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

Protein crystallography data

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

Other elements in 4csh:

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:

Zinc (Zn) 4 atoms
Sodium (Na) 4 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 4csh

Go back to Calcium Binding Sites List in 4csh
Calcium 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 Calcium with other atoms in the Ca 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:Ca1167

b:10.2
occ:1.00
 OD1 A:ASP47 2.3 15.1 1.0
OD1 A:ASP45 2.3 10.3 1.0
OD2 A:ASP56 2.4 8.2 1.0
O A:TYR49 2.4 11.2 1.0
O A:HIS51 2.4 8.7 1.0
O A:HOH2085 2.5 12.5 1.0
OD1 A:ASP56 2.7 10.2 1.0
CG A:ASP56 2.9 8.8 1.0
CG A:ASP47 3.4 16.8 1.0
CG A:ASP45 3.4 10.5 1.0
C A:TYR49 3.6 12.0 1.0
C A:HIS51 3.6 9.7 1.0
OD2 A:ASP47 3.8 18.0 1.0
N A:TYR49 4.1 11.9 1.0
OD2 A:ASP45 4.2 10.7 1.0
N A:HIS51 4.2 10.1 1.0
OH A:TYR32 4.3 8.3 1.0
CA A:ASP45 4.3 10.7 1.0
C A:TYR50 4.3 11.4 1.0
CB A:ASP45 4.3 10.8 1.0
N A:ASP47 4.4 17.8 1.0
O A:HOH2098 4.4 29.3 1.0
CB A:ASP56 4.4 9.1 1.0
N A:GLY48 4.4 14.7 1.0
CA A:TYR49 4.4 12.0 1.0
CA A:HIS51 4.5 9.5 1.0
N A:ALA46 4.5 11.9 1.0
N A:GLN53 4.5 11.4 1.0
N A:TYR50 4.6 11.4 1.0
CG A:GLN53 4.6 16.5 1.0
N A:ALA52 4.6 9.8 1.0
CB A:ASP47 4.6 18.4 1.0
CA A:ALA52 4.7 10.8 1.0
O A:TYR50 4.7 10.7 1.0
CA A:TYR50 4.7 12.5 1.0
C A:ASP45 4.7 10.8 1.0
CB A:TYR50 4.7 13.6 1.0
CA A:ASP47 4.8 18.1 1.0
CB A:GLN53 4.9 13.9 1.0
C A:GLY48 5.0 11.8 1.0
C A:ASP47 5.0 18.8 1.0

Calcium binding site 2 out of 4 in 4csh

Go back to Calcium Binding Sites List in 4csh
Calcium 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 Calcium with other atoms in the Ca 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:Ca1166

b:12.3
occ:1.00
 O B:TYR49 2.3 12.1 1.0
OD1 B:ASP47 2.4 13.5 1.0
OD2 B:ASP56 2.4 7.9 1.0
OD1 B:ASP45 2.4 7.4 1.0
O B:HIS51 2.4 8.2 1.0
O B:HOH2088 2.4 10.8 1.0
OD1 B:ASP56 2.8 7.6 1.0
CG B:ASP56 2.9 6.9 1.0
CG B:ASP47 3.4 13.8 1.0
CG B:ASP45 3.5 7.7 1.0
C B:TYR49 3.5 12.1 1.0
C B:HIS51 3.6 8.6 1.0
OD2 B:ASP47 3.8 15.8 1.0
N B:TYR49 4.1 12.1 1.0
OD2 B:ASP45 4.2 8.0 1.0
N B:HIS51 4.2 9.4 1.0
OH B:TYR32 4.2 7.9 1.0
C B:TYR50 4.3 10.5 1.0
CA B:ASP45 4.4 7.6 1.0
CA B:TYR49 4.4 12.8 1.0
CB B:ASP45 4.4 7.3 1.0
CA B:HIS51 4.4 8.4 1.0
N B:GLN53 4.4 9.1 1.0
CB B:ASP56 4.4 6.9 1.0
N B:TYR50 4.5 10.9 1.0
N B:ASP47 4.5 13.1 1.0
CG B:GLN53 4.5 11.6 1.0
O B:HOH2101 4.6 28.0 1.0
N B:ALA52 4.6 8.1 1.0
N B:GLY48 4.6 15.2 1.0
N B:ALA46 4.6 9.6 1.0
O B:TYR50 4.7 11.2 1.0
CA B:ALA52 4.7 8.1 1.0
CB B:TYR50 4.7 12.2 1.0
CA B:TYR50 4.7 11.4 1.0
CB B:ASP47 4.7 14.2 1.0
CB B:GLN53 4.7 10.0 1.0
C B:ASP45 4.8 8.3 1.0
CA B:ASP47 5.0 13.8 1.0

