Sodium in PDB 3b1n: Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Adp-Mizoribine

All present enzymatic activity of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Adp-Mizoribine:
2.7.1.143;

The structure of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Adp-Mizoribine, PDB code: 3b1n was solved by Y.Yasutake, H.Ota, E.Hino, S.Sakasegawa, T.Tamura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.31 / 1.55
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	44.583, 164.654, 182.540, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.8

The binding sites of Sodium atom in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Adp-Mizoribine (pdb code 3b1n). 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 Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Adp-Mizoribine, PDB code: 3b1n:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Adp-Mizoribine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Adp-Mizoribine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:11.0 occ:1.00 O A:ALA186 2.3 9.7 1.0 O A:ARG213 2.3 9.9 1.0 O A:GLU184 2.4 11.3 1.0 O A:ILE183 2.4 9.8 1.0 O A:HOH392 2.4 16.4 1.0 C A:GLU184 3.0 10.2 1.0 C A:ALA186 3.4 9.3 1.0 C A:ARG213 3.5 10.1 1.0 N A:ALA186 3.5 10.4 1.0 CA A:GLU184 3.5 9.6 1.0 C A:ILE183 3.5 8.4 1.0 CG1 A:VAL214 3.7 10.9 1.0 C A:LEU185 3.8 11.0 1.0 N A:LEU185 3.9 9.1 1.0 CA A:ALA186 4.0 9.6 1.0 N A:GLU184 4.0 9.9 1.0 O A:HOH630 4.0 35.1 1.0 CA A:VAL214 4.1 9.5 1.0 N A:VAL214 4.2 9.9 1.0 O A:LEU185 4.2 13.1 1.0 CA A:LEU185 4.3 11.2 1.0 N A:THR187 4.5 10.3 1.0 CB A:ALA186 4.5 10.7 1.0 CB A:VAL214 4.5 9.1 1.0 CA A:ARG213 4.6 11.0 1.0 O A:HOH347 4.6 34.2 1.0 CB A:ARG213 4.7 10.8 1.0 CA A:ILE183 4.8 8.6 1.0 CA A:THR187 4.9 9.5 1.0 CB A:GLU184 4.9 9.0 1.0

Sodium binding site 2 out of 2 in the Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Adp-Mizoribine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Burkholderia Thailandensis Nucleoside Kinase (Bthnk) in Complex with Adp-Mizoribine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:22.0 occ:1.00 O B:ARG213 2.2 21.6 1.0 O B:ALA186 2.3 18.1 1.0 O B:GLU184 2.4 21.5 1.0 O B:ILE183 2.4 18.9 1.0 O B:HOH552 2.5 27.3 1.0 C B:GLU184 3.0 20.1 1.0 C B:ALA186 3.4 17.6 1.0 C B:ARG213 3.4 21.6 1.0 N B:ALA186 3.4 18.4 1.0 C B:ILE183 3.6 20.0 1.0 CA B:GLU184 3.6 21.7 1.0 CG1 B:VAL214 3.7 21.7 1.0 C B:LEU185 3.8 19.8 1.0 O B:HOH590 3.8 41.7 1.0 N B:LEU185 3.9 20.4 1.0 CA B:ALA186 3.9 17.9 1.0 CA B:VAL214 4.1 21.0 1.0 N B:GLU184 4.1 20.3 1.0 N B:VAL214 4.2 21.5 1.0 O B:LEU185 4.2 19.9 1.0 CA B:LEU185 4.3 19.6 1.0 CB B:ALA186 4.5 16.7 1.0 CB B:VAL214 4.5 20.8 1.0 CA B:ARG213 4.5 22.6 1.0 N B:THR187 4.5 16.5 1.0 CB B:ARG213 4.6 22.6 1.0 CA B:ILE183 4.8 18.9 1.0 CA B:THR187 4.9 17.1 1.0

Y.Yasutake, H.Ota, E.Hino, S.Sakasegawa, T.Tamura. Structures of Burkholderia Thailandensis Nucleoside Kinase: Implications For the Catalytic Mechanism and Nucleoside Selectivity Acta Crystallogr.,Sect.D V. 67 945 2011.
ISSN: ISSN 0907-4449
PubMed: 22101821
DOI: 10.1107/S0907444911038777