Rubidium in PDB 8ayp: Nak C-Di Mutant with Rb+ and BA2+

The structure of Nak C-Di Mutant with Rb+ and BA2+, PDB code: 8ayp 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)	44.68 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.171, 177.495, 68.042, 90, 90, 90
R / Rfree (%)	22.6 / 26.7

The structure of Nak C-Di Mutant with Rb+ and BA2+ also contains other interesting chemical elements:

Barium

(Ba)

4 atoms

The binding sites of Rubidium atom in the Nak C-Di Mutant with Rb+ and BA2+ (pdb code 8ayp). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 4 binding sites of Rubidium where determined in the Nak C-Di Mutant with Rb+ and BA2+, PDB code: 8ayp:
Jump to Rubidium binding site number: 1; 2; 3; 4;

Rubidium binding site 1 out of 4 in the Nak C-Di Mutant with Rb+ and BA2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Nak C-Di Mutant with Rb+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb203 b:41.4 occ:0.37 OG1 A:THR63 2.7 29.4 1.0 OG1 B:THR63 2.8 30.4 1.0 O A:THR63 3.2 31.7 1.0 O B:THR63 3.2 31.5 1.0 CB A:THR63 3.3 34.6 1.0 CB B:THR63 3.4 31.7 1.0 BA A:BA206 3.4 84.3 0.2 C A:THR63 3.9 32.9 1.0 C B:THR63 4.0 33.7 1.0 RB A:RB204 4.1 26.3 0.6 CA A:THR63 4.3 33.6 1.0 CA B:THR63 4.3 32.5 1.0 CG2 A:THR63 4.5 29.6 1.0 CG2 B:THR63 4.5 32.3 1.0 O A:THR62 4.9 28.5 1.0 O B:THR62 4.9 28.0 1.0 N A:VAL64 4.9 29.4 1.0 N B:VAL64 5.0 29.7 1.0

Rubidium binding site 2 out of 4 in the Nak C-Di Mutant with Rb+ and BA2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Nak C-Di Mutant with Rb+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb204 b:26.3 occ:0.64 O B:THR63 2.8 31.5 1.0 O A:THR63 2.8 31.7 1.0 O B:VAL64 2.9 26.1 1.0 O A:VAL64 2.9 26.8 1.0 C B:VAL64 3.6 35.1 1.0 C A:VAL64 3.6 29.6 1.0 C B:THR63 3.9 33.7 1.0 C A:THR63 4.0 32.9 1.0 RB A:RB203 4.1 41.4 0.4 CA B:VAL64 4.2 34.7 1.0 CA A:VAL64 4.2 33.4 1.0 N A:GLY65 4.4 31.6 1.0 N B:GLY65 4.5 32.5 1.0 N B:VAL64 4.5 29.7 1.0 N A:VAL64 4.6 29.4 1.0 CA A:GLY65 4.7 36.9 1.0 BA A:BA205 4.8 89.0 0.3 CA B:GLY65 4.8 37.8 1.0

Rubidium binding site 3 out of 4 in the Nak C-Di Mutant with Rb+ and BA2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Nak C-Di Mutant with Rb+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Rb210 b:47.7 occ:0.32 OG1 C:THR63 2.8 45.8 1.0 OG1 D:THR63 2.8 47.3 1.0 O D:THR63 3.0 56.7 1.0 O C:THR63 3.1 49.5 1.0 CB D:THR63 3.3 44.2 1.0 CB C:THR63 3.4 51.6 1.0 C D:THR63 3.8 54.0 1.0 C C:THR63 3.9 51.2 1.0 RB D:RB209 4.1 37.6 0.6 BA C:BA211 4.1 97.5 0.2 CA D:THR63 4.2 52.9 1.0 CA C:THR63 4.3 50.5 1.0 CG2 C:THR63 4.5 48.8 1.0 CG2 D:THR63 4.5 42.7 1.0 O D:THR62 4.9 49.6 1.0 N D:VAL64 4.9 51.0 1.0 O C:THR62 4.9 54.3 1.0 N C:VAL64 4.9 49.3 1.0

Rubidium binding site 4 out of 4 in the Nak C-Di Mutant with Rb+ and BA2+


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Nak C-Di Mutant with Rb+ and BA2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Rb209 b:37.6 occ:0.63 O D:THR63 2.5 56.7 1.0 O D:VAL64 2.8 56.5 1.0 O C:THR63 3.1 49.5 1.0 C D:VAL64 3.3 52.5 1.0 O C:VAL64 3.4 50.2 1.0 C D:THR63 3.6 54.0 1.0 N D:GLY65 3.9 48.8 1.0 CA D:VAL64 3.9 52.0 1.0 RB C:RB210 4.1 47.7 0.3 C C:VAL64 4.1 55.4 1.0 CA D:GLY65 4.1 64.2 1.0 N D:VAL64 4.2 51.0 1.0 C C:THR63 4.2 51.2 1.0 BA D:BA210 4.4 102.5 0.3 CA D:THR63 4.6 52.9 1.0 CA C:VAL64 4.7 52.8 1.0 N C:GLY65 4.8 53.8 1.0 CB D:THR63 4.9 44.2 1.0 N C:VAL64 4.9 49.3 1.0

F.K.Schackert, J.Biedermann, S.Abdolvand, S.Minniberger, C.Song, A.J.R.Plested, P.Carloni, H.Sun. Mechanism of Calcium Permeation in A Glutamate Receptor Ion Channel. J.Chem.Inf.Model. 2023.
ISSN: ESSN 1549-960X
PubMed: 36758214
DOI: 10.1021/ACS.JCIM.2C01494