Calcium binding site 3 out of 4 in 4csh

Go back to Calcium Binding Sites List in 4csh
Calcium 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 Calcium with other atoms in the Ca 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:Ca1166

b:10.3
occ:1.00
 OD1 C:ASP45 2.3 8.3 1.0
OD1 C:ASP47 2.3 10.0 1.0
O C:TYR49 2.3 11.2 1.0
O C:HIS51 2.4 10.2 1.0
OD2 C:ASP56 2.5 11.9 1.0
O C:HOH2067 2.5 7.4 1.0
OD1 C:ASP56 2.8 10.8 1.0
CG C:ASP56 3.0 10.9 1.0
CG C:ASP45 3.3 9.0 1.0
CG C:ASP47 3.4 11.3 1.0
C C:TYR49 3.5 10.1 1.0
C C:HIS51 3.6 8.5 1.0
OD2 C:ASP47 3.9 12.2 1.0
N C:TYR49 4.0 9.5 1.0
OD2 C:ASP45 4.1 9.2 1.0
OH C:TYR32 4.2 8.0 1.0
N C:HIS51 4.2 8.8 1.0
CB C:ASP45 4.3 8.8 1.0
CA C:ASP45 4.3 8.7 1.0
N C:ASP47 4.4 10.3 1.0
CA C:TYR49 4.4 10.1 1.0
C C:TYR50 4.4 9.0 1.0
N C:GLY48 4.4 9.6 1.0
CB C:ASP56 4.5 10.8 1.0
CA C:HIS51 4.5 8.7 1.0
N C:GLN53 4.5 9.3 1.0
N C:ALA46 4.5 9.4 1.0
N C:TYR50 4.5 10.2 1.0
N C:ALA52 4.6 8.1 1.0
O C:HOH2080 4.6 24.2 1.0
CG C:GLN53 4.6 10.9 1.0
CA C:ALA52 4.7 8.7 1.0
CB C:ASP47 4.7 10.6 1.0
CB C:TYR50 4.7 10.9 1.0
CA C:TYR50 4.7 9.7 1.0
C C:ASP45 4.7 8.8 1.0
O C:TYR50 4.8 9.9 1.0
CA C:ASP47 4.9 10.2 1.0
CB C:GLN53 4.9 10.4 1.0
C C:GLY48 4.9 9.7 1.0

Calcium binding site 4 out of 4 in 4csh

Go back to Calcium Binding Sites List in 4csh
Calcium 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 Calcium with other atoms in the Ca 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:Ca1166

b:10.5
occ:1.00
 OD2 D:ASP56 2.4 11.9 1.0
O D:TYR49 2.4 7.2 1.0
OD1 D:ASP47 2.4 11.9 1.0
OD1 D:ASP45 2.4 11.3 1.0
O D:HOH2059 2.5 10.0 1.0
O D:HIS51 2.5 10.8 1.0
OD1 D:ASP56 2.7 10.5 1.0
CG D:ASP56 2.9 10.4 1.0
CG D:ASP47 3.4 13.3 1.0
CG D:ASP45 3.5 11.5 1.0
C D:TYR49 3.6 9.2 1.0
C D:HIS51 3.6 9.5 1.0
OD2 D:ASP47 3.8 13.5 1.0
N D:TYR49 4.1 10.1 1.0
OD2 D:ASP45 4.2 11.2 1.0
N D:HIS51 4.2 9.1 1.0
OH D:TYR32 4.3 9.5 1.0
C D:TYR50 4.3 9.2 1.0
CA D:ASP45 4.4 10.0 1.0
CB D:ASP45 4.4 10.5 1.0
CB D:ASP56 4.4 9.8 1.0
N D:ASP47 4.4 12.7 1.0
N D:GLN53 4.4 10.8 1.0
CA D:TYR49 4.4 9.1 1.0
N D:GLY48 4.5 11.6 1.0
CA D:HIS51 4.5 9.5 1.0
N D:ALA46 4.5 11.4 1.0
N D:ALA52 4.6 9.8 1.0
CG D:GLN53 4.6 13.0 1.0
N D:TYR50 4.6 9.2 1.0
CA D:ALA52 4.7 10.0 1.0
CB D:ASP47 4.7 12.8 1.0
CB D:TYR50 4.7 11.7 1.0
O D:HOH2075 4.7 28.1 1.0
CA D:TYR50 4.7 9.7 1.0
O D:TYR50 4.8 8.2 1.0
C D:ASP45 4.8 10.8 1.0
CB D:GLN53 4.8 12.5 1.0
CA D:ASP47 4.9 13.3 1.0

Reference:

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
Page generated: Tue Jul 8 19:17:35 2025

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