Sodium in PDB 4i0w: Structure of the Clostridium Perfringens Cspb Protease

The structure of Structure of the Clostridium Perfringens Cspb Protease, PDB code: 4i0w was solved by C.M.Adams, B.E.Eckenroth, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.73 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.876, 138.112, 140.038, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 18.1

The structure of Structure of the Clostridium Perfringens Cspb Protease also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Structure of the Clostridium Perfringens Cspb Protease (pdb code 4i0w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Clostridium Perfringens Cspb Protease, PDB code: 4i0w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Clostridium Perfringens Cspb Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Clostridium Perfringens Cspb Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Na603 b:34.6 occ:1.00 O B:HOH877 2.4 38.3 0.8 O B:ASN287 2.4 20.5 1.0 O B:HOH834 2.5 25.7 0.6 OD1 B:ASN290 2.5 27.6 1.0 O B:HOH999 2.5 50.7 1.0 OG B:SER291 2.7 29.3 1.0 CG B:ASN290 3.6 27.7 1.0 C B:ASN287 3.6 19.1 1.0 CB B:SER291 4.0 26.2 1.0 N B:SER291 4.0 24.8 1.0 CB B:PHE455 4.1 21.3 1.0 O B:HOH924 4.2 49.4 1.0 CA B:SER291 4.2 24.6 1.0 ND2 B:ASN290 4.2 31.8 1.0 C B:ASN290 4.2 25.1 1.0 CB B:ASN287 4.3 18.9 1.0 N B:ASN290 4.4 23.1 1.0 O B:HOH1002 4.5 65.8 1.0 CA B:GLU288 4.5 18.5 1.0 O B:HOH861 4.5 44.9 1.0 N B:GLU288 4.5 18.3 1.0 CA B:ASN287 4.6 19.0 1.0 O B:HOH800 4.6 33.5 0.8 CA B:PHE455 4.6 22.4 1.0 O B:ASN290 4.6 27.6 1.0 CA B:ASN290 4.7 24.5 1.0 OE2 B:GLU288 4.7 27.6 1.0 CB B:ASN290 4.8 25.4 1.0 C B:GLU288 4.8 19.8 1.0 O B:PHE455 4.9 20.8 1.0 N B:GLY289 4.9 19.7 1.0

Sodium binding site 2 out of 2 in the Structure of the Clostridium Perfringens Cspb Protease


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Clostridium Perfringens Cspb Protease within 5.0Å range: probe atom residue distance (Å) B Occ D:Na602 b:33.4 occ:1.00 O D:HOH831 2.3 32.8 0.8 O D:HOH877 2.3 27.9 0.7 O D:ASN287 2.4 17.1 1.0 OD1 D:ASN290 2.6 20.6 1.0 OG D:SER291 2.8 25.1 1.0 C D:ASN287 3.6 17.8 1.0 CG D:ASN290 3.7 21.0 1.0 CB D:SER291 4.1 23.3 1.0 N D:SER291 4.2 19.2 1.0 CB D:PHE455 4.2 19.0 1.0 CB D:ASN287 4.2 17.7 1.0 O1 D:EDO606 4.3 52.4 1.0 ND2 D:ASN290 4.3 24.5 1.0 CA D:SER291 4.3 22.4 1.0 C D:ASN290 4.4 20.4 1.0 O D:HOH883 4.4 38.7 0.8 CA D:GLU288 4.5 17.9 1.0 N D:GLU288 4.5 16.2 1.0 N D:ASN290 4.5 19.9 1.0 O D:HOH962 4.5 38.8 1.0 CA D:ASN287 4.5 17.1 1.0 O D:HOH878 4.6 52.7 1.0 OE2 D:GLU288 4.7 25.5 1.0 CA D:PHE455 4.7 18.8 1.0 O D:ASN290 4.7 22.1 1.0 O D:HOH768 4.8 29.0 1.0 CA D:ASN290 4.8 19.8 1.0 C D:GLU288 4.8 17.2 1.0 CB D:ASN290 4.9 21.2 1.0 O D:PHE455 5.0 18.9 1.0 O D:HOH815 5.0 37.7 1.0

C.M.Adams, B.E.Eckenroth, E.E.Putnam, S.Doublie, A.Shen. Structural and Functional Analysis of the Cspb Protease Required For Clostridium Spore Germination. Plos Pathog. V. 9 03165 2013.
ISSN: ISSN 1553-7366
PubMed: 23408892
DOI: 10.1371/JOURNAL.PPAT.1003165