Calcium in PDB 5kmd: Structure of Cavab in Complex with Amlodipine

The structure of Structure of Cavab in Complex with Amlodipine, PDB code: 5kmd was solved by L.Tang, T.M.Gamal El-Din, T.M.Swanson, D.C.Pryde, T.Scheuer, N.Zheng, W.A.Catterall, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.85 / 3.20
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	125.640, 125.530, 191.700, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 27.7

The structure of Structure of Cavab in Complex with 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 Amlodipine (pdb code 5kmd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Cavab in Complex with Amlodipine, PDB code: 5kmd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Cavab in Complex with 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 Amlodipine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1301 b:56.3 occ:1.00 N C:ASP1178 3.6 32.1 1.0 OD1 C:ASP1177 3.9 20.8 1.0 O C:LEU1176 3.9 22.5 1.0 N B:ASP1178 4.1 54.1 1.0 CA C:ASP1177 4.1 33.8 1.0 OD1 D:ASP1177 4.1 38.1 1.0 CA D:CA1301 4.3 39.1 1.0 O B:LEU1176 4.3 94.6 1.0 C C:ASP1177 4.3 29.8 1.0 CA C:ASP1178 4.5 38.5 1.0 OD1 B:ASP1177 4.6 27.9 1.0 N D:ASP1178 4.6 44.3 1.0 OD1 A:ASP1177 4.7 39.8 1.0 C C:LEU1176 4.8 38.2 1.0 CA B:ASP1178 4.8 56.0 1.0 CG C:ASP1177 4.9 30.7 1.0 CA B:ASP1177 4.9 53.3 1.0 CB C:ASP1177 4.9 29.3 1.0 N C:ASP1177 4.9 48.3 1.0 C B:ASP1177 5.0 54.9 1.0 N A:ASP1178 5.0 70.2 1.0

Calcium binding site 2 out of 2 in the Structure of Cavab in Complex with 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 Amlodipine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1301 b:39.1 occ:1.00 CB D:ASP1178 3.3 50.3 1.0 CG D:ASP1178 3.3 65.2 1.0 OD2 D:ASP1178 3.3 67.0 1.0 CB A:ASP1178 3.7 72.7 1.0 CA D:ASP1178 3.8 55.4 1.0 CG A:ASP1178 4.0 80.2 1.0 OD1 D:ASP1178 4.0 72.6 1.0 OD1 A:ASP1177 4.2 39.8 1.0 OD1 A:ASP1178 4.2 78.7 1.0 N D:ASP1178 4.2 44.3 1.0 CA C:CA1301 4.3 56.3 1.0 OD1 C:ASP1178 4.3 29.6 1.0 CA A:ASP1178 4.4 67.8 1.0 N A:ASP1178 4.6 70.2 1.0 OD2 A:ASP1178 4.6 84.9 1.0 OD2 B:ASP1178 4.7 57.5 1.0 CA C:ASP1178 4.8 38.5 1.0 CB C:ASP1178 4.8 38.4 1.0 CG C:ASP1178 4.9 42.8 1.0 OD1 D:ASP1177 4.9 38.1 1.0 CB B:ASP1178 5.0 55.3 1.0

L.Tang, T.M.El-Din, T.M.Swanson, D.C.Pryde, T.Scheuer, N.Zheng, W.A.Catterall. Structural Basis For Inhibition of A Voltage-Gated Ca(2+) Channel By Ca(2+) Antagonist Drugs. Nature V. 537 117 2016.
ISSN: ESSN 1476-4687
PubMed: 27556947
DOI: 10.1038/NATURE19102