Sodium in PDB 7oor: Nak C-Di Mutant with Na+ and K+

The structure of Nak C-Di Mutant with Na+ and K+, PDB code: 7oor 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)	40.62 / 1.47
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.25, 88.49, 49.66, 90, 90, 90
R / Rfree (%)	14.7 / 18.3

The structure of Nak C-Di Mutant with Na+ and K+ also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Nak C-Di Mutant with Na+ and K+ (pdb code 7oor). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Nak C-Di Mutant with Na+ and K+, PDB code: 7oor:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Nak C-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nak C-Di Mutant with Na+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na216 b:84.7 occ:0.50 NA A:NA217 2.2 71.2 0.5 O A:HOH308 2.2 43.2 0.6 NA B:NA208 2.3 42.7 0.7 O A:CYS66 3.1 29.5 1.0 HA A:ASP67 3.5 33.2 1.0 HA B:ASP67 3.6 37.2 1.0 O B:CYS66 3.7 34.6 1.0 C A:CYS66 3.9 25.8 1.0 NA B:NA207 4.0 52.2 0.7 NA B:NA209 4.3 35.4 0.8 O A:HOH322 4.3 36.8 1.0 CA A:ASP67 4.3 27.7 1.0 HB3 A:ASP67 4.4 39.7 1.0 N A:ASP67 4.5 25.4 1.0 CA B:ASP67 4.6 31.1 1.0 C B:CYS66 4.6 32.8 1.0 HA A:CYS66 4.8 30.2 1.0 H A:CYS66 4.8 27.1 1.0 CA A:CYS66 4.9 25.1 1.0 CB A:ASP67 4.9 33.1 1.0 N B:ASP67 5.0 29.5 1.0

Sodium binding site 2 out of 5 in the Nak C-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Nak C-Di Mutant with Na+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na217 b:71.2 occ:0.50 NA A:NA216 2.2 84.7 0.5 HA A:ASP67 2.9 33.2 1.0 HA B:ASP67 3.2 37.2 1.0 HB3 A:ASP67 3.5 39.7 1.0 CA A:ASP67 3.7 27.7 1.0 HB2 A:ASP67 3.9 39.7 1.0 CB A:ASP67 3.9 33.1 1.0 O A:HOH308 3.9 43.2 0.6 O A:CYS66 4.0 29.5 1.0 O B:ASP67 4.1 31.6 1.0 CA B:ASP67 4.1 31.1 1.0 NA B:NA208 4.3 42.7 0.7 HB2 B:ASP67 4.3 44.4 1.0 C B:ASP67 4.5 29.6 1.0 O B:CYS66 4.5 34.6 1.0 N A:ASP67 4.6 25.4 1.0 HB3 B:ASP67 4.6 44.4 1.0 C A:CYS66 4.6 25.8 1.0 CB B:ASP67 4.6 37.0 1.0 C A:ASP67 4.7 25.9 1.0 O A:ASP67 4.8 28.8 1.0

Sodium binding site 3 out of 5 in the Nak C-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Nak C-Di Mutant with Na+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na207 b:52.2 occ:0.69 NA B:NA208 2.3 42.7 0.7 O A:HOH322 2.4 36.8 1.0 HA3 B:GLY65 2.6 25.5 1.0 O A:HOH308 2.8 43.2 0.6 O A:VAL64 2.9 19.1 1.0 O B:VAL64 3.2 18.9 1.0 NA B:NA209 3.2 35.4 0.8 HA3 A:GLY65 3.2 20.2 1.0 CA B:GLY65 3.5 21.3 1.0 K A:K202 3.6 15.2 0.5 H B:CYS66 3.9 37.6 1.0 CA A:GLY65 3.9 16.9 1.0 C B:GLY65 4.0 25.0 1.0 C A:GLY65 4.0 18.5 1.0 NA A:NA216 4.0 84.7 0.5 C A:VAL64 4.0 15.5 1.0 HA2 B:GLY65 4.0 25.5 1.0 C B:VAL64 4.1 15.8 1.0 N A:CYS66 4.1 22.6 1.0 N B:CYS66 4.2 31.4 1.0 H A:CYS66 4.2 27.1 1.0 N B:GLY65 4.3 17.7 1.0 O B:CYS66 4.4 34.6 1.0 O A:GLY65 4.4 20.3 1.0 N A:GLY65 4.5 16.1 1.0 HA A:CYS66 4.5 30.2 1.0 O A:CYS66 4.6 29.5 1.0 O B:GLY65 4.6 26.6 1.0 HA2 A:GLY65 4.7 20.2 1.0 CA A:CYS66 4.8 25.1 1.0

Sodium binding site 4 out of 5 in the Nak C-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Nak C-Di Mutant with Na+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:42.7 occ:0.70 O A:HOH308 2.2 43.2 0.6 NA B:NA209 2.2 35.4 0.8 NA B:NA207 2.3 52.2 0.7 NA A:NA216 2.3 84.7 0.5 O A:HOH322 3.2 36.8 1.0 O B:CYS66 3.2 34.6 1.0 HA3 B:GLY65 3.8 25.5 1.0 C B:CYS66 3.9 32.8 1.0 H B:CYS66 3.9 37.6 1.0 N B:CYS66 4.0 31.4 1.0 HA B:ASP67 4.1 37.2 1.0 C B:GLY65 4.1 25.0 1.0 NA A:NA217 4.3 71.2 0.5 O B:VAL64 4.4 18.9 1.0 O A:CYS66 4.4 29.5 1.0 CA B:CYS66 4.5 33.4 1.0 CA B:GLY65 4.5 21.3 1.0 O B:GLY65 4.5 26.6 1.0 N B:ASP67 4.6 29.5 1.0 HA B:CYS66 4.7 40.0 1.0 CA B:ASP67 4.8 31.1 1.0 HA A:CYS66 5.0 30.2 1.0

Sodium binding site 5 out of 5 in the Nak C-Di Mutant with Na+ and K+


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Nak C-Di Mutant with Na+ and K+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na209 b:35.4 occ:0.76 NA B:NA208 2.2 42.7 0.7 O B:GLY65 3.0 26.6 1.0 C B:GLY65 3.2 25.0 1.0 NA B:NA207 3.2 52.2 0.7 O B:VAL64 3.2 18.9 1.0 HA3 B:GLY65 3.5 25.5 1.0 N B:CYS66 3.6 31.4 1.0 HG12 B:VAL64 3.7 21.8 1.0 CA B:GLY65 3.8 21.3 1.0 HA B:CYS66 3.9 40.0 1.0 H B:CYS66 4.0 37.6 1.0 C B:CYS66 4.0 32.8 1.0 C B:VAL64 4.0 15.8 1.0 CA B:CYS66 4.1 33.4 1.0 O B:CYS66 4.1 34.6 1.0 O B:HOH312 4.1 28.7 0.5 O A:HOH308 4.2 43.2 0.6 O A:HOH322 4.3 36.8 1.0 NA A:NA216 4.3 84.7 0.5 N B:GLY65 4.4 17.7 1.0 HG13 B:VAL64 4.4 21.8 1.0 CG1 B:VAL64 4.5 18.2 1.0 N B:ASP67 4.6 29.5 1.0 HA2 B:GLY65 4.7 25.5 1.0 O B:HOH312 4.7 30.2 0.5 H B:ASP67 4.9 35.4 1.0 HA B:ASP67 4.9 37.2 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.