Zinc in PDB 2vo9: Crystal Structure of the Enzymatically Active Domain of the Listeria Monocytogenes Bacteriophage 500 Endolysin PLY500

The structure of Crystal Structure of the Enzymatically Active Domain of the Listeria Monocytogenes Bacteriophage 500 Endolysin PLY500, PDB code: 2vo9 was solved by I.P.Korndoerfer, A.Kanitz, A.Skerra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	59.787, 95.180, 182.578, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.4

The binding sites of Zinc atom in the Crystal Structure of the Enzymatically Active Domain of the Listeria Monocytogenes Bacteriophage 500 Endolysin PLY500 (pdb code 2vo9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of the Enzymatically Active Domain of the Listeria Monocytogenes Bacteriophage 500 Endolysin PLY500, PDB code: 2vo9:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of the Enzymatically Active Domain of the Listeria Monocytogenes Bacteriophage 500 Endolysin PLY500


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Enzymatically Active Domain of the Listeria Monocytogenes Bacteriophage 500 Endolysin PLY500 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:35.6 occ:1.00 OD2 A:ASP87 2.0 25.4 1.0 NE2 A:HIS80 2.0 21.1 1.0 ND1 A:HIS133 2.0 23.1 1.0 CG A:ASP87 2.8 26.4 1.0 CE1 A:HIS80 3.0 23.8 1.0 OD1 A:ASP87 3.0 28.4 1.0 CE1 A:HIS133 3.0 23.7 1.0 CG A:HIS133 3.1 22.3 1.0 CD2 A:HIS80 3.1 23.6 1.0 CB A:HIS133 3.4 22.8 1.0 O3 A:SO4502 3.8 34.0 1.0 O1 A:SO4502 3.9 30.4 1.0 CA A:HIS133 4.0 21.8 1.0 OD2 A:ASP130 4.0 23.4 1.0 O A:HOH2120 4.1 21.6 1.0 NE2 A:HIS133 4.1 23.0 1.0 ND1 A:HIS80 4.1 19.7 1.0 CD2 A:HIS133 4.2 22.4 1.0 CG A:HIS80 4.2 20.0 1.0 CB A:ASP87 4.3 23.1 1.0 O A:VAL86 4.5 23.2 1.0 S A:SO4502 4.5 33.5 1.0 O A:HOH2132 4.5 28.1 1.0 N A:ASP87 4.6 22.6 1.0 C A:VAL86 4.6 23.4 1.0 CA A:ASP87 4.7 22.4 1.0 CG A:ASP130 4.8 23.2 1.0 OD1 A:ASP130 4.9 21.2 1.0 N A:HIS133 4.9 20.6 1.0 CB A:ALA85 5.0 19.4 1.0 C A:HIS133 5.0 23.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of the Enzymatically Active Domain of the Listeria Monocytogenes Bacteriophage 500 Endolysin PLY500


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Enzymatically Active Domain of the Listeria Monocytogenes Bacteriophage 500 Endolysin PLY500 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:36.5 occ:1.00 O B:HOH2146 1.9 24.5 1.0 NE2 B:HIS80 2.0 24.0 1.0 OD2 B:ASP87 2.0 23.1 1.0 ND1 B:HIS133 2.0 22.8 1.0 CG B:ASP87 2.9 26.0 1.0 CE1 B:HIS80 2.9 24.1 1.0 CE1 B:HIS133 3.0 22.6 1.0 CG B:HIS133 3.1 19.4 1.0 CD2 B:HIS80 3.1 24.6 1.0 OD1 B:ASP87 3.1 26.2 1.0 CB B:HIS133 3.4 21.5 1.0 O B:HOH2092 3.8 30.9 1.0 O1 B:SO4502 3.9 41.1 1.0 OD2 B:ASP130 4.0 24.0 1.0 CA B:HIS133 4.0 19.5 1.0 ND1 B:HIS80 4.1 24.6 1.0 NE2 B:HIS133 4.1 20.3 1.0 O B:HOH2130 4.1 19.4 1.0 O2 B:SO4502 4.2 43.1 1.0 CG B:HIS80 4.2 24.6 1.0 CD2 B:HIS133 4.2 21.0 1.0 CB B:ASP87 4.3 24.2 1.0 O B:HOH2148 4.5 40.0 1.0 N B:ASP87 4.6 22.8 1.0 O B:VAL86 4.6 23.2 1.0 CA B:ASP87 4.6 21.4 1.0 S B:SO4502 4.6 39.2 1.0 C B:VAL86 4.7 21.4 1.0 CG B:ASP130 4.7 25.1 1.0 OD1 B:ASP130 4.8 24.2 1.0 CB B:ALA85 5.0 20.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of the Enzymatically Active Domain of the Listeria Monocytogenes Bacteriophage 500 Endolysin PLY500


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Enzymatically Active Domain of the Listeria Monocytogenes Bacteriophage 500 Endolysin PLY500 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:35.9 occ:1.00 NE2 C:HIS80 2.0 23.6 1.0 OD2 C:ASP87 2.1 25.3 1.0 ND1 C:HIS133 2.1 22.1 1.0 CG C:ASP87 2.9 24.6 1.0 CE1 C:HIS80 3.0 22.8 1.0 CE1 C:HIS133 3.0 22.5 1.0 CD2 C:HIS80 3.0 24.0 1.0 CG C:HIS133 3.1 23.9 1.0 OD1 C:ASP87 3.1 27.0 1.0 CB C:HIS133 3.4 20.6 1.0 O C:HOH2048 3.8 28.1 1.0 OD2 C:ASP130 3.9 24.6 1.0 CA C:HIS133 4.0 21.3 1.0 O3 C:SO4502 4.0 41.6 1.0 ND1 C:HIS80 4.1 21.7 1.0 NE2 C:HIS133 4.2 25.4 1.0 CG C:HIS80 4.2 21.9 1.0 CD2 C:HIS133 4.2 24.7 1.0 CB C:ASP87 4.3 22.8 1.0 O1 C:SO4502 4.4 37.1 1.0 O C:VAL86 4.5 23.4 1.0 N C:ASP87 4.6 23.3 1.0 CA C:ASP87 4.6 22.0 1.0 C C:VAL86 4.7 24.1 1.0 S C:SO4502 4.7 42.1 1.0 CG C:ASP130 4.7 24.3 1.0 N C:HIS133 4.9 20.5 1.0 OD1 C:ASP130 5.0 21.6 1.0 C C:HIS133 5.0 21.9 1.0 CB C:ALA85 5.0 19.0 1.0

I.P.Korndorfer, A.Kanitz, J.Danzer, M.Zimmer, M.J.Loessner, A.Skerra. Structural Analysis of the L-Alanoyl-D-Glutamate Endopeptidase Domain of Listeria Bacteriophage Endolysin PLY500 Reveals A New Member of the Las Peptidase Family. Acta Crystallogr.,Sect.D V. 64 644 2008.
ISSN: ISSN 0907-4449
PubMed: 18560152
DOI: 10.1107/S0907444908007890