Sodium in PDB 4tme: Crystal Structure of Eutl From Clostridium Perfringens Bound to Ethanolamine

The structure of Crystal Structure of Eutl From Clostridium Perfringens Bound to Ethanolamine, PDB code: 4tme was solved by M.C.Thompson, T.O.Yeates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	83.04 / 1.70
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.960, 87.960, 251.910, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 16.2

The binding sites of Sodium atom in the Crystal Structure of Eutl From Clostridium Perfringens Bound to Ethanolamine (pdb code 4tme). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Eutl From Clostridium Perfringens Bound to Ethanolamine, PDB code: 4tme:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Eutl From Clostridium Perfringens Bound to Ethanolamine


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 Eutl From Clostridium Perfringens Bound to Ethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:21.9 occ:1.00 OD1 C:ASN74 2.3 28.0 1.0 OD1 A:ASN74 2.3 27.6 1.0 OD1 B:ASN74 2.3 26.5 1.0 O C:HOH479 2.3 40.9 1.0 O A:HOH497 2.4 40.3 1.0 O B:HOH510 2.5 42.9 1.0 CG B:ASN74 3.4 24.5 1.0 CG C:ASN74 3.4 25.6 1.0 CG A:ASN74 3.4 25.7 1.0 CB B:ASN74 4.2 23.8 1.0 CB A:ASN74 4.2 24.0 1.0 CB C:ASN74 4.3 24.6 1.0 ND2 C:ASN74 4.4 23.1 1.0 ND2 B:ASN74 4.4 24.5 1.0 ND2 A:ASN74 4.4 24.8 1.0 CA A:ASN74 4.5 23.5 1.0 CA B:ASN74 4.5 23.7 1.0 CA C:ASN74 4.6 24.8 1.0 O C:GLY73 5.0 29.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Eutl From Clostridium Perfringens Bound to Ethanolamine


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 Eutl From Clostridium Perfringens Bound to Ethanolamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:45.7 occ:1.00 O B:HOH432 2.3 43.8 1.0 O B:LEU165 2.3 32.9 1.0 O B:ALA168 2.3 35.8 1.0 O B:HOH529 2.4 38.0 1.0 O B:HOH573 2.4 45.6 1.0 O B:HOH433 2.6 54.7 1.0 C B:ALA168 3.4 37.6 1.0 C B:LEU165 3.6 30.2 1.0 CA B:ASP169 4.1 34.1 1.0 N B:ASP169 4.1 35.5 1.0 O C:HOH509 4.2 48.2 1.0 N B:ALA168 4.2 31.9 1.0 N B:VAL170 4.2 29.6 1.0 O B:LYS166 4.2 31.3 0.7 C B:LYS166 4.3 31.2 0.7 CA B:LYS166 4.4 31.0 0.7 O B:VAL170 4.4 33.0 1.0 CA B:ALA168 4.4 34.9 1.0 C B:LYS166 4.4 31.1 0.3 N B:LYS166 4.4 29.6 0.7 CA B:LYS166 4.4 31.6 0.3 N B:LYS166 4.4 29.6 0.3 CA B:LEU165 4.5 27.9 1.0 O B:LYS166 4.6 31.6 0.3 C B:ASP169 4.7 31.9 1.0 N B:ALA167 4.9 31.2 1.0 OE1 C:GLU22 4.9 35.5 0.5

M.C.Thompson, D.Cascio, D.J.Leibly, T.O.Yeates. An Allosteric Model For Control of Pore Opening By Substrate Binding in the Eutl Microcompartment Shell Protein. Protein Sci. 2015.
ISSN: ESSN 1469-896X
PubMed: 25752492
DOI: 10.1002/PRO.2672