Zinc in PDB 6yj1: The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin

The structure of The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin, PDB code: 6yj1 was solved by M.Dunne, P.Ernst, A.Sobieraj, A.Pluckthun, M.J.Loessner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.43 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.890, 56.380, 110.490, 90.00, 92.84, 90.00
R / Rfree (%)	25.1 / 31

The binding sites of Zinc atom in the The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin (pdb code 6yj1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin, PDB code: 6yj1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:26.5 occ:1.00 O A:HOH323 1.9 23.5 1.0 OD1 A:ASP53 2.0 23.8 1.0 ND1 A:HIS135 2.0 23.5 1.0 NE2 A:HIS49 2.1 19.8 1.0 CG A:ASP53 2.7 23.9 1.0 OD2 A:ASP53 2.8 23.4 1.0 CE1 A:HIS135 2.9 22.8 1.0 CD2 A:HIS49 3.0 17.6 1.0 CG A:HIS135 3.0 26.1 1.0 CE1 A:HIS49 3.1 20.8 1.0 CB A:HIS135 3.4 26.4 1.0 NE2 A:HIS135 4.0 25.4 1.0 CG A:HIS49 4.1 16.1 1.0 ND1 A:HIS49 4.1 16.0 1.0 CD2 A:HIS135 4.1 24.0 1.0 CB A:ASP53 4.1 21.6 1.0 CA A:HIS135 4.2 25.4 1.0 NH1 A:ARG32 4.4 24.8 1.0 NE2 A:HIS133 4.5 32.3 1.0 CA A:ASP53 4.6 22.1 1.0 N A:ASP53 4.6 24.0 1.0 NE2 A:HIS97 4.7 31.8 1.0 O A:HOH339 4.7 38.8 1.0 NH2 A:ARG32 4.8 25.4 1.0 O A:PHE52 4.9 23.6 1.0 C A:PHE52 4.9 22.8 1.0 CD2 A:HIS133 4.9 34.7 1.0 CB A:ALA51 5.0 23.1 1.0

Zinc binding site 2 out of 2 in the The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The M23 Peptidase Domain of the Staphylococcal Phage 2638A Endolysin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:28.2 occ:1.00 ND1 B:HIS135 1.8 18.6 1.0 OD1 B:ASP53 1.9 25.1 1.0 NE2 B:HIS49 2.0 22.1 1.0 O B:HOH337 2.3 26.4 1.0 CE1 B:HIS135 2.7 18.4 1.0 CG B:ASP53 2.7 22.4 1.0 CD2 B:HIS49 2.9 20.4 1.0 OD2 B:ASP53 2.9 25.9 1.0 CG B:HIS135 2.9 22.6 1.0 CE1 B:HIS49 3.0 20.8 1.0 CB B:HIS135 3.4 25.9 1.0 NE2 B:HIS135 3.9 20.7 1.0 CD2 B:HIS135 4.0 21.4 1.0 ND1 B:HIS49 4.0 19.1 1.0 CG B:HIS49 4.0 21.7 1.0 CA B:HIS135 4.1 25.4 1.0 CB B:ASP53 4.1 21.7 1.0 NH1 B:ARG32 4.3 20.8 1.0 NE2 B:HIS133 4.4 35.9 1.0 CA B:ASP53 4.5 25.9 1.0 N B:ASP53 4.6 26.1 1.0 O B:PHE52 4.7 24.0 1.0 NH2 B:ARG32 4.7 23.0 1.0 CD2 B:HIS133 4.8 31.5 1.0 NE2 B:HIS97 4.8 36.5 1.0 C B:PHE52 4.8 25.0 1.0 CZ B:ARG32 4.9 23.3 1.0

A.Sobieraj, M.Dunne, P.Ernst, A.Pluckthun, M.J.Loessner. (Casp Target) Crystal Structure of the M23 Peptidase Domain of Staphylococcal Phage 2638A Endolysin To Be Published.