Sodium in PDB 5j72: CWP6 From Clostridium Difficile

All present enzymatic activity of CWP6 From Clostridium Difficile:
3.5.1.28;

The structure of CWP6 From Clostridium Difficile, PDB code: 5j72 was solved by M.Renko, A.Usenik, D.Turk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.85 / 1.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.357, 212.916, 84.931, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.1

The structure of CWP6 From Clostridium Difficile also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Calcium	(Ca)	6 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Sodium atom in the CWP6 From Clostridium Difficile (pdb code 5j72). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the CWP6 From Clostridium Difficile, PDB code: 5j72:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CWP6 From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:26.0 occ:1.00 O A:SER442 2.1 22.4 1.0 O A:LYS419 2.3 24.3 1.0 O A:LYS445 2.3 35.6 1.0 O A:LEU416 2.3 27.1 1.0 O A:SER417 2.6 29.6 1.0 C A:SER417 3.2 26.9 1.0 C A:SER442 3.2 23.0 1.0 C A:LYS419 3.4 24.5 1.0 C A:LYS445 3.5 35.3 1.0 C A:LEU416 3.5 27.9 1.0 CB A:ALA448 3.6 47.9 1.0 CA A:SER417 3.7 27.4 1.0 N A:LYS419 3.8 23.8 1.0 CA A:LEU443 4.0 25.1 1.0 C A:GLU418 4.0 28.1 1.0 N A:SER417 4.1 28.0 1.0 N A:LEU443 4.1 23.7 1.0 N A:GLU418 4.1 27.0 1.0 CA A:SER442 4.2 23.6 1.0 CA A:LYS419 4.2 22.5 1.0 N A:ALA448 4.2 44.7 1.0 N A:LYS445 4.2 30.1 1.0 N A:HIS446 4.3 35.5 1.0 CB A:SER442 4.4 26.9 1.0 CA A:HIS446 4.4 39.5 1.0 O A:GLU418 4.4 27.1 1.0 CA A:LYS445 4.4 32.6 1.0 N A:THR420 4.5 26.5 1.0 C A:LEU443 4.5 24.8 1.0 CA A:GLU418 4.5 25.7 1.0 CA A:ALA448 4.5 48.0 1.0 CG2 A:THR420 4.6 26.5 1.0 CA A:THR420 4.7 26.0 1.0 N A:ASN447 4.7 42.0 1.0 C A:HIS446 4.7 41.6 1.0 CA A:LEU416 4.7 23.2 1.0 CD2 A:LEU443 4.8 21.5 1.0 N A:SER444 4.9 27.2 1.0 O A:ASN415 4.9 24.0 1.0

Sodium binding site 2 out of 3 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of CWP6 From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ B:Na704 b:22.1 occ:1.00 O B:LYS419 2.2 24.0 1.0 O B:SER442 2.2 20.7 1.0 O B:LEU416 2.4 19.9 1.0 O B:LYS445 2.4 27.4 1.0 O B:SER417 2.5 25.1 1.0 C B:SER417 3.2 22.6 1.0 C B:SER442 3.3 21.2 1.0 C B:LYS419 3.4 22.0 1.0 C B:LEU416 3.5 23.0 1.0 C B:LYS445 3.6 30.4 1.0 CA B:SER417 3.7 21.2 1.0 CB B:ALA448 3.7 32.6 1.0 N B:LYS419 3.8 26.1 1.0 C B:GLU418 4.0 31.9 1.0 N B:GLU418 4.0 23.5 1.0 CA B:LEU443 4.0 17.5 1.0 N B:SER417 4.1 21.3 1.0 CA B:LYS419 4.1 22.3 1.0 N B:LEU443 4.1 21.7 1.0 N B:ALA448 4.2 34.3 1.0 CA B:SER442 4.3 21.8 1.0 N B:LYS445 4.3 26.4 1.0 CA B:HIS446 4.3 31.0 1.0 N B:HIS446 4.4 28.4 1.0 O B:GLU418 4.4 30.0 1.0 N B:THR420 4.4 22.2 1.0 CA B:GLU418 4.5 27.9 1.0 CA B:LYS445 4.5 31.2 1.0 C B:LEU443 4.5 20.9 1.0 CB B:SER442 4.6 22.8 1.0 N B:ASN447 4.6 36.3 1.0 CA B:ALA448 4.7 34.8 1.0 C B:HIS446 4.7 33.9 1.0 CA B:LEU416 4.7 21.4 1.0 CA B:THR420 4.7 21.1 1.0 CG2 B:THR420 4.8 23.6 1.0 CD2 B:LEU443 4.8 20.0 1.0 N B:SER444 4.9 19.6 1.0

Sodium binding site 3 out of 3 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of CWP6 From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ B:Na705 b:44.4 occ:0.50 O B:ASP592 2.8 22.6 1.0 O B:HOH1208 2.8 64.6 1.0 C B:ASN593 3.3 24.0 1.0 O B:HOH1408 3.4 68.0 1.0 N B:GLY594 3.5 19.5 1.0 CA B:ASN593 3.6 23.8 1.0 O B:ASN593 3.7 26.3 1.0 C B:ASP592 3.8 24.3 1.0 CA B:GLY594 4.0 18.8 1.0 N B:ASN593 4.2 22.5 1.0 O B:HOH1224 4.2 43.0 1.0 CA B:ASP592 5.0 20.9 1.0 CB B:ASN593 5.0 27.4 1.0

A.Usenik, M.Renko, M.Mihelic, N.Lindic, J.Borisek, A.Perdih, G.Pretnar, U.Muller, D.Turk. The CWB2 Cell Wall-Anchoring Module Is Revealed By the Crystal Structures of the Clostridium Difficile Cell Wall Proteins CWP8 and CWP6. Structure V. 25 514 2017.
ISSN: ISSN 1878-4186
PubMed: 28132783
DOI: 10.1016/J.STR.2016.12.018