Calcium 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:

Rubidium	(Rb)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 5 binding sites of Calcium where determined in the Nak C-Di Mutant with Rb+ and CA2+, PDB code: 8ayq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Nak C-Di Mutant with Rb+ and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca203 b:144.2 occ:0.50 HE2 A:PHE91 4.1 79.9 1.0 HZ B:PHE91 4.4 87.0 1.0 OG1 B:THR63 4.5 63.8 1.0 HG21 B:THR63 4.5 74.3 1.0 OG1 A:THR63 4.6 56.0 1.0 HG21 A:THR63 4.7 65.7 1.0 CE2 A:PHE91 4.7 66.5 1.0 CZ B:PHE91 4.8 72.4 1.0 HZ A:PHE91 4.8 73.0 1.0 HE1 B:PHE91 4.9 91.3 1.0 RB A:RB202 4.9 62.9 0.6

Calcium binding site 2 out of 5 in the Nak C-Di Mutant with Rb+ and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca204 b:97.4 occ:0.50 CA A:CA204 0.0 97.4 0.5 O B:HOH304 2.4 83.8 1.0 CA A:CA204 2.7 92.5 0.5 HB2 A:ASP67 3.0 102.2 1.0 HB2 B:ASP67 3.3 106.0 1.0 HA A:ASP67 3.6 99.4 1.0 HB3 A:ASP67 3.6 102.2 1.0 HA B:ASP67 3.6 101.3 1.0 CB A:ASP67 3.7 85.0 1.0 O B:ASP67 3.7 81.8 1.0 CB B:ASP67 4.0 88.2 1.0 CA A:ASP67 4.1 82.7 1.0 CA B:ASP67 4.2 84.2 1.0 O A:ASP67 4.2 71.4 1.0 HB3 B:ASP67 4.3 106.0 1.0 C B:ASP67 4.4 84.0 1.0 C A:ASP67 4.7 77.8 1.0 CG A:ASP67 5.0 85.7 1.0

Calcium binding site 3 out of 5 in the Nak C-Di Mutant with Rb+ and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Nak C-Di Mutant with Rb+ and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:92.5 occ:0.50 CA A:CA204 0.0 92.5 0.5 HA B:ASP67 2.6 101.3 1.0 HA A:ASP67 2.7 99.4 1.0 CA A:CA204 2.7 97.4 0.5 HB3 A:ASP67 3.4 102.2 1.0 CA A:ASP67 3.5 82.7 1.0 CA B:CA201 3.5 109.5 0.5 CA B:ASP67 3.6 84.2 1.0 HB2 A:ASP67 3.7 102.2 1.0 CB A:ASP67 3.8 85.0 1.0 O B:CYS66 3.9 86.6 1.0 HB2 B:ASP67 4.0 106.0 1.0 HB3 B:ASP67 4.1 106.0 1.0 CB B:ASP67 4.1 88.2 1.0 N A:ASP67 4.2 83.8 1.0 O A:CYS66 4.3 85.1 1.0 O B:ASP67 4.3 81.8 1.0 C B:ASP67 4.3 84.0 1.0 N B:ASP67 4.4 82.3 1.0 C A:CYS66 4.5 83.1 1.0 C B:CYS66 4.5 76.9 1.0 C A:ASP67 4.6 77.8 1.0 O B:HOH304 4.6 83.8 1.0 O A:ASP67 4.7 71.4 1.0 H A:ASP67 4.7 100.7 1.0

Calcium binding site 4 out of 5 in the Nak C-Di Mutant with Rb+ and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Nak C-Di Mutant with Rb+ and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:109.5 occ:0.50 O B:CYS66 3.5 86.6 1.0 CA A:CA204 3.5 92.5 0.5 O A:CYS66 4.3 85.1 1.0 HA3 B:GLY65 4.4 70.3 1.0 C B:CYS66 4.4 76.9 1.0 HA3 A:GLY65 4.4 88.0 1.0 H A:CYS66 4.5 73.8 1.0 N A:CYS66 4.5 61.3 1.0 HA B:ASP67 4.5 101.3 1.0 H B:CYS66 4.5 72.2 1.0 C A:CYS66 4.6 83.1 1.0 N B:CYS66 4.6 60.0 1.0 HA A:CYS66 4.6 89.4 1.0 O A:VAL64 4.7 55.7 1.0 HA A:ASP67 4.8 99.4 1.0 C A:GLY65 4.8 58.7 1.0 C B:GLY65 4.8 69.1 1.0 CA A:CYS66 4.9 74.3 1.0

Calcium binding site 5 out of 5 in the Nak C-Di Mutant with Rb+ and CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Nak C-Di Mutant with Rb+ and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:140.8 occ:0.50 HA3 D:GLY65 3.7 140.7 1.0 O D:CYS66 4.1 122.2 1.0 N D:CYS66 4.3 108.3 1.0 C D:GLY65 4.3 119.4 1.0 H D:CYS66 4.4 130.2 1.0 HA D:CYS66 4.5 139.9 1.0 CA D:GLY65 4.5 117.1 1.0 C D:CYS66 4.5 125.4 1.0 O D:VAL64 4.7 108.9 1.0 CA D:CYS66 4.7 116.5 1.0 O D:GLY65 4.7 126.8 1.0 HA2 D:GLY65 4.9 140.7 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