Sodium in PDB 4y8f: Crystal Structure of Triosephosphate Isomerase From Clostridium Perfringens

All present enzymatic activity of Crystal Structure of Triosephosphate Isomerase From Clostridium Perfringens:
5.3.1.1;

The structure of Crystal Structure of Triosephosphate Isomerase From Clostridium Perfringens, PDB code: 4y8f was solved by S.Romero-Romero, A.Rodriguez-Romero, D.A.Fernandez-Velasco, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.59 / 1.54
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.255, 49.555, 71.502, 90.00, 119.11, 90.00
R / Rfree (%)	14.7 / 18.1

The binding sites of Sodium atom in the Crystal Structure of Triosephosphate Isomerase From Clostridium Perfringens (pdb code 4y8f). 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 Triosephosphate Isomerase From Clostridium Perfringens, PDB code: 4y8f:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Triosephosphate Isomerase From Clostridium Perfringens


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 Triosephosphate Isomerase From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:28.9 occ:1.00 O A:HOH767 2.2 37.0 1.0 O A:HOH517 2.4 34.1 1.0 O A:ILE230 2.4 11.8 1.0 O A:MET225 2.5 18.7 1.0 O A:LYS227 2.7 19.8 1.0 O A:HOH766 3.3 22.4 1.0 C A:MET225 3.5 15.8 1.0 C A:ILE230 3.6 9.3 1.0 C A:LYS227 3.9 14.7 1.0 N A:ILE230 4.1 10.4 1.0 N A:LYS227 4.2 15.4 1.0 CA A:MET225 4.2 16.2 1.0 CA A:ILE230 4.3 8.8 1.0 O A:HOH490 4.3 26.7 1.0 C A:ALA226 4.4 13.7 1.0 N A:ALA226 4.5 12.8 1.0 CB A:ILE230 4.5 11.3 1.0 N A:ASP231 4.6 8.1 1.0 CA A:LYS227 4.7 15.6 1.0 CA A:ALA226 4.7 13.8 1.0 C A:SER228 4.7 15.6 1.0 O A:SER228 4.7 15.3 1.0 CE A:MET225 4.8 15.5 1.0 O A:HOH420 4.8 20.7 1.0 O A:ALA226 4.8 18.4 1.0 O A:GLN224 4.9 13.7 1.0 CA A:ASP231 4.9 9.9 1.0 N A:SER228 4.9 13.7 1.0 CB A:MET225 4.9 14.4 1.0 N A:ASP229 5.0 13.6 1.0 C A:ASP229 5.0 13.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Triosephosphate Isomerase From Clostridium Perfringens


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 Triosephosphate Isomerase From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:50.9 occ:1.00 OE1 A:GLU187 2.5 46.9 1.0 O A:HOH672 2.5 32.8 1.0 CD A:GLU187 2.8 41.4 1.0 O A:HOH601 2.9 16.9 1.0 OE2 A:GLU187 3.0 44.8 1.0 CA A:GLN184 3.7 14.6 1.0 CB A:GLU187 3.8 16.3 1.0 CG A:GLN184 3.8 20.6 1.0 CG A:GLU187 3.8 25.6 1.0 CB A:GLN184 4.2 16.6 1.0 N A:GLN184 4.3 14.2 1.0 O A:ASP183 4.3 16.2 1.0 O A:HOH734 4.5 36.7 1.0 O A:HOH726 4.5 43.9 1.0 O A:GLN184 4.5 13.2 1.0 C A:ASP183 4.6 14.3 1.0 C A:GLN184 4.6 14.7 1.0 OD2 A:ASP183 4.8 49.5 1.0 NH1 A:ARG136 4.9 26.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Triosephosphate Isomerase From Clostridium Perfringens


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 Triosephosphate Isomerase From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:47.4 occ:1.00 O A:SER215 2.6 18.7 1.0 CG2 A:THR179 2.6 44.1 1.0 NE2 A:GLN224 3.4 10.9 0.7 O A:HOH626 3.6 30.4 1.0 CB A:THR179 3.6 44.1 1.0 C A:SER215 3.6 17.4 1.0 OH A:TYR212 3.8 17.4 1.0 CB A:SER215 3.9 24.8 1.0 O A:ALA180 3.9 27.7 1.0 CA A:SER215 4.0 20.6 1.0 CE2 A:TYR212 4.1 13.0 1.0 N A:SER215 4.1 13.9 1.0 OG1 A:THR179 4.2 47.9 1.0 OG A:SER215 4.3 27.3 1.0 CZ A:TYR212 4.4 12.8 1.0 CG2 A:THR220 4.7 21.3 1.0 CD A:GLN224 4.7 15.8 0.7 O A:HOH770 4.7 47.8 1.0 N A:VAL216 4.8 14.7 1.0 CB A:THR220 4.8 19.4 1.0 OG1 A:THR220 4.9 19.8 1.0 N A:ALA180 4.9 30.9 1.0 CA A:THR179 4.9 34.3 1.0 C A:ALA180 5.0 24.5 1.0 C A:GLY214 5.0 18.0 1.0

S.Romero-Romero, M.Costas, A.Rodriguez-Romero, D.Alejandro Fernandez-Velasco. Reversibility and Two State Behaviour in the Thermal Unfolding of Oligomeric Tim Barrel Proteins. Phys Chem Chem Phys V. 17 20699 2015.
ISSN: ESSN 1463-9084
PubMed: 26206330
DOI: 10.1039/C5CP01599E