Calcium in PDB 5kmh: Structure of Cavab in Complex with Br-Verapamil

The structure of Structure of Cavab in Complex with Br-Verapamil, PDB code: 5kmh 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)	29.83 / 3.20
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	125.535, 125.525, 191.960, 90.00, 90.00, 90.00
R / Rfree (%)	25.1 / 29.4

The structure of Structure of Cavab in Complex with Br-Verapamil also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Calcium atom in the Structure of Cavab in Complex with Br-Verapamil (pdb code 5kmh). 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 Br-Verapamil, PDB code: 5kmh:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of Cavab in Complex with Br-Verapamil


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 Br-Verapamil within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1301 b:99.1 occ:1.00 N A:ASP1178 3.4 57.4 1.0 O A:LEU1176 3.7 65.9 1.0 OD1 B:ASP1177 4.0 42.1 1.0 OD1 A:ASP1177 4.0 54.1 1.0 CA D:CA1301 4.0 43.9 1.0 CA A:ASP1177 4.1 58.3 1.0 CA A:CA1302 4.2 88.5 1.0 CA A:ASP1178 4.2 57.0 1.0 C A:ASP1177 4.3 45.7 1.0 N C:ASP1178 4.4 43.2 1.0 O C:LEU1176 4.5 36.2 1.0 N B:ASP1178 4.5 43.4 1.0 C A:LEU1176 4.7 64.8 1.0 O B:LEU1176 4.9 42.4 1.0 CA B:ASP1177 4.9 53.9 1.0 CB A:ASP1178 4.9 58.0 1.0 N A:ASP1177 5.0 60.7 1.0 CG A:ASP1177 5.0 57.4 1.0

Calcium binding site 2 out of 3 in the Structure of Cavab in Complex with Br-Verapamil


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 Br-Verapamil within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1302 b:88.5 occ:1.00 O A:LEU1176 3.7 65.9 1.0 C13 C:6U81302 3.8 66.4 1.0 CA A:CA1301 4.2 99.1 1.0 O B:LEU1176 4.4 42.4 1.0 CB A:LEU1176 4.5 64.4 1.0 N11 C:6U81302 4.5 67.2 1.0 C12 C:6U81302 4.5 78.6 1.0 O A:THR1175 4.6 35.2 1.0 C10 C:6U81302 4.6 72.8 1.0 O C:LEU1176 4.6 36.2 1.0 C A:LEU1176 4.7 64.8 1.0 C14 C:6U81302 5.0 85.6 1.0

Calcium binding site 3 out of 3 in the Structure of Cavab in Complex with Br-Verapamil


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 Br-Verapamil within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1301 b:43.9 occ:1.00 OD1 D:ASP1178 3.5 99.2 1.0 CB A:ASP1178 4.0 58.0 1.0 CA A:CA1301 4.0 99.1 1.0 OD1 A:ASