Zinc in PDB 1yb0: Structure of Plyl

The structure of Structure of Plyl, PDB code: 1yb0 was solved by L.Y.Low, C.Yang, M.Perego, A.Osterman, R.C.Liddington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.24 / 1.86
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	163.181, 163.181, 37.292, 90.00, 90.00, 120.00
R / Rfree (%)	20.6 / 24.2

The binding sites of Zinc atom in the Structure of Plyl (pdb code 1yb0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Structure of Plyl, PDB code: 1yb0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Structure of Plyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Plyl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn160 b:23.0 occ:1.00 ND1 A:HIS29 2.2 19.5 1.0 ND1 A:HIS129 2.3 22.4 1.0 SG A:CYS137 2.3 21.0 1.0 O4 A:PO4161 2.4 58.7 1.0 O2 A:PO4161 2.7 59.1 1.0 P A:PO4161 3.0 63.0 1.0 CG A:HIS29 3.1 21.3 1.0 CG A:HIS129 3.1 21.3 1.0 CE1 A:HIS29 3.2 20.2 1.0 CB A:CYS137 3.3 20.5 1.0 CB A:HIS129 3.3 19.2 1.0 CE1 A:HIS129 3.3 24.4 1.0 CB A:HIS29 3.4 19.6 1.0 O A:HOH253 3.8 31.0 1.0 O3 A:PO4161 4.0 58.9 1.0 CA A:HIS29 4.1 21.1 1.0 O1 A:PO4161 4.2 61.0 1.0 CD2 A:HIS29 4.3 20.3 1.0 NE2 A:HIS29 4.3 21.4 1.0 CD2 A:HIS129 4.3 23.0 1.0 NE2 A:HIS129 4.4 23.6 1.0 O A:ALA74 4.4 23.6 1.0 OE2 A:GLU90 4.5 33.0 1.0 CA A:CYS137 4.7 19.4 1.0 O A:ASN30 4.7 22.1 1.0 CA A:HIS129 4.8 19.1 1.0 N A:ASN30 4.8 20.7 1.0 O A:HOH163 5.0 20.4 1.0

Zinc binding site 2 out of 3 in the Structure of Plyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Plyl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn160 b:22.7 occ:1.00 O2 B:PO41161 2.0 27.6 1.0 ND1 B:HIS29 2.1 22.6 1.0 ND1 B:HIS129 2.2 19.4 1.0 SG B:CYS137 2.3 20.6 1.0 CG B:HIS129 3.1 18.5 1.0 CE1 B:HIS29 3.1 22.4 1.0 CG B:HIS29 3.1 22.8 1.0 P B:PO41161 3.2 29.6 1.0 CE1 B:HIS129 3.2 21.2 1.0 CB B:HIS129 3.3 18.0 1.0 CB B:CYS137 3.3 19.5 1.0 CB B:HIS29 3.4 21.4 1.0 O4 B:PO41161 3.5 28.4 1.0 O3 B:PO41161 3.8 27.2 1.0 O B:ALA74 4.2 22.5 1.0 NE2 B:HIS29 4.2 23.4 1.0 CA B:HIS29 4.2 20.5 1.0 CD2 B:HIS129 4.2 17.9 1.0 CD2 B:HIS29 4.2 24.1 1.0 NE2 B:HIS129 4.3 18.5 1.0 O1 B:PO41161 4.3 31.8 1.0 O B:HOH1180 4.5 27.2 1.0 NZ B:LYS135 4.6 29.0 1.0 CD B:LYS135 4.7 23.5 1.0 OE2 B:GLU90 4.7 27.0 1.0 CE B:LYS135 4.7 23.0 1.0 CA B:CYS137 4.7 19.0 1.0 CA B:HIS129 4.8 20.3 1.0 O B:ASN30 4.9 21.9 1.0 N B:ASN30 4.9 21.2 1.0

Zinc binding site 3 out of 3 in the Structure of Plyl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Plyl within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn160 b:28.2 occ:1.00 ND1 C:HIS29 2.2 24.4 1.0 SG C:CYS137 2.3 27.1 1.0 ND1 C:HIS129 2.3 23.9 1.0 O4 C:PO42161 2.6 67.2 1.0 O3 C:PO42161 2.7 65.4 1.0 P C:PO42161 2.9 65.9 1.0 O1 C:PO42161 2.9 62.5 1.0 CG C:HIS29 3.1 29.8 1.0 CG C:HIS129 3.2 23.6 1.0 CB C:CYS137 3.2 27.7 1.0 CB C:HIS29 3.3 27.8 1.0 CE1 C:HIS29 3.3 27.0 1.0 CE1 C:HIS129 3.3 26.2 1.0 CB C:HIS129 3.3 26.4 1.0 CA C:HIS29 4.1 27.1 1.0 O C:ALA74 4.1 27.0 1.0 CD2 C:HIS29 4.3 27.3 1.0 O2 C:PO42161 4.3 67.2 1.0 CD2 C:HIS129 4.3 25.8 1.0 OE2 C:GLU90 4.3 39.6 1.0 NE2 C:HIS29 4.3 26.5 1.0 NE2 C:HIS129 4.4 24.4 1.0 N C:ASN30 4.6 30.7 1.0 CA C:CYS137 4.7 25.8 1.0 O C:ASN30 4.7 31.6 1.0 CA C:HIS129 4.8 26.6 1.0 C C:HIS29 5.0 32.1 1.0 C C:CYS137 5.0 29.9 1.0

L.Y.Low, C.Yang, M.Perego, A.Osterman, R.C.Liddington. Structure and Lytic Activity of A Bacillus Anthracis Prophage Endolysin J.Biol.Chem. V. 280 35433 2005.
ISSN: ISSN 0021-9258
PubMed: 16103125
DOI: 10.1074/JBC.M502723200