Calcium in PDB 5kmf: Structure of Cavab in Complex with Nimodipine

The structure of Structure of Cavab in Complex with Nimodipine, PDB code: 5kmf 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)	29.79 / 3.20
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	125.280, 125.365, 191.625, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.6

The binding sites of Calcium atom in the Structure of Cavab in Complex with Nimodipine (pdb code 5kmf). 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 Nimodipine, PDB code: 5kmf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Cavab in Complex with Nimodipine


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 Nimodipine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1301 b:46.0 occ:1.00 OD1 C:ASP1178 3.2 43.3 1.0 OD1 A:ASP1178 3.2 56.2 1.0 CG C:ASP1178 3.3 55.8 1.0 CG A:ASP1178 3.4 61.2 1.0 CB A:ASP1178 3.4 50.7 1.0 CB C:ASP1178 3.5 46.4 1.0 CA C:ASP1178 3.8 49.3 1.0 OD1 A:ASP1177 4.0 47.0 1.0 OD2 C:ASP1178 4.0 70.6 1.0 OD2 A:ASP1178 4.1 67.4 1.0 CA A:ASP1178 4.2 62.9 1.0 CA D:CA1305 4.3 96.6 1.0 N C:ASP1178 4.3 37.2 1.0 N A:ASP1178 4.6 65.0 1.0 CG D:ASP1178 4.6 68.6 1.0 OD1 D:ASP1178 4.8 57.1 1.0 CB D:ASP1178 4.8 53.1 1.0 OD2 D:ASP1178 4.8 68.2 1.0 CA D:ASP1178 5.0 53.1 1.0

Calcium binding site 2 out of 2 in the Structure of Cavab in Complex with Nimodipine


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 Nimodipine within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1305 b:96.6 occ:1.00 C36 B:MC31301 3.9 75.7 1.0 OD1 D:ASP1177 4.0 54.6 1.0 N D:ASP1178 4.0 55.0 1.0 N B:ASP1178 4.0 49.1 1.0 O D:LEU1176 4.0 35.7 1.0 O B:LEU1176 4.1 87.9 1.0 OD1 B:ASP1177 4.2 44.1 1.0 CA D:ASP1177 4.2 37.1 1.0 CA C:CA1301 4.3 46.0 1.0 CA B:ASP1177 4.5 60.3 1.0 OD1 A:ASP1177 4.5 47.0 1.0 OD1 C:ASP1177 4.5 39.6 1.0 C D:ASP1177 4.6 44.0 1.0 C B:ASP1177 4.8 57.9 1.0 N A:ASP1178 4.9 65.0 1.0 N C:ASP1178 4.9 37.2 1.0 CA D:ASP1178 4.9 53.1 1.0 CG D:ASP1177 4.9 50.5 1.0 C35 B:MC31301 4.9 83.8 1.0 CA B:ASP1178 4.9 42.1 1.0 C D:LEU1176 5.0 53.7 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