Sodium in PDB 6orj: Central Spike of Phikz Phage Tail

The structure of Central Spike of Phikz Phage Tail, PDB code: 6orj was solved by P.G.Leiman, C.Browning, M.M.Shneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.89 / 2.37
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	82.595, 82.595, 345.930, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 20.6

The structure of Central Spike of Phikz Phage Tail also contains other interesting chemical elements:

Chlorine

(Cl)

5 atoms

The binding sites of Sodium atom in the Central Spike of Phikz Phage Tail (pdb code 6orj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Central Spike of Phikz Phage Tail, PDB code: 6orj:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Central Spike of Phikz Phage Tail


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Central Spike of Phikz Phage Tail within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:29.2 occ:0.33 O A:ASN96 2.4 26.7 1.0 O A:HOH442 2.4 32.0 1.0 C A:ASN96 3.5 22.9 1.0 CA A:ASN96 3.9 18.5 1.0 CB A:ASN96 4.1 25.8 1.0 O A:HOH574 4.1 46.9 1.0 OD1 A:ASN96 4.4 38.7 1.0 N A:GLU97 4.6 23.7 1.0 CG A:ASN96 4.7 34.2 1.0

Sodium binding site 2 out of 3 in the Central Spike of Phikz Phage Tail


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Central Spike of Phikz Phage Tail within 5.0Å range: probe atom residue distance (Å) B Occ A:Na308 b:67.8 occ:1.00 OH A:TYR240 2.3 45.3 1.0 O A:HOH610 2.4 63.5 1.0 O A:HOH528 2.4 61.4 1.0 O A:HOH494 2.4 41.1 1.0 O A:HOH530 2.5 63.8 1.0 CZ A:TYR240 3.5 42.7 1.0 O A:HOH551 4.1 70.7 1.0 CE2 A:TYR240 4.1 37.4 1.0 NZ A:LYS242 4.3 49.2 1.0 O A:HOH607 4.4 61.0 1.0 CE1 A:TYR240 4.5 35.8 1.0

Sodium binding site 3 out of 3 in the Central Spike of Phikz Phage Tail


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Central Spike of Phikz Phage Tail within 5.0Å range: probe atom residue distance (Å) B Occ A:Na309 b:35.5 occ:1.00 O A:SER139 2.5 28.3 1.0 O A:HOH472 2.5 26.5 1.0 OD1 A:ASP105 2.5 33.4 1.0 O A:HOH507 2.5 38.0 1.0 OD2 A:ASP105 2.7 35.9 1.0 CG A:ASP105 2.9 27.7 1.0 C A:SER139 3.5 26.2 1.0 O A:HOH437 3.6 26.5 1.0 CB A:SER139 3.7 32.6 1.0 N A:SER139 3.8 28.8 1.0 CA A:SER139 3.9 25.5 1.0 CG A:ARG40 4.1 33.8 1.0 O A:PRO103 4.1 23.4 1.0 O A:ARG40 4.3 37.0 1.0 CB A:ASP105 4.4 26.4 1.0 CB A:THR102 4.4 31.2 1.0 NE A:ARG40 4.7 40.1 1.0 OG1 A:THR102 4.7 31.0 1.0 N A:VAL140 4.7 22.3 1.0 CE1 A:HIS168 4.8 36.5 1.0 CG2 A:THR102 4.8 20.3 1.0 OG A:SER139 4.9 30.4 1.0 O A:HOH441 4.9 24.7 1.0 CA A:ARG40 4.9 44.3 1.0 CA A:ASP105 4.9 27.5 1.0 N A:ASP105 4.9 27.3 1.0 CD A:ARG40 5.0 42.8 1.0

P.G.Leiman, C.Browning, M.M.Shneider. Central Spike of Phikz Phage Tail To Be Published.