Sodium in PDB 9iok: Crystal Structure of Sortase E From Thermobifida Fusca

The structure of Crystal Structure of Sortase E From Thermobifida Fusca, PDB code: 9iok was solved by V.Sharma, S.Murmu, A.Megta, R.P.Roy, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.56 / 1.80
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	111.111, 111.111, 70.023, 90, 90, 90
R / Rfree (%)	17.8 / 19.6

The structure of Crystal Structure of Sortase E From Thermobifida Fusca also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Sortase E From Thermobifida Fusca (pdb code 9iok). 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 Sortase E From Thermobifida Fusca, PDB code: 9iok:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Sortase E From Thermobifida Fusca


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 Sortase E From Thermobifida Fusca within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:23.5 occ:1.00 O B:SER114 2.3 17.3 1.0 O A:SER114 2.3 19.1 1.0 O B:HOH469 2.3 27.5 1.0 OD1 B:ASP120 2.5 21.3 1.0 OD1 A:ASP120 2.5 18.6 1.0 C A:SER114 3.4 20.0 1.0 CG B:ASP120 3.4 21.0 1.0 C B:SER114 3.4 17.5 1.0 CG A:ASP120 3.5 18.5 1.0 N A:SER114 3.7 19.8 1.0 N B:SER114 3.8 18.6 1.0 CB A:VAL113 3.8 20.8 1.0 CG2 A:VAL113 3.8 23.3 1.0 CG2 B:VAL113 3.8 22.6 1.0 CB B:VAL113 3.9 21.5 1.0 CA A:SER114 3.9 17.6 1.0 CB B:ASP120 3.9 19.8 1.0 CA B:SER114 4.0 17.6 1.0 CB A:ASP120 4.0 18.9 1.0 CB A:SER114 4.1 20.7 1.0 CB B:SER114 4.3 19.0 1.0 CA B:ASP120 4.3 18.6 1.0 CA A:ASP120 4.4 18.2 1.0 OD2 B:ASP120 4.4 19.9 1.0 OD2 A:ASP120 4.5 17.9 1.0 N A:GLY115 4.5 17.9 1.0 C A:VAL113 4.5 19.3 1.0 N B:GLY115 4.5 19.4 1.0 C B:VAL113 4.5 18.1 1.0 CA A:VAL113 4.7 18.7 1.0 CA A:GLY115 4.8 19.5 1.0 CA B:VAL113 4.8 19.3 1.0 CG1 A:VAL113 4.8 24.9 1.0 CA B:GLY115 4.8 19.7 1.0 CG1 B:VAL113 4.8 21.9 1.0 OG A:SER114 4.9 21.0 1.0 OG B:SER114 5.0 20.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Sortase E From Thermobifida Fusca


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 Sortase E From Thermobifida Fusca within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:27.5 occ:1.00 O A:HOH474 2.4 33.2 1.0 O A:VAL111 2.5 22.5 1.0 O A:PRO125 2.6 16.7 1.0 N A:PRO125 3.3 15.9 1.0 C A:GLY124 3.3 17.8 1.0 CD A:PRO125 3.4 15.8 1.0 CA A:GLY124 3.5 20.7 1.0 C A:PRO125 3.6 15.4 1.0 C A:VAL111 3.7 20.8 1.0 N A:VAL113 3.7 18.4 1.0 O A:GLY124 3.8 18.4 1.0 CG1 A:VAL113 3.8 24.9 1.0 CA A:PRO125 4.0 14.8 1.0 CA A:VAL112 4.1 18.3 1.0 CG A:PRO125 4.1 15.9 1.0 N A:GLY124 4.2 24.5 1.0 CG2 A:VAL113 4.3 23.3 1.0 C A:VAL112 4.3 18.1 1.0 O A:HOH413 4.3 27.7 1.0 N A:VAL112 4.3 18.8 1.0 CB A:VAL113 4.4 20.8 1.0 CA A:VAL113 4.7 18.7 1.0 CB A:PRO125 4.7 16.5 1.0 N A:GLY126 4.8 16.1 1.0 CB A:TRP110 4.8 17.6 1.0 CA A:VAL111 4.9 20.2 1.0 C A:TYR123 4.9 30.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Sortase E From Thermobifida Fusca


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 Sortase E From Thermobifida Fusca within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:27.2 occ:1.00 O B:HOH468 2.4 38.2 1.0 O B:VAL111 2.5 19.6 1.0 O B:PRO125 2.6 14.9 1.0 N B:PRO125 3.2 14.5 1.0 C B:GLY124 3.3 14.8 1.0 CD B:PRO125 3.4 15.5 1.0 CA B:GLY124 3.6 19.0 1.0 C B:PRO125 3.6 15.3 1.0 C B:VAL111 3.6 18.8 1.0 N B:VAL113 3.7 17.5 1.0 CG1 B:VAL113 3.8 21.9 1.0 O B:GLY124 3.8 15.7 1.0 CA B:PRO125 3.9 15.6 1.0 CA B:VAL112 4.0 17.4 1.0 CG B:PRO125 4.2 16.6 1.0 CG2 B:VAL113 4.2 22.6 1.0 N B:VAL112 4.3 17.1 1.0 C B:VAL112 4.3 18.6 1.0 N B:GLY124 4.3 21.1 1.0 CB B:VAL113 4.4 21.5 1.0 O B:HOH409 4.5 27.2 1.0 CA B:VAL113 4.6 19.3 1.0 CB B:PRO125 4.7 17.4 1.0 N B:GLY126 4.8 15.1 1.0 CB B:TRP110 4.8 14.4 1.0 O B:HOH454 4.8 33.8 1.0 CA B:VAL111 4.8 19.2 1.0 C B:TYR123 5.0 27.7 1.0

V.Sharma, S.Murmu, A.Megta, R.P.Roy, V.Krishnan. Crystal Structure Analysis of Sortase E From Thermobifida Fusca To Be Published.