Sodium in PDB 5e3b: Structure of Macrodomain Protein From Streptomyces Coelicolor

The structure of Structure of Macrodomain Protein From Streptomyces Coelicolor, PDB code: 5e3b was solved by J.Lalic, M.Posavec Marjanovic, D.Perina, I.Sabljic, R.Zaja, B.Plese, M.Imesek, G.Bucca, M.Ahel, H.Cetkovic, M.Luic, A.Mikoc, I.Ahel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.43 / 1.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.819, 103.819, 33.254, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.3

The binding sites of Sodium atom in the Structure of Macrodomain Protein From Streptomyces Coelicolor (pdb code 5e3b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Macrodomain Protein From Streptomyces Coelicolor, PDB code: 5e3b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Macrodomain Protein 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 Macrodomain Protein From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1000 b:30.5 occ:1.00 OD1 A:ASP156 1.8 18.7 0.4 CG A:ASP156 2.9 17.2 0.4 O A:HOH1155 2.9 29.5 1.0 O A:VAL154 3.0 15.4 1.0 NH1 A:ARG124 3.1 24.0 1.0 NE A:ARG124 3.3 19.8 1.0 O A:VAL7 3.4 18.6 1.0 OD2 A:ASP156 3.5 16.0 0.4 N A:VAL7 3.6 17.3 1.0 CB A:TYR6 3.6 17.1 1.0 N A:ASP156 3.7 19.0 1.0 CZ A:ARG124 3.7 19.0 1.0 C A:VAL154 3.8 15.4 1.0 CA A:TYR6 3.8 16.3 1.0 C A:TYR6 4.0 17.5 1.0 CB A:ASP156 4.0 17.7 0.4 CB A:ASP156 4.0 20.7 0.6 C A:TYR155 4.0 14.9 1.0 C A:VAL7 4.1 16.1 1.0 CG1 A:VAL154 4.1 16.2 1.0 CD1 A:TYR6 4.1 20.7 1.0 CA A:TYR155 4.2 14.8 1.0 N A:TYR155 4.3 14.8 1.0 CG A:TYR6 4.4 21.0 1.0 CA A:ASP156 4.4 17.9 0.4 CA A:ASP156 4.4 18.7 0.6 CA A:VAL7 4.4 18.1 1.0 CD A:ARG124 4.5 19.4 1.0 CB A:VAL154 4.6 14.9 1.0 O A:TYR155 4.7 16.3 1.0 CA A:VAL154 4.8 14.4 1.0 CB A:ARG124 4.9 21.0 1.0 O A:TYR6 4.9 18.6 1.0

Sodium binding site 2 out of 2 in the Structure of Macrodomain Protein 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 Macrodomain Protein From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1001 b:35.9 occ:1.00 OD2 A:ASP156 2.3 16.0 0.4 OD2 A:ASP156 2.6 20.3 0.6 O A:HOH1155 2.9 29.5 1.0 CG A:ASP156 3.0 17.2 0.4 CB A:ASP156 3.2 17.7 0.4 CB A:ASP156 3.3 20.7 0.6 CG A:ASP156 3.4 21.2 0.6 OD1 A:ASP156 4.1 18.7 0.4 CD A:ARG8 4.4 30.7 1.0 CB A:ARG8 4.6 24.2 1.0 OD1 A:ASP156 4.6 17.4 0.6 CA A:ASP156 4.7 17.9 0.4 CA A:ASP156 4.8 18.7 0.6 CG A:ARG8 5.0 24.9 1.0

J.Lalic, M.Posavec Marjanovic, L.Palazzo, D.Perina, I.Sabljic, R.Zaja, T.Colby, B.Plese, M.Halasz, G.Jankevicius, G.Bucca, M.Ahel, I.Matic, H.Cetkovic, M.Luic, A.Mikoc, I.Ahel. Disruption of Macrodomain Protein SCO6735 Increases Antibiotic Production in Streptomyces Coelicolor. J.Biol.Chem. V. 291 23175 2016.
ISSN: ESSN 1083-351X
PubMed: 27634042
DOI: 10.1074/JBC.M116.721894