Chlorine 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
Sodium	(Na)	3 atoms

The binding sites of Chlorine atom in the CWP6 From Clostridium Difficile (pdb code 5j72). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the CWP6 From Clostridium Difficile, PDB code: 5j72:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of CWP6 From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl704 b:25.6 occ:1.00 OH A:TYR425 2.9 22.8 1.0 N A:LYS19 3.0 19.2 1.0 NE2 A:GLN159 3.1 19.6 1.0 O A:HOH960 3.2 23.3 1.0 N A:SER20 3.7 17.4 1.0 CG A:GLN159 3.8 19.4 1.0 CB A:LYS19 3.8 20.5 1.0 CZ A:TYR425 3.9 22.8 1.0 CA A:LYS19 3.9 20.3 1.0 CD A:GLN159 4.0 20.7 1.0 CA A:ARG18 4.0 21.7 1.0 C A:ARG18 4.0 20.2 1.0 CD2 A:LEU396 4.0 18.1 1.0 CE1 A:TYR425 4.0 22.7 1.0 C A:LYS19 4.2 17.4 1.0 CG A:LYS19 4.3 27.9 1.0 O A:GLN159 4.5 19.6 1.0 CB A:SER20 4.5 20.9 1.0 CD1 A:LEU396 4.6 18.2 1.0 CB A:ARG18 4.7 19.7 1.0 O A:GLN17 4.7 20.4 1.0 CA A:SER20 4.7 18.6 1.0 CD1 A:LEU392 4.8 16.5 1.0 CG A:LEU396 4.9 16.0 1.0 O A:SER20 4.9 19.7 1.0

Chlorine binding site 2 out of 5 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of CWP6 From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl705 b:55.5 occ:1.00 O A:HOH1060 2.2 53.3 1.0 O A:HOH1442 2.8 64.5 1.0 O B:HOH1139 2.8 35.2 1.0 NH2 A:ARG602 3.1 22.5 1.0 ND2 A:ASN603 3.1 35.1 1.0 NE A:ARG602 3.5 29.6 1.0 CZ A:ARG602 3.7 26.7 1.0 OD1 A:ASN603 3.8 37.1 1.0 O A:HOH846 3.9 39.8 1.0 CG A:ASN603 3.9 35.1 1.0 CE2 A:TYR599 4.2 25.8 1.0 CD1 B:TYR78 4.3 24.6 1.0 O B:HOH1388 4.5 56.9 1.0 CD2 A:TYR599 4.6 25.4 1.0 CE1 B:TYR78 4.6 29.8 1.0 O B:HOH1458 4.8 55.6 1.0 CD A:ARG602 4.8 31.9 1.0 CZ A:TYR599 4.9 32.1 1.0

Chlorine binding site 3 out of 5 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of CWP6 From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl706 b:56.4 occ:1.00 O A:HOH844 2.6 47.5 1.0 O A:HOH842 2.6 44.2 1.0 O A:HOH1203 2.8 32.1 1.0 OE1 A:GLN17 2.9 18.5 1.0 NH1 A:ARG18 3.1 34.0 1.0 O A:LYS26 3.1 20.2 1.0 C A:LYS26 3.6 18.7 1.0 CD A:GLN17 3.8 22.9 1.0 CZ A:ARG18 4.0 35.1 1.0 O A:HOH1435 4.0 54.8 1.0 CB A:LYS26 4.0 24.6 1.0 NE2 A:GLN17 4.0 17.6 1.0 NE A:ARG18 4.0 39.5 1.0 N A:SER27 4.1 16.8 1.0 CA A:SER27 4.1 19.3 1.0 OD1 A:ASN28 4.1 25.1 1.0 N A:ASN28 4.1 18.5 1.0 CG A:ASN28 4.3 22.7 1.0 ND2 A:ASN28 4.4 23.3 1.0 CA A:LYS26 4.4 18.7 1.0 C A:SER27 4.5 21.5 1.0 O A:HOH1415 4.6 50.6 1.0 O A:HOH1050 4.6 50.9 1.0 O A:HOH1049 4.8 27.7 1.0

Chlorine binding site 4 out of 5 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of CWP6 From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl706 b:25.5 occ:1.00 OH B:TYR425 2.9 21.4 1.0 N B:LYS19 3.1 19.2 1.0 O B:HOH1024 3.1 22.7 1.0 NE2 B:GLN159 3.2 21.3 1.0 CG B:GLN159 3.7 22.9 1.0 N B:SER20 3.8 21.3 1.0 CZ B:TYR425 3.8 23.2 1.0 CA B:ARG18 3.9 22.1 1.0 CD B:GLN159 3.9 24.4 1.0 C B:ARG18 3.9 21.0 1.0 CA B:LYS19 4.0 19.5 1.0 CE1 B:TYR425 4.0 23.7 1.0 CD2 B:LEU396 4.0 22.6 1.0 CB B:LYS19 4.1 22.8 1.0 C B:LYS19 4.3 20.8 1.0 CG B:LYS19 4.4 30.3 1.0 O B:GLN159 4.5 22.9 1.0 CB B:SER20 4.6 23.1 1.0 CB B:ARG18 4.6 18.8 0.7 O B:GLN17 4.6 18.4 1.0 CD1 B:LEU396 4.6 16.4 1.0 CB B:ARG18 4.7 19.1 0.3 CA B:SER20 4.8 20.4 1.0 CD1 B:LEU392 4.8 21.8 1.0 CG B:LEU396 4.9 19.6 1.0 O B:SER20 4.9 20.1 1.0

Chlorine binding site 5 out of 5 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of CWP6 From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl707 b:37.5 occ:1.00 O B:HOH1333 2.8 50.1 1.0 O B:HOH1035 3.1 37.6 1.0 N B:ILE383 3.2 26.4 1.0 N B:VAL384 3.3 21.9 1.0 O B:HOH1234 3.4 57.0 1.0 NH1 B:ARG149 3.5 32.4 1.0 CB B:ILE382 3.8 28.3 1.0 CB B:VAL384 3.8 26.2 1.0 CG1 B:VAL384 3.9 24.7 1.0 CB B:ALA176 3.9 59.9 1.0 CB B:ILE383 4.0 27.3 1.0 CA B:ILE383 4.0 23.6 1.0 NH2 B:ARG149 4.1 37.1 1.0 C B:ILE382 4.1 28.9 1.0 C B:ILE383 4.1 22.6 1.0 CA B:ILE382 4.2 29.2 1.0 CZ B:ARG149 4.2 35.4 1.0 CA B:VAL384 4.2 23.9 1.0 CG2 B:ILE382 4.5 30.4 1.0 CG1 B:ILE383 4.7 35.3 1.0 O B:HOH1207 4.8 58.7 1.0 CG1 B:ILE382 4.9 30.2 1.0 O B:GLY173 4.9 32.0 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