Chlorine 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
Calcium	(Ca)	5 atoms

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

Chlorine binding site 1 out of 2 in the Nak C-Di Mutant with Rb+ and CA2+


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl208 b:85.7 occ:1.00 HH11 A:ARG49 2.7 100.4 1.0 HD2 A:PRO50 3.1 86.5 1.0 NH1 A:ARG49 3.4 83.6 1.0 HH12 A:ARG49 3.5 100.4 1.0 HD2 A:ARG49 3.5 90.1 1.0 HB3 A:ARG49 3.6 78.1 1.0 CD A:PRO50 4.1 72.0 1.0 HG2 A:ARG49 4.2 81.5 1.0 HG2 A:PRO50 4.3 82.2 1.0 CD A:ARG49 4.4 74.9 1.0 HD3 A:PRO50 4.4 86.5 1.0 CB A:ARG49 4.4 65.7 1.0 CZ A:ARG49 4.5 79.4 1.0 CG A:ARG49 4.5 67.7 1.0 CG A:PRO50 4.8 68.3 1.0 H A:ILE51 4.8 80.4 1.0 NE A:ARG49 4.9 72.8 1.0 HA A:ARG49 5.0 77.0 1.0 HB2 A:PRO50 5.0 92.5 1.0 HG22 A:ILE51 5.0 80.1 1.0 N A:PRO50 5.0 71.0 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Nak C-Di Mutant with Rb+ and CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl210 b:61.9 occ:1.00 HD2 B:PRO50 2.8 93.8 1.0 HB3 B:ARG49 2.8 95.9 1.0 H B:ILE51 3.0 87.4 1.0 HH11 B:ARG49 3.1 109.2 1.0 HG22 B:ILE51 3.1 79.2 1.0 HO4 B:MPD204 3.3 106.7 1.0 HG2 B:PRO50 3.4 81.4 1.0 CD B:PRO50 3.5 78.1 1.0 HH12 B:ARG49 3.5 109.2 1.0 NH1 B:ARG49 3.5 90.8 1.0 HB2 B:PRO50 3.5 90.7 1.0 O4 B:MPD204 3.7 88.8 1.0 CB B:ARG49 3.8 79.8 1.0 N B:PRO50 3.8 75.0 1.0 H32 B:MPD204 3.8 112.3 1.0 CG B:PRO50 3.8 67.7 1.0 N B:ILE51 3.8 72.7 1.0 HG21 B:ILE51 3.9 79.2 1.0 CG2 B:ILE51 3.9 65.8 1.0 HB B:ILE51 3.9 78.1 1.0 CB B:PRO50 4.1 75.4 1.0 HB2 B:ARG49 4.1 95.9 1.0 HD2 B:ARG49 4.3 106.9 1.0 HD3 B:PRO50 4.3 93.8 1.0 C B:ARG49 4.3 68.8 1.0 CB B:ILE51 4.4 65.0 1.0 CA B:PRO50 4.4 72.2 1.0 HA B:ARG49 4.4 84.3 1.0 CA B:ARG49 4.5 70.1 1.0 CZ B:ARG49 4.5 81.6 1.0 HG2 B:ARG49 4.6 106.5 1.0 CG B:ARG49 4.6 88.6 1.0 C B:PRO50 4.6 68.1 1.0 C3 B:MPD204 4.6 93.4 1.0 HG23 B:ILE51 4.7 79.2 1.0 C4 B:MPD204 4.7 91.0 1.0 CA B:ILE51 4.8 67.4 1.0 HG3 B:PRO50 4.8 81.4 1.0 CD B:ARG49 4.8 89.0 1.0 HB3 B:PRO50 5.0 90.7 1.0 H31 B:MPD204 5.0 112.3 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