Zinc in PDB 3qay: Catalytic Domain of CD27L Endolysin Targeting Clostridia Difficile

The structure of Catalytic Domain of CD27L Endolysin Targeting Clostridia Difficile, PDB code: 3qay was solved by M.J.Mayer, V.Garefaliki, R.Spoerl, A.Narbad, R.Meijers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	36.507, 69.737, 78.818, 101.72, 102.00, 105.24
R / Rfree (%)	18.4 / 24.6

The binding sites of Zinc atom in the Catalytic Domain of CD27L Endolysin Targeting Clostridia Difficile (pdb code 3qay). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Catalytic Domain of CD27L Endolysin Targeting Clostridia Difficile, PDB code: 3qay:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Catalytic Domain of CD27L Endolysin Targeting Clostridia Difficile


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of CD27L Endolysin Targeting Clostridia Difficile within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn180 b:9.0 occ:1.00 ND1 A:HIS84 2.0 8.9 1.0 NE2 A:HIS9 2.0 8.8 1.0 OE2 A:GLU26 2.1 10.1 1.0 O4 A:PO4181 2.2 26.6 1.0 O A:HOH1468 2.4 13.8 1.0 O A:HOH1469 2.9 33.1 1.0 CE1 A:HIS84 2.9 9.7 1.0 CD A:GLU26 2.9 9.8 1.0 CD2 A:HIS9 3.0 9.6 1.0 CE1 A:HIS9 3.0 10.0 1.0 CG A:HIS84 3.1 8.1 1.0 P A:PO4181 3.1 29.9 1.0 OE1 A:GLU26 3.1 11.1 1.0 O1 A:PO4181 3.3 28.5 1.0 O3 A:PO4181 3.4 26.6 1.0 CB A:HIS84 3.5 7.4 1.0 O A:LEU85 3.9 9.3 1.0 NE2 A:HIS84 4.0 9.5 1.0 ND1 A:HIS9 4.1 10.7 1.0 CG A:HIS9 4.1 9.3 1.0 CD2 A:HIS84 4.1 9.1 1.0 CA A:HIS84 4.3 7.1 1.0 CG A:GLU26 4.3 9.1 1.0 O A:HOH694 4.4 17.4 1.0 O2 A:PO4181 4.5 27.1 1.0 N A:LEU85 4.5 7.7 1.0 OE2 A:GLU144 4.6 18.5 1.0 O A:HOH186 4.9 5.6 1.0 C A:HIS84 5.0 7.3 1.0 O A:HOH427 5.0 18.2 1.0

Zinc binding site 2 out of 4 in the Catalytic Domain of CD27L Endolysin Targeting Clostridia Difficile


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of CD27L Endolysin Targeting Clostridia Difficile within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn180 b:9.6 occ:1.00 OE2 B:GLU26 2.0 8.7 1.0 ND1 B:HIS84 2.1 9.3 1.0 NE2 B:HIS9 2.1 9.4 1.0 O2 B:PO4181 2.4 48.1 1.0 O B:HOH909 2.4 11.3 1.0 O B:HOH1470 2.7 19.9 1.0 CD B:GLU26 2.9 7.1 1.0 CE1 B:HIS84 3.0 9.3 1.0 CD2 B:HIS9 3.0 9.4 1.0 OE1 B:GLU26 3.1 5.9 1.0 CG B:HIS84 3.1 8.6 1.0 CE1 B:HIS9 3.1 9.7 1.0 CB B:HIS84 3.4 8.2 1.0 P B:PO4181 3.6 49.2 1.0 O3 B:PO4181 3.7 48.9 1.0 O B:LEU85 3.9 9.8 1.0 NE2 B:HIS84 4.1 9.7 1.0 ND1 B:HIS9 4.2 10.3 1.0 CG B:HIS9 4.2 9.7 1.0 CD2 B:HIS84 4.2 9.7 1.0 CA B:HIS84 4.2 8.0 1.0 CG B:GLU26 4.2 8.1 1.0 O B:HOH617 4.3 13.6 1.0 OE2 B:GLU144 4.4 17.4 1.0 N B:LEU85 4.4 8.5 1.0 O4 B:PO4181 4.5 48.5 1.0 O1 B:PO4181 4.7 48.0 1.0 C B:HIS84 4.9 8.1 1.0 O B:HOH226 5.0 8.8 1.0 C B:LEU85 5.0 9.5 1.0

