Sodium in PDB 5ji5: Crystal Structure of A Histone Deacetylase Superfamily Protein From Burkholderia Phymatumphymatum

The structure of Crystal Structure of A Histone Deacetylase Superfamily Protein From Burkholderia Phymatumphymatum, PDB code: 5ji5 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.80 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	66.380, 127.870, 68.680, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 23.5

The structure of Crystal Structure of A Histone Deacetylase Superfamily Protein From Burkholderia Phymatumphymatum also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of A Histone Deacetylase Superfamily Protein From Burkholderia Phymatumphymatum (pdb code 5ji5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of A Histone Deacetylase Superfamily Protein From Burkholderia Phymatumphymatum, PDB code: 5ji5:

Sodium binding site 1 out of 1 in the Crystal Structure of A Histone Deacetylase Superfamily Protein From Burkholderia Phymatumphymatum


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 A Histone Deacetylase Superfamily Protein From Burkholderia Phymatumphymatum within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:32.1 occ:1.00 O A:ILE185 2.6 15.8 1.0 O A:HOH536 2.7 20.4 1.0 O A:HIS165 2.8 9.7 1.0 O A:ASP163 2.9 17.8 1.0 OD1 A:ASP161 3.3 9.5 1.0 C A:HIS165 3.5 18.0 1.0 CG A:ASP161 3.6 18.1 1.0 CA A:HIS166 3.7 13.7 1.0 CB A:PHE186 3.7 14.2 1.0 C A:ILE185 3.7 10.8 1.0 O A:ASP161 3.8 25.2 1.0 N A:GLY167 3.8 9.5 1.0 C A:ASP163 3.9 17.8 1.0 N A:HIS166 3.9 17.3 1.0 OD2 A:ASP161 4.0 17.1 1.0 C A:HIS166 4.1 12.7 1.0 CA A:PHE186 4.2 14.8 1.0 CB A:SER184 4.2 14.6 1.0 OG A:SER184 4.2 18.7 1.0 N A:ASP163 4.2 9.9 1.0 CB A:ASP161 4.3 9.7 1.0 C A:ASP161 4.3 18.1 1.0 CA A:ASP163 4.4 17.8 1.0 N A:PHE186 4.4 11.0 1.0 CB A:ASP163 4.5 9.5 1.0 N A:ILE185 4.5 13.4 1.0 CE1 A:HIS125 4.6 10.2 1.0 N A:HIS165 4.6 15.8 1.0 C A:VAL164 4.7 18.4 1.0 CA A:HIS165 4.7 14.9 1.0 C A:PHE162 4.8 11.7 1.0 O A:VAL164 4.8 13.8 1.0 CA A:ILE185 4.8 11.9 1.0 CG A:PHE186 4.9 14.4 1.0 N A:PHE162 4.9 10.2 1.0 CB A:HIS166 4.9 15.0 1.0 ND1 A:HIS125 4.9 11.2 1.0 CA A:ASP161 4.9 14.1 1.0 N A:VAL164 5.0 10.2 1.0 CA A:PHE162 5.0 14.3 1.0 CA A:GLY167 5.0 9.3 1.0

D.M.Dranow, J.Abendroth, D.Lorimer, T.E.Edwards. Crystal Structure of A Histone Deacetylase Superfamily Protein From Burkholderia Phymatumphymatum To Be Published.