 42.3 1.0 O B:HOH2109 2.4 29.9 1.0 OG K:SER175 3.1 29.6 0.5 CB D:SER175 3.9 25.7 1.0 CB K:SER175 4.1 19.8 0.5 OG D:SER175 4.1 36.0 1.0 CB B:SER175 4.1 24.3 1.0 OG B:SER175 4.2 24.9 1.0 CB K:SER175 4.2 24.2 0.5 OG K:SER175 4.4 18.6 0.5 O D:HOH2116 4.5 39.2 1.0 OD1 K:ASP171 4.6 23.6 1.0 OD1 B:ASP171 4.7 25.8 1.0 OD2 B:ASP171 4.7 25.5 1.0 OD1 D:ASP171 4.7 29.3 1.0 OD2 K:ASP171 4.8 23.4 1.0 OD2 D:ASP171 5.0 28.2 1.0

Sodium binding site 4 out of 4 in the Dpsc 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 Dpsc From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ L:Na1300 b:27.5 occ:1.00 O L:HOH2099 2.2 45.2 1.0 O L:HOH2042 2.3 37.1 1.0 O L:HOH2044 2.3 34.4 1.0 O L:HOH2100 2.4 47.9 1.0 O L:HOH2098 2.4 24.0 1.0 O L:HOH2041 2.6 25.9 1.0 O K:HOH2073 3.8 41.5 1.0 CA L:GLY93 4.1 17.8 1.0 O K:HOH2031 4.2 30.2 1.0 O L:HOH2020 4.4 20.8 1.0 O L:HOH2051 4.5 34.7 1.0 N L:GLY93 4.6 18.5 1.0 OD2 L:ASP89 4.6 26.1 1.0 O L:ASP89 4.6 18.2 1.0 OD1 L:ASP89 4.7 27.9 1.0 O K:HOH2032 4.8 52.1 1.0 O L:HOH2033 4.8 22.4 1.0 CG L:ASP89 4.9 24.2 1.0 O L:HOH2046 5.0 45.0 1.0

M.D.Hitchings, P.D.Townsend, E.Pohl, P.D.Facey, D.H.Jones, P.J.Dyson, R.Del Sol. A Tale of Tails: Deciphering the Contribution of Terminal Tails to the Biochemical Properties of Two Dps Proteins From Streptomyces Coelicolor Cell.Mol.Life Sci. 2014.
ISSN: ESSN 1420-9071
PubMed: 24915944
DOI: 10.1007/S00018-014-1658-4