Sodium in PDB 7oq2: Nak S-Di Mutant Soaked in Na+

The structure of Nak S-Di Mutant Soaked in Na+, PDB code: 7oq2 was solved by S.Minniberger, A.J.R.Plested, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.73 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.204, 88.173, 49.389, 90, 90, 90
R / Rfree (%)	18.6 / 23.3

The structure of Nak S-Di Mutant Soaked in Na+ also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Nak S-Di Mutant Soaked in Na+ (pdb code 7oq2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Nak S-Di Mutant Soaked in Na+, PDB code: 7oq2:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Nak S-Di Mutant Soaked in Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nak S-Di Mutant Soaked in Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na215 b:38.5 occ:0.39 O B:HOH306 2.7 40.8 1.0 HA A:ASP67 3.2 27.9 1.0 HA B:ASP67 3.3 41.6 1.0 HB3 A:ASP67 3.7 31.1 1.0 HB2 A:ASP67 3.7 31.1 1.0 CB A:ASP67 4.0 25.9 1.0 NA A:NA216 4.0 40.3 0.4 CA A:ASP67 4.0 23.2 1.0 O B:ASP67 4.1 41.3 1.0 CA B:ASP67 4.2 34.8 1.0 O B:SER66 4.5 28.0 1.0 C B:ASP67 4.5 37.0 1.0 HB2 B:ASP67 4.5 52.1 1.0 O B:HOH329 4.6 29.9 0.4 O A:SER66 4.6 27.1 1.0 HB3 B:ASP67 4.8 52.1 1.0 CB B:ASP67 4.8 43.4 1.0 O B:HOH316 4.8 33.0 1.0 O A:ASP67 4.8 28.6 1.0 C A:ASP67 4.9 24.0 1.0 N A:ASP67 4.9 21.9 1.0

Sodium binding site 2 out of 4 in the Nak S-Di Mutant Soaked in Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Nak S-Di Mutant Soaked in Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na216 b:40.3 occ:0.41 NA A:NA217 2.2 30.3 0.2 O B:HOH306 2.3 40.8 1.0 O B:HOH329 2.3 29.9 0.4 O B:HOH329 2.4 28.8 0.6 O A:HOH315 2.7 33.3 1.0 O B:SER66 3.7 28.0 1.0 O A:SER66 4.0 27.1 1.0 NA A:NA215 4.0 38.5 0.4 HA3 A:GLY65 4.3 22.6 1.0 HA3 B:GLY65 4.4 25.5 1.0 O B:HOH320 4.5 34.0 1.0 HA B:ASP67 4.7 41.6 1.0 C B:SER66 4.7 32.2 1.0 C A:SER66 4.7 22.4 1.0 HA A:ASP67 4.8 27.9 1.0 O B:HOH316 4.8 33.0 1.0 C A:GLY65 4.8 20.6 1.0 O A:VAL64 4.8 19.8 1.0 N A:SER66 5.0 20.8 1.0

Sodium binding site 3 out of 4 in the Nak S-Di Mutant Soaked in Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Nak S-Di Mutant Soaked in Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na217 b:30.3 occ:0.18 NA A:NA216 2.2 40.3 0.4 O B:HOH329 2.3 28.8 0.6 O A:HOH315 2.7 33.3 1.0 HA3 A:GLY65 3.2 22.6 1.0 O A:VAL64 3.2 19.8 1.0 O B:HOH329 3.3 29.9 0.4 K A:K219 3.3 14.5 0.5 HA3 B:GLY65 3.3 25.5 1.0 O B:VAL64 3.4 17.2 1.0 CA A:GLY65 4.1 18.8 1.0 CA B:GLY65 4.2 21.2 1.0 O B:HOH306 4.2 40.8 1.0 C A:VAL64 4.3 18.9 1.0 C A:GLY65 4.5 20.6 1.0 C B:VAL64 4.5 25.4 1.0 O B:HOH320 4.5 34.0 1.0 C B:GLY65 4.6 27.4 1.0 N A:GLY65 4.7 15.9 1.0 HA2 A:GLY65 4.7 22.6 1.0 O A:GLY65 4.8 23.1 1.0 HA2 B:GLY65 4.8 25.5 1.0 N B:GLY65 4.8 21.4 1.0 O B:SER66 4.9 28.0 1.0 O B:GLY65 4.9 22.5 1.0

Sodium binding site 4 out of 4 in the Nak S-Di Mutant Soaked in Na+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Nak S-Di Mutant Soaked in Na+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na205 b:41.2 occ:0.36 O A:HOH343 2.5 50.8 1.0 OG1 B:THR63 3.7 18.8 1.0 HZ B:PHE91 3.9 27.5 0.4 HG1 B:THR63 3.9 22.6 1.0 OG1 A:THR63 3.9 16.9 1.0 HE2 B:PHE91 4.0 31.9 0.4 K A:K218 4.0 21.4 0.5 HG1 A:THR63 4.1 20.4 1.0 HZ A:PHE91 4.4 39.7 1.0 HG21 B:THR63 4.4 25.1 1.0 HZ B:PHE91 4.5 27.1 0.6 CZ B:PHE91 4.5 22.9 0.4 HG21 A:THR63 4.6 24.3 1.0 CE2 B:PHE91 4.6 26.6 0.4 CB B:THR63 4.8 15.3 1.0 CZ A:PHE91 4.8 33.1 1.0 HB B:THR63 4.9 18.4 1.0 CZ B:PHE91 4.9 22.5 0.6 HE2 A:PHE91 4.9 38.0 1.0 CG2 B:THR63 5.0 20.9 1.0 CB A:THR63 5.0 19.2 1.0

S.Minniberger, S.Abdolvand, S.Braunbeck, H.Sun, A.J.R.Plested. Asymmetry and Ion Selectivity Properties in the Bacterial Channel Nak Mimicking Ionotropic Glutamate Receptors To Be Published.