Zinc 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:

Calcium	(Ca)	6 atoms
Chlorine	(Cl)	5 atoms
Sodium	(Na)	3 atoms

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

Zinc binding site 1 out of 2 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of CWP6 From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn707 b:36.1 occ:0.69 O A:HOH1278 2.2 46.7 1.0 O A:HOH1240 2.2 49.9 1.0 ND1 A:HIS539 2.2 25.7 1.0 OE1 A:GLU486 2.2 29.7 1.0 NE2 A:HIS469 2.2 34.9 1.0 O A:HOH912 2.3 46.5 1.0 CD A:GLU486 3.0 34.9 1.0 OE2 A:GLU486 3.1 31.2 1.0 CE1 A:HIS539 3.2 25.4 1.0 CD2 A:HIS469 3.2 31.4 1.0 CG A:HIS539 3.3 25.3 1.0 CE1 A:HIS469 3.4 30.3 1.0 CB A:HIS539 3.6 25.4 1.0 O A:HOH1433 3.8 62.9 1.0 O A:TYR540 4.3 33.9 1.0 NE2 A:HIS539 4.3 25.0 1.0 CD2 A:HIS539 4.4 23.3 1.0 CG A:HIS469 4.4 32.0 1.0 CG A:GLU486 4.4 28.4 1.0 ND1 A:HIS469 4.5 26.5 1.0 CA A:HIS539 4.5 22.2 1.0 N A:TYR540 4.7 27.0 1.0 OE2 A:GLU612 4.8 43.3 1.0 O B:HOH984 4.8 30.2 1.0 O A:HOH1363 4.8 29.1 1.0 OE1 A:GLU612 5.0 38.7 1.0

Zinc binding site 2 out of 2 in the CWP6 From Clostridium Difficile


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of CWP6 From Clostridium Difficile within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn710 b:47.1 occ:0.70 NE2 B:HIS469 2.2 27.3 1.0 ND1 B:HIS539 2.2 22.6 1.0 O B:HOH1235 2.2 42.5 1.0 OE1 B:GLU486 2.2 33.1 1.0 O B:HOH1321 2.3 48.0 1.0 O B:HOH1196 2.6 59.8 1.0 CD B:GLU486 3.1 41.9 1.0 CD2 B:HIS469 3.1 23.5 1.0 CE1 B:HIS539 3.2 25.9 1.0 CG B:HIS539 3.2 23.5 1.0 CE1 B:HIS469 3.2 30.1 1.0 OE2 B:GLU486 3.3 37.3 1.0 CB B:HIS539 3.5 21.3 1.0 O B:HOH1306 3.7 49.6 1.0 O B:HOH1312 3.9 75.1 1.0 O B:TYR540 4.1 39.1 1.0 CG B:HIS469 4.3 23.9 1.0 NE2 B:HIS539 4.3 25.1 1.0 ND1 B:HIS469 4.3 26.4 1.0 CD2 B:HIS539 4.3 21.9 1.0 CG B:GLU486 4.5 29.8 1.0 CA B:HIS539 4.5 20.9 1.0 N B:TYR540 4.6 25.5 1.0 O B:HOH1406 4.6 26.8 1.0 OE1 B:GLU612 4.8 46.1 1.0 O A:HOH1408 4.8 52.9 1.0 OE2 B:GLU612 4.8 51.6 1.0 O A:HOH861 5.0 30.5 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