Sodium in PDB 3cbt: Crystal Structure of SC4828, A Unique Phosphatase From Streptomyces Coelicolor

All present enzymatic activity of Crystal Structure of SC4828, A Unique Phosphatase From Streptomyces Coelicolor:
3.1.3.5;

The structure of Crystal Structure of SC4828, A Unique Phosphatase From Streptomyces Coelicolor, PDB code: 3cbt was solved by A.U.Singer, X.Xu, C.Chang, H.Zheng, A.M.Edwards, A.Joachimiak, A.F.Yakunin, A.Savchenko, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.87 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.738, 77.271, 80.044, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 21.5

The structure of Crystal Structure of SC4828, A Unique Phosphatase From Streptomyces Coelicolor also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of SC4828, A Unique Phosphatase From Streptomyces Coelicolor (pdb code 3cbt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of SC4828, A Unique Phosphatase From Streptomyces Coelicolor, PDB code: 3cbt:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of SC4828, A Unique Phosphatase 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 Crystal Structure of SC4828, A Unique Phosphatase From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:18.5 occ:1.00 OE2 A:GLU210 2.6 14.2 1.0 O A:PRO204 2.6 11.3 1.0 NE1 A:TRP130 2.7 12.0 1.0 N A:TRP209 3.2 10.7 1.0 O A:PHE205 3.3 14.4 1.0 CE2 A:TRP130 3.5 9.6 1.0 CB A:TRP209 3.6 11.8 1.0 CZ2 A:TRP130 3.6 10.0 1.0 N A:GLY208 3.7 11.4 1.0 C A:PRO204 3.7 11.5 1.0 C A:PHE205 3.8 12.4 1.0 CA A:TRP209 3.8 11.5 1.0 CD A:GLU210 3.8 11.7 1.0 N A:GLU210 3.9 11.3 1.0 CD1 A:TRP130 3.9 11.3 1.0 CA A:PHE205 3.9 11.6 1.0 CD1 A:TRP209 4.0 11.8 1.0 NA A:NA420 4.0 20.3 1.0 C A:GLY208 4.1 10.5 1.0 CG A:TRP209 4.2 11.2 1.0 N A:ASP207 4.2 11.2 1.0 CA A:GLY208 4.2 11.2 1.0 N A:PHE205 4.3 11.8 1.0 C A:ASP207 4.3 10.6 1.0 C A:TRP209 4.3 11.2 1.0 CD2 A:LEU119 4.4 11.2 1.0 OE1 A:GLU210 4.5 15.6 1.0 CA A:ASP207 4.7 11.6 1.0 N A:ALA206 4.7 12.0 1.0 CD2 A:TRP130 4.9 10.3 1.0 CA A:PRO204 4.9 12.7 1.0 CB A:PRO204 4.9 12.7 1.0 CB A:ASP207 5.0 12.4 1.0 CB A:GLU210 5.0 10.2 1.0 CH2 A:TRP130 5.0 9.9 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of SC4828, A Unique Phosphatase 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 Crystal Structure of SC4828, A Unique Phosphatase From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:18.2 occ:1.00 O A:HOH523 2.4 18.9 1.0 OE1 A:GLU113 2.5 13.9 1.0 O A:TRP115 2.6 12.4 1.0 N A:ARG110 2.7 12.0 1.0 CD A:GLU113 3.4 12.6 1.0 CA A:ALA109 3.5 10.3 1.0 CG A:GLU113 3.5 13.0 1.0 C A:ALA109 3.6 11.1 1.0 CB A:GLU113 3.6 12.4 1.0 C A:TRP115 3.7 10.1 1.0 CA A:ARG110 3.8 12.5 1.0 CD1 A:TRP115 3.8 12.7 1.0 CB A:ARG110 3.8 12.8 1.0 CG A:ARG110 3.9 13.7 1.0 NE1 A:TRP115 3.9 13.9 1.0 O A:HOH532 4.0 19.9 1.0 O A:ARG110 4.1 12.7 1.0 CA A:SER116 4.2 9.7 1.0 O A:LEU108 4.3 11.3 1.0 O A:HOH531 4.4 23.1 1.0 CB A:ALA109 4.4 11.7 1.0 N A:SER116 4.4 10.7 1.0 C A:ARG110 4.5 13.6 1.0 CG A:TRP115 4.5 11.2 1.0 N A:ALA109 4.6 10.5 1.0 CE2 A:TRP115 4.7 13.5 1.0 OE2 A:GLU113 4.7 15.3 1.0 NE A:ARG110 4.7 16.0 1.0 C A:LEU108 4.8 11.1 1.0 CA A:TRP115 4.8 10.6 1.0 O A:GLU113 4.8 11.8 1.0 O A:ALA109 4.9 11.3 1.0 CA A:GLU113 4.9 12.0 1.0 CD A:ARG110 4.9 15.6 1.0 N A:TRP115 4.9 10.5 1.0 C A:SER116 4.9 10.7 1.0 CD2 A:TRP115 5.0 11.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of SC4828, A Unique Phosphatase 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 Crystal Structure of SC4828, A Unique Phosphatase From Streptomyces Coelicolor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na420 b:20.3 occ:1.00 O A:HOH598 2.4 26.6 1.0 O A:HOH536 2.4 23.5 1.0 O A:PHE205 2.5 14.4 1.0 OE1 A:GLU210 2.5 15.6 1.0 N A:GLY208 2.7 11.4 1.0 OE2 A:GLU210 3.2 14.2 1.0 C A:ALA206 3.2 12.5 1.0 CD A:GLU210 3.3 11.7 1.0 CA A:GLY208 3.4 11.2 1.0 O A:ALA206 3.4 12.8 1.0 N A:ASP207 3.4 11.2 1.0 CA A:ALA206 3.6 12.0 1.0 C A:PHE205 3.6 12.4 1.0 O A:HOH519 3.7 21.6 1.0 C A:ASP207 3.9 10.6 1.0 NA A:NA401 4.0 18.5 1.0 N A:ALA206 4.0 12.0 1.0 CA A:ASP207 4.2 11.6 1.0 C A:GLY208 4.6 10.5 1.0 O A:HOH637 4.6 31.2 1.0 CZ2 A:TRP130 4.7 10.0 1.0 O A:HOH616 4.7 20.4 1.0 CG A:GLU210 4.8 11.7 1.0 NE1 A:TRP201 4.8 13.0 1.0 O A:PRO204 4.8 11.3 1.0 N A:TRP209 4.8 10.7 1.0 O A:HOH665 4.8 34.1 1.0 O A:HOH638 4.9 36.0 1.0 CA A:PHE205 4.9 11.6 1.0 CB A:ALA206 5.0 13.0 1.0 O A:ASP207 5.0 11.5 1.0

A.U.Singer, M.Proudfoot, G.Brown, X.Xu, C.Chang, H.Zhang, A.M.Edwards, A.Joachimiak, A.Savchenko, A.F.Yakunin. Crystal Structure of SC4828, A Unique Phosphatase From Streptomyces Coelicolor. To Be Published.