Zinc binding site 3 out of 4 in the Catalytic Domain of CD27L Endolysin Targeting Clostridia Difficile


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalytic Domain of CD27L Endolysin Targeting Clostridia Difficile within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn180 b:10.7 occ:1.00 ND1 C:HIS84 1.9 10.3 1.0 O1 C:PO4181 2.0 46.1 1.0 NE2 C:HIS9 2.1 10.9 1.0 OE2 C:GLU26 2.2 10.0 1.0 O C:HOH1471 2.3 7.5 1.0 O4 C:PO4181 2.8 46.1 1.0 CE1 C:HIS84 2.8 9.7 1.0 P C:PO4181 2.8 47.0 1.0 CD C:GLU26 3.0 8.8 1.0 CG C:HIS84 3.0 9.4 1.0 CD2 C:HIS9 3.0 10.6 1.0 CE1 C:HIS9 3.1 11.2 1.0 OE1 C:GLU26 3.1 8.6 1.0 CB C:HIS84 3.5 9.0 1.0 O2 C:PO4181 3.5 47.1 1.0 NE2 C:HIS84 4.0 10.0 1.0 O C:LEU85 4.1 10.9 1.0 CD2 C:HIS84 4.1 9.0 1.0 O3 C:PO4181 4.2 47.2 1.0 ND1 C:HIS9 4.2 10.9 1.0 CG C:HIS9 4.2 10.4 1.0 CA C:HIS84 4.3 8.5 1.0 O C:HOH210 4.4 13.6 1.0 CG C:GLU26 4.4 8.9 1.0 N C:LEU85 4.6 9.2 1.0 OE2 C:GLU144 4.7 18.2 1.0 O C:HOH239 5.0 14.6 1.0

Zinc binding site 4 out of 4 in the Catalytic Domain of CD27L Endolysin Targeting Clostridia Difficile


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalytic Domain of CD27L Endolysin Targeting Clostridia Difficile within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn180 b:13.4 occ:1.00 ND1 D:HIS84 2.0 10.9 1.0 NE2 D:HIS9 2.0 11.9 1.0 OE2 D:GLU26 2.1 12.5 1.0 O4 D:PO4181 2.2 50.0 1.0 O D:HOH1472 2.2 17.8 1.0 O3 D:PO4181 2.4 50.2 1.0 P D:PO4181 2.7 51.2 1.0 CE1 D:HIS84 2.9 10.8 1.0 CD D:GLU26 2.9 11.3 1.0 CE1 D:HIS9 3.0 12.3 1.0 CD2 D:HIS9 3.0 10.9 1.0 CG D:HIS84 3.1 9.8 1.0 OE1 D:GLU26 3.1 10.6 1.0 O2 D:PO4181 3.4 50.4 1.0 CB D:HIS84 3.5 10.4 1.0 O D:LEU85 4.0 13.5 1.0 O1 D:PO4181 4.0 50.5 1.0 NE2 D:HIS84 4.0 10.8 1.0 ND1 D:HIS9 4.1 12.5 1.0 CG D:HIS9 4.1 11.2 1.0 CD2 D:HIS84 4.2 9.8 1.0 O D:HOH756 4.3 10.3 1.0 CG D:GLU26 4.3 10.8 1.0 CA D:HIS84 4.4 10.1 1.0 OE2 D:GLU144 4.4 18.7 1.0 N D:LEU85 4.6 11.3 1.0 O D:HOH248 4.8 9.8 1.0 O D:HOH515 4.8 34.1 1.0 O D:HOH1198 4.9 33.5 1.0

M.J.Mayer, V.Garefalaki, R.Spoerl, A.Narbad, R.Meijers. Structure-Based Modification of A Clostridium Difficile-Targeting Endolysin Affects Activity and Host Range. J.Bacteriol. V. 193 5477 2011.
ISSN: ISSN 0021-9193
PubMed: 21803993
DOI: 10.1128/JB.00439-11