Zinc in PDB 4csh: Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K

The structure of Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K, PDB code: 4csh was solved by M.Sanz-Gaitero, R.Keary, C.Garcia-Doval, A.Coffey, M.J.Van Raaij, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.85 / 1.79
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	39.220, 61.470, 73.130, 91.49, 98.62, 89.99
R / Rfree (%)	17.486 / 20.106

The structure of Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Sodium	(Na)	4 atoms

The binding sites of Zinc atom in the Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K (pdb code 4csh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K, PDB code: 4csh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1170 b:27.1 occ:0.67 SG A:CYS54 2.2 13.3 1.0 O A:HOH2094 2.3 19.1 1.0 O A:HOH2212 2.5 42.0 1.0 O A:HOH2097 2.6 36.5 1.0 O3S A:MES1168 3.3 34.0 1.0 O A:GLY116 3.4 13.1 1.0 O2S A:MES1168 3.5 28.9 1.0 CB A:CYS54 3.6 10.0 1.0 S A:MES1168 3.8 38.7 1.0 C8 A:MES1168 3.9 38.1 1.0 ND1 A:HIS117 4.2 10.0 1.0 N A:CYS54 4.2 10.4 1.0 CA A:HIS117 4.3 9.0 1.0 C A:GLY116 4.4 11.1 1.0 OE1 A:GLN53 4.4 20.0 1.0 CA A:CYS54 4.5 9.7 1.0 O A:HOH2171 4.5 23.4 1.0 CB A:ALA76 4.6 10.4 1.0 N A:HIS117 4.8 9.5 1.0 CB A:HIS117 4.9 9.0 1.0 N A:GLN55 4.9 9.7 1.0 C7 A:MES1168 4.9 37.8 1.0 CG A:HIS117 5.0 9.5 1.0

Zinc binding site 2 out of 4 in the Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1169 b:27.9 occ:0.67 SG B:CYS54 2.2 13.6 1.0 O B:HOH2100 2.4 33.2 1.0 O B:HOH2098 2.5 20.4 1.0 O B:GLY116 3.3 9.9 1.0 O2S B:MES1167 3.5 34.1 1.0 O1S B:MES1167 3.5 29.7 1.0 CB B:CYS54 3.6 9.9 1.0 S B:MES1167 3.8 38.3 1.0 C8 B:MES1167 3.9 36.7 1.0 ND1 B:HIS117 4.2 7.6 1.0 N B:CYS54 4.3 9.6 1.0 CA B:HIS117 4.3 8.8 1.0 C B:GLY116 4.4 9.8 1.0 OE1 B:GLN53 4.4 15.6 1.0 CA B:CYS54 4.6 9.3 1.0 CB B:ALA76 4.6 10.9 1.0 O B:HOH2171 4.6 20.4 1.0 CB B:HIS117 4.9 8.5 1.0 N B:HIS117 4.9 9.1 1.0 C3 B:MES1167 5.0 37.9 1.0 N B:GLN55 5.0 8.2 1.0

Zinc binding site 3 out of 4 in the Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1169 b:17.5 occ:0.67 O C:HOH2172 2.0 41.0 1.0 O C:HOH2079 2.2 24.3 1.0 SG C:CYS54 2.3 15.7 1.0 O C:HOH2075 2.8 17.6 1.0 O C:GLY116 3.3 16.1 1.0 O3S C:MES1167 3.5 26.5 1.0 O2S C:MES1167 3.5 29.6 1.0 CB C:CYS54 3.6 12.0 1.0 S C:MES1167 3.8 34.9 1.0 C8 C:MES1167 3.9 33.9 1.0 ND1 C:HIS117 4.2 13.7 1.0 N C:CYS54 4.3 10.3 1.0 CA C:HIS117 4.3 14.1 1.0 C C:GLY116 4.4 14.8 1.0 O C:HOH2135 4.5 29.2 1.0 CA C:CYS54 4.5 10.9 1.0 CB C:ALA76 4.6 14.1 1.0 OE1 C:GLN53 4.7 12.6 1.0 N C:HIS117 4.8 14.0 1.0 CB C:HIS117 4.9 13.9 1.0 N C:GLN55 4.9 9.8 1.0

Zinc binding site 4 out of 4 in the Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Native Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1169 b:14.9 occ:0.67 O D:HOH2074 2.1 35.2 1.0 SG D:CYS54 2.2 14.2 1.0 O D:HOH2071 2.8 17.0 1.0 O D:GLY116 3.4 15.2 1.0 O1S D:MES1167 3.5 24.5 1.0 O2S D:MES1167 3.5 24.4 1.0 CB D:CYS54 3.5 12.7 1.0 S D:MES1167 3.8 35.9 1.0 C8 D:MES1167 3.9 32.1 1.0 N D:CYS54 4.2 11.8 1.0 ND1 D:HIS117 4.3 16.4 1.0 CA D:HIS117 4.4 13.7 1.0 C D:GLY116 4.4 13.8 1.0 CA D:CYS54 4.4 11.7 1.0 CB D:ALA76 4.5 13.4 1.0 OE1 D:GLN53 4.7 14.4 1.0 N D:GLN55 4.8 11.0 1.0 N D:HIS117 4.9 15.2 1.0 CB D:HIS117 4.9 15.7 1.0 C7 D:MES1167 4.9 30.6 1.0

M.Sanz-Gaitero, R.Keary, C.Garcia-Doval, A.Coffey, M.J.Van Raaij. Crystal Structure of the Lytic Chapk Domain of the Endolysin Lysk From Staphylococcus Aureus Bacteriophage K. Virol.J. V. 11 133 2014.
ISSN: ISSN 1743-422X
PubMed: 25064136
DOI: 10.1186/1743-422X-11-133