Sodium 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
Zinc	(Zn)	4 atoms

The binding sites of Sodium 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 Sodium atom.
In total 4 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4;

Sodium 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 Sodium with other atoms in the Na 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:Na1169 b:34.0 occ:1.00 O A:HOH2145 2.3 31.7 1.0 O A:HOH2143 2.5 23.1 1.0 OD1 A:ASN93 2.5 20.4 1.0 O A:THR97 2.7 45.8 1.0 O A:LYS94 2.7 57.9 1.0 CG A:ASN93 3.5 20.6 1.0 CE2 A:TYR152 3.7 13.5 1.0 CD2 A:TYR152 3.7 13.6 1.0 C A:THR97 3.7 41.8 1.0 ND2 A:ASN93 3.8 20.0 1.0 C A:LYS94 3.8 52.0 1.0 N A:THR97 3.8 48.5 1.0 O A:PRO95 3.9 59.1 1.0 CB A:THR97 4.0 44.4 1.0 CA A:THR97 4.0 44.3 1.0 C A:PRO95 4.0 58.9 1.0 CA A:PRO95 4.1 65.1 1.0 CZ A:TYR152 4.3 14.0 1.0 N A:PRO95 4.4 62.5 1.0 CG A:TYR152 4.4 11.9 1.0 N A:LYS94 4.7 32.7 1.0 C A:SER96 4.7 51.9 1.0 OG1 A:THR97 4.8 41.1 1.0 N A:SER96 4.8 50.9 1.0 C A:ASN93 4.9 24.5 1.0 CB A:ASN93 4.9 19.5 1.0 CA A:LYS94 4.9 41.8 1.0 OH A:TYR152 4.9 16.7 1.0 CE1 A:TYR152 4.9 12.2 1.0 N A:VAL98 5.0 36.5 1.0 CD1 A:TYR152 5.0 12.4 1.0 O A:THR127 5.0 26.0 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na1168 b:37.9 occ:1.00 O B:HOH2150 2.1 34.6 1.0 O B:HOH2147 2.3 28.1 1.0 OD1 B:ASN93 2.6 20.3 1.0 O B:THR97 2.8 37.1 1.0 O B:LYS94 2.8 44.7 1.0 CG B:ASN93 3.5 21.7 1.0 CE2 B:TYR152 3.6 11.6 1.0 CD2 B:TYR152 3.6 12.3 1.0 O B:PRO95 3.8 47.5 1.0 C B:THR97 3.8 33.0 1.0 ND2 B:ASN93 3.8 20.2 1.0 C B:LYS94 3.8 45.6 1.0 N B:THR97 3.9 39.5 1.0 C B:PRO95 4.0 47.9 1.0 CA B:PRO95 4.0 52.6 1.0 O B:HOH2145 4.1 48.6 1.0 CB B:THR97 4.1 35.2 1.0 CA B:THR97 4.1 34.9 1.0 CZ B:TYR152 4.2 13.0 1.0 CG B:TYR152 4.3 11.2 1.0 N B:PRO95 4.4 51.2 1.0 C B:SER96 4.7 43.4 1.0 N B:LYS94 4.7 32.6 1.0 N B:SER96 4.8 41.0 1.0 CE1 B:TYR152 4.8 12.7 1.0 CD1 B:TYR152 4.9 12.2 1.0 OH B:TYR152 4.9 15.8 1.0 OG1 B:THR97 4.9 30.6 1.0 CB B:ASN93 4.9 20.2 1.0 C B:ASN93 4.9 26.0 1.0 O B:THR127 4.9 23.8 1.0 CA B:LYS94 4.9 39.4 1.0 N B:VAL98 5.0 28.3 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na1168 b:49.5 occ:1.00 O C:HOH2121 2.2 24.4 0.5 O C:HOH2123 2.2 44.2 1.0 O C:THR97 2.4 41.6 1.0 OD1 C:ASN93 2.6 24.1 1.0 O C:LYS94 3.0 46.5 1.0 CE2 C:TYR152 3.4 18.9 1.0 C C:THR97 3.5 42.6 1.0 O C:HOH2122 3.5 19.9 0.5 CD2 C:TYR152 3.6 19.5 1.0 CG C:ASN93 3.6 26.5 1.0 N C:THR97 3.8 48.8 1.0 O C:PRO95 3.9 57.4 1.0 CA C:THR97 3.9 45.5 1.0 ND2 C:ASN93 4.0 25.1 1.0 CB C:THR97 4.0 43.6 1.0 CZ C:TYR152 4.0 19.4 1.0 C C:LYS94 4.1 49.8 1.0 C C:PRO95 4.2 54.4 1.0 CG C:TYR152 4.3 19.2 1.0 CA C:PRO95 4.3 54.0 1.0 OH C:TYR152 4.5 21.3 1.0 C C:SER96 4.6 54.3 1.0 N C:VAL98 4.6 38.1 1.0 CE1 C:TYR152 4.7 18.9 1.0 N C:PRO95 4.7 53.2 1.0 CD1 C:TYR152 4.8 18.9 1.0 O C:THR127 4.8 30.6 1.0 OG1 C:THR97 4.9 39.4 1.0 N C:LYS94 4.9 40.3 1.0 N C:SER96 4.9 55.0 1.0 CG2 C:THR97 5.0 44.5 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na1168 b:48.6 occ:1.00 O D:HOH2115 2.0 22.4 0.5 O D:THR97 2.7 50.8 1.0 OD1 D:ASN93 2.7 28.1 1.0 O D:HOH2114 2.8 19.3 0.5 O D:LYS94 2.9 54.1 1.0 CG D:ASN93 3.6 31.2 1.0 C D:THR97 3.7 49.3 1.0 CE1 D:TYR152 3.7 28.0 1.0 O D:PRO95 3.8 61.5 1.0 CD1 D:TYR152 3.8 26.1 1.0 N D:THR97 3.9 52.6 1.0 ND2 D:ASN93 3.9 28.1 1.0 C D:LYS94 3.9 55.1 1.0 C D:PRO95 4.0 56.9 1.0 CA D:THR97 4.1 50.6 1.0 CA D:PRO95 4.1 59.7 1.0 CB D:THR97 4.1 46.8 1.0 CZ D:TYR152 4.2 28.2 1.0 CG D:TYR152 4.3 26.1 1.0 N D:PRO95 4.5 57.7 1.0 CE2 D:TYR152 4.6 26.4 1.0 C D:SER96 4.7 56.0 1.0 CD2 D:TYR152 4.7 26.5 1.0 OH D:TYR152 4.7 28.4 1.0 O D:THR127 4.8 38.0 1.0 N D:SER96 4.8 56.7 1.0 N D:LYS94 4.8 42.6 1.0 N D:VAL98 4.9 45.2 1.0 OG1 D:THR97 5.0 45.6 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