Rubidium in PDB 8ayq: Nak C-Di Mutant with Rb+ and CA2+

The structure of Nak C-Di Mutant with Rb+ and CA2+, PDB code: 8ayq 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)	33.78 / 2.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	67.57, 175.508, 67.347, 90, 90, 90
R / Rfree (%)	25.5 / 30

The structure of Nak C-Di Mutant with Rb+ and CA2+ also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Calcium	(Ca)	5 atoms

The binding sites of Rubidium atom in the Nak C-Di Mutant with Rb+ and CA2+ (pdb code 8ayq). 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 CA2+, PDB code: 8ayq:
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 CA2+


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 CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb201 b:54.8 occ:0.46 O A:THR63 2.7 63.7 1.0 O B:THR63 2.9 67.1 1.0 O B:VAL64 3.0 59.7 1.0 O A:VAL64 3.1 55.7 1.0 RB A:RB202 3.4 62.9 0.6 HA A:VAL64 3.6 75.9 1.0 C A:VAL64 3.6 55.5 1.0 C B:VAL64 3.6 60.3 1.0 C A:THR63 3.9 86.0 1.0 HA B:VAL64 3.9 81.8 1.0 HA3 B:GLY65 3.9 70.3 1.0 CA A:VAL64 4.1 63.1 1.0 C B:THR63 4.1 58.6 1.0 CA B:VAL64 4.3 68.1 1.0 HA3 A:GLY65 4.3 88.0 1.0 N B:GLY65 4.4 55.6 1.0 N A:VAL64 4.5 84.3 1.0 N A:GLY65 4.5 55.2 1.0 HB A:THR63 4.6 68.1 1.0 CA B:GLY65 4.7 58.5 1.0 N B:VAL64 4.7 56.5 1.0 HB B:THR63 4.7 71.8 1.0 CA A:GLY65 5.0 73.2 1.0

Rubidium binding site 2 out of 4 in the Nak C-Di Mutant with Rb+ and CA2+


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 CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Rb202 b:62.9 occ:0.55 HB B:THR63 2.8 71.8 1.0 O B:THR63 2.9 67.1 1.0 HB A:THR63 2.9 68.1 1.0 O A:THR63 2.9 63.7 1.0 OG1 A:THR63 3.1 56.0 1.0 OG1 B:THR63 3.3 63.8 1.0 RB A:RB201 3.4 54.8 0.5 CB A:THR63 3.4 56.6 1.0 CB B:THR63 3.4 59.7 1.0 C B:THR63 3.7 58.6 1.0 C A:THR63 3.7 86.0 1.0 CA B:THR63 4.2 63.9 1.0 CA A:THR63 4.3 65.5 1.0 HA B:VAL64 4.4 81.8 1.0 HA A:VAL64 4.4 75.9 1.0 HG21 A:THR63 4.6 65.7 1.0 HG21 B:THR63 4.6 74.3 1.0 CG2 A:THR63 4.6 55.4 1.0 N B:VAL64 4.6 56.5 1.0 HA B:THR63 4.6 76.9 1.0 CG2 B:THR63 4.7 61.8 1.0 N A:VAL64 4.7 84.3 1.0 HA A:THR63 4.7 78.8 1.0 CA A:CA203 4.9 144.2 0.5 CA B:VAL64 4.9 68.1 1.0

Rubidium binding site 3 out of 4 in the Nak C-Di Mutant with Rb+ and CA2+


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 CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Rb201 b:121.9 occ:0.50 O C:THR63 2.6 106.0 1.0 HB C:THR63 2.7 101.2 1.0 OG1 C:THR63 3.4 95.4 1.0 CB C:THR63 3.4 84.2 1.0 RB C:RB202 3.6 66.5 0.4 C C:THR63 3.6 87.2 1.0 CA C:THR63 4.1 78.8 1.0 HA C:THR63 4.4 94.7 1.0 HA C:VAL64 4.5 112.0 1.0 HG21 C:THR63 4.6 91.1 1.0 CG2 C:THR63 4.6 75.8 1.0 N C:VAL64 4.7 88.4 1.0

Rubidium binding site 4 out of 4 in the Nak C-Di Mutant with Rb+ and CA2+


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 CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Rb202 b:66.5 occ:0.44 O C:THR63 3.1 106.0 1.0 O C:VAL64 3.1 94.0 1.0 HA3 C:GLY65 3.5 135.9 1.0 RB C:RB201 3.6 121.9 0.5 C C:VAL64 3.6 88.6 1.0 HA C:VAL64 4.1 112.0 1.0 C C:THR63 4.2 87.2 1.0 N C:GLY65 4.2 74.0 1.0 CA C:GLY65 4.3 113.1 1.0 CA C:VAL64 4.4 93.2 1.0 HA2 C:GLY65 4.7 135.9 1.0 N C:VAL64 4.7 88.4 1.0 H C:GLY65 4.8 88.9 1.0 HB C:THR63 5.0 101.2 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