Sodium in PDB 8a35: Nak C-Di Mutant with Rb+ and Na+

The structure of Nak C-Di Mutant with Rb+ and Na+, PDB code: 8a35 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)	34.03 / 2.05
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	68.062, 68.062, 90.268, 90, 90, 90
R / Rfree (%)	19.2 / 21.7

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

Rubidium

(Rb)

4 atoms

The binding sites of Sodium atom in the Nak C-Di Mutant with Rb+ and Na+ (pdb code 8a35). 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 C-Di Mutant with Rb+ and Na+, PDB code: 8a35:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Nak C-Di Mutant with Rb+ and Na+


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 Rb+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:86.8 occ:0.25 HO4 A:MPD204 2.1 86.1 1.0 H31 A:MPD204 2.2 94.5 1.0 O4 A:MPD204 2.7 72.3 1.0 C3 A:MPD204 3.0 79.2 1.0 H32 A:MPD204 3.0 94.5 1.0 C4 A:MPD204 3.3 81.1 1.0 H53 A:MPD204 3.8 107.2 1.0 H4 A:MPD204 4.1 96.7 1.0 C5 A:MPD204 4.1 89.9 1.0 H13 A:MPD204 4.2 107.0 1.0 C2 A:MPD204 4.3 86.3 1.0 HO2 A:MPD204 4.4 102.9 1.0 H52 A:MPD204 4.6 107.2 1.0 O2 A:MPD204 4.7 86.2 1.0 C1 A:MPD204 4.7 89.6 1.0 H51 A:MPD204 4.9 107.2 1.0

Sodium binding site 2 out of 4 in the Nak C-Di Mutant with Rb+ and Na+


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 Rb+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na206 b:104.3 occ:0.25 HO2 A:MPD204 2.2 102.9 1.0 O2 A:MPD204 2.9 86.2 1.0 H13 A:MPD204 3.9 107.0 1.0 H31 A:MPD204 4.0 94.5 1.0 C2 A:MPD204 4.0 86.3 1.0 H12 A:MPD204 4.1 107.0 1.0 C1 A:MPD204 4.2 89.6 1.0 O A:ASP67 4.2 81.2 1.0 CB A:ASP67 4.3 86.2 1.0 C3 A:MPD204 4.5 79.2 1.0 CA A:ASP67 4.5 79.5 1.0 H32 A:MPD204 4.6 94.5 1.0 C A:ASP67 4.8 81.2 1.0

Sodium binding site 3 out of 4 in the Nak C-Di Mutant with Rb+ and Na+


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 Rb+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na208 b:52.5 occ:0.25 CE2 B:PHE91 4.6 57.6 1.0 CZ B:PHE91 4.9 50.8 1.0

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


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 Rb+ and Na+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Na209 b:92.9 occ:0.25 O B:CYS66 3.6 79.9 1.0 C B:CYS66 4.7 59.5 1.0 N B:CYS66 4.7 57.4 1.0 O B:VAL64 4.7 59.0 1.0

S.Minniberger, S.Abdolvand, S.Braunbeck, H.Sun, A.J.R.Plested. Asymmetry and Ion Selectivity Properties of Bacterial Channel Nak Mutants Derived From Ionotropic Glutamate Receptors. J.Mol.Biol. 67970 2023.
ISSN: ESSN 1089-8638
PubMed: 36682679
DOI: 10.1016/J.JMB.2023.167970