Sodium in PDB 8dtq: Crystal Structure of Staphylococcus Aureus PSK41 Cop

The structure of Crystal Structure of Staphylococcus Aureus PSK41 Cop, PDB code: 8dtq was solved by W.G.Walton, T.C.Eakes, M.R.Redinbo, K.J.Mclaughlin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.58 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.46, 56.261, 46.018, 90, 104.34, 90
R / Rfree (%)	18.8 / 22.3

The structure of Crystal Structure of Staphylococcus Aureus PSK41 Cop also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of Staphylococcus Aureus PSK41 Cop (pdb code 8dtq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Staphylococcus Aureus PSK41 Cop, PDB code: 8dtq:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Staphylococcus Aureus PSK41 Cop


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Staphylococcus Aureus PSK41 Cop within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:17.2 occ:1.00 O A:HOH213 3.0 30.8 1.0 O B:HOH238 3.1 19.2 1.0 O B:HOH256 3.1 24.4 1.0 N B:PHE69 3.2 14.8 1.0 NH1 A:ARG5 3.5 20.4 1.0 CD2 A:LEU9 3.6 16.7 1.0 CB B:PHE69 3.9 16.5 1.0 CB B:SER62 3.9 21.0 1.0 CA B:ASP68 3.9 17.2 1.0 C B:ASP68 4.0 14.8 1.0 O B:VAL67 4.1 19.5 1.0 CA B:PHE69 4.1 15.3 1.0 OE2 A:GLU77 4.2 19.6 0.5 OE2 A:GLU77 4.2 19.6 0.5 O B:HOH224 4.5 21.7 1.0 CZ A:ARG5 4.5 20.5 1.0 OG B:SER62 4.5 25.1 1.0 NH2 A:ARG5 4.7 22.8 1.0 OD1 B:ASP68 4.7 26.8 1.0 O B:HOH223 4.7 47.4 1.0 N B:ASP68 4.8 16.4 1.0 C B:VAL67 4.8 17.9 1.0 CB B:ASP68 4.8 20.2 1.0 CD2 B:LEU59 4.9 17.8 1.0 CD A:GLU77 4.9 20.6 0.5 CD A:GLU77 4.9 20.6 0.5 C B:SER62 5.0 18.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Staphylococcus Aureus PSK41 Cop


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Staphylococcus Aureus PSK41 Cop within 5.0Å range: probe atom residue distance (Å) B Occ A:Na105 b:30.5 occ:1.00 ND1 A:HIS41 3.0 30.6 0.7 N A:THR38 3.6 38.6 1.0 CA A:VAL37 3.8 36.1 1.0 CG A:HIS41 3.9 31.0 0.7 CG2 A:THR38 3.9 42.1 1.0 CG A:HIS41 4.0 34.0 0.3 CB A:HIS41 4.0 31.2 0.7 CB A:HIS41 4.0 33.4 0.3 CB A:VAL37 4.0 34.5 1.0 CE1 A:HIS41 4.0 31.4 0.7 ND1 A:HIS41 4.1 34.4 0.3 C A:VAL37 4.2 37.5 1.0 CG1 A:VAL37 4.3 33.8 1.0 OG1 A:THR38 4.3 42.3 1.0 CD2 A:HIS41 4.5 33.8 0.3 CB A:THR38 4.5 41.5 1.0 CA A:THR38 4.7 40.2 1.0 CE1 A:HIS41 4.7 33.7 0.3 O A:SER36 4.8 37.7 1.0 NE2 A:HIS41 4.9 34.0 0.3

Sodium binding site 3 out of 4 in the Crystal Structure of Staphylococcus Aureus PSK41 Cop


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Staphylococcus Aureus PSK41 Cop within 5.0Å range: probe atom residue distance (Å) B Occ A:Na106 b:46.7 occ:1.00 NZ A:LYS74 3.1 28.7 1.0 NE2 B:HIS70 3.5 24.6 1.0 CD B:LYS74 3.6 27.9 1.0 CD2 B:HIS70 3.7 23.3 1.0 CE A:LYS74 3.8 24.9 1.0 CD A:LYS74 3.9 21.9 1.0 CE B:LYS74 4.0 33.6 1.0 NZ B:LYS74 4.6 36.9 1.0 CD2 A:HIS70 4.6 31.9 1.0 NE2 A:HIS70 4.7 33.9 1.0 CE1 B:HIS70 4.8 22.9 1.0 O A:HOH247 4.9 50.4 1.0 CG B:LYS74 5.0 24.5 1.0 CG B:HIS70 5.0 20.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Staphylococcus Aureus PSK41 Cop


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Staphylococcus Aureus PSK41 Cop within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:30.1 occ:1.00 NE B:ARG44 3.1 28.2 1.0 ND1 B:HIS41 3.2 29.8 0.8 NH2 B:ARG44 3.2 29.3 1.0 CD2 B:HIS41 3.3 25.7 0.2 NZ B:LYS50 3.5 37.0 1.0 CZ B:ARG44 3.6 29.2 1.0 CE B:LYS50 3.7 35.4 1.0 CE1 B:HIS41 4.0 29.6 0.8 CD B:LYS50 4.1 33.1 1.0 O B:HOH214 4.1 42.6 1.0 NE2 B:HIS41 4.1 25.9 0.2 CG B:HIS41 4.1 25.0 0.2 CD B:ARG44 4.2 27.8 1.0 CG B:HIS41 4.2 27.3 0.8 O B:HOH253 4.2 43.9 1.0 CA B:HIS41 4.3 22.3 0.8 CA B:HIS41 4.3 22.9 0.2 CB B:HIS41 4.4 24.3 0.8 O B:HOH266 4.5 42.0 1.0 CB B:HIS41 4.5 23.9 0.2 O B:HOH269 4.6 37.9 1.0 CG B:LYS50 4.8 32.2 1.0 CB B:ARG44 4.9 26.2 1.0 NH1 B:ARG44 4.9 31.2 1.0

A.Sarosh, K.J.Mclaughlin, N.Firth. Conjugative PSK41-Family Plasmids of Staphylococcus Aureus Encode A Cryptic Repressor of Replication To Be Published.