Calcium in PDB 6ke5: Structure of Cavab in Complex with Diltiazem and Amlodipine

The structure of Structure of Cavab in Complex with Diltiazem and Amlodipine, PDB code: 6ke5 was solved by L.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.71 / 2.80
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	124.730, 124.990, 191.940, 90.00, 90.00, 90.00
R / Rfree (%)	24.9 / 29.2

The structure of Structure of Cavab in Complex with Diltiazem and Amlodipine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Structure of Cavab in Complex with Diltiazem and Amlodipine (pdb code 6ke5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of Cavab in Complex with Diltiazem and Amlodipine, PDB code: 6ke5:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Cavab in Complex with Diltiazem and Amlodipine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Cavab in Complex with Diltiazem and Amlodipine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1302 b:50.7 occ:1.00 OD2 A:ASP1178 2.6 50.2 1.0 CG A:ASP1178 3.3 47.9 1.0 CB A:ASP1178 3.4 39.8 1.0 OD1 C:ASP1178 3.6 35.3 1.0 CA D:CA1302 3.9 54.5 1.0 CB C:ASP1178 3.9 33.0 1.0 CB D:ASP1178 4.0 25.1 1.0 CG C:ASP1178 4.1 33.3 1.0 CB B:ASP1178 4.1 27.3 1.0 CA A:ASP1178 4.2 32.4 1.0 N A:ASP1178 4.2 33.0 1.0 OD1 B:ASP1178 4.3 31.5 1.0 OD1 A:ASP1178 4.3 35.5 1.0 CG B:ASP1178 4.3 31.6 1.0 CA B:ASP1178 4.3 29.4 1.0 CA D:ASP1178 4.3 29.8 1.0 CA C:ASP1178 4.4 32.6 1.0 N D:ASP1178 4.6 29.1 1.0 CG D:ASP1178 4.6 29.8 1.0 OD1 A:ASP1177 4.6 39.3 1.0 OD1 C:ASP1177 4.6 31.7 1.0 OD1 D:ASP1178 4.7 30.1 1.0 N B:ASP1178 4.7 31.1 1.0 N C:ASP1178 4.7 31.5 1.0

Calcium binding site 2 out of 3 in the Structure of Cavab in Complex with Diltiazem and Amlodipine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Cavab in Complex with Diltiazem and Amlodipine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1303 b:55.4 occ:1.00 O C:LEU1176 3.4 32.8 1.0 O C:THR1175 3.6 31.0 1.0 C C:LEU1176 3.8 29.8 1.0 CA C:ASP1177 3.9 31.3 1.0 CA D:CA1302 4.0 54.5 1.0 C21 C:D6C1302 4.1 47.8 1.0 N C:ASP1177 4.1 29.5 1.0 O A:LEU1176 4.1 31.7 1.0 CB C:LEU1176 4.2 33.1 1.0 CB C:ASP1177 4.5 27.7 1.0 OD1 C:ASP1177 4.6 31.7 1.0 CA C:LEU1176 4.6 29.7 1.0 C C:THR1175 4.7 30.9 1.0 CB A:LEU1176 4.9 27.0 1.0 O D:LEU1176 5.0 32.8 1.0

Calcium binding site 3 out of 3 in the Structure of Cavab in Complex with Diltiazem and Amlodipine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Cavab in Complex with Diltiazem and Amlodipine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1302 b:54.5 occ:1.00 N D:ASP1178 3.3 29.1 1.0 OD1 B:ASP1177 3.5 31.2 1.0 O D:LEU1176 3.5 32.8 1.0 OD1 A:ASP1177 3.7 39.3 1.0 CA A:CA1302 3.9 50.7 1.0 N B:ASP1178 3.9 31.1 1.0 CA C:CA1303 4.0 55.4 1.0 CA D:ASP1178 4.1 29.8 1.0 CA B:ASP1177 4.1 33.0 1.0 C D:ASP1177 4.3 31.0 1.0 CA D:ASP1177 4.3 32.0 1.0 O B:LEU1176 4.3 36.2 1.0 OD1 D:ASP1177 4.4 31.1 1.0 C B:ASP1177 4.5 31.2 1.0 CG B:ASP1177 4.6 27.9 1.0 C D:LEU1176 4.6 31.7 1.0 N C:ASP1178 4.8 31.5 1.0 CB B:ASP1177 4.8 28.6 1.0 CA B:ASP1178 4.8 29.4 1.0 OD1 C:ASP1177 4.9 31.7 1.0 CB D:ASP1178 4.9 25.1 1.0 CG A:ASP1177 5.0 36.5 1.0 N D:ASP1177 5.0 33.0 1.0

L.Tang, T.M.Gamal El-Din, M.J.Lenaeus, N.Zheng, W.A.Catterall. Structural Basis For Diltiazem Block of A Voltage-Gated CA2+Channel. Mol.Pharmacol. V. 96 485 2019.
ISSN: ESSN 1521-0111
PubMed: 31391290
DOI: 10.1124/MOL.119.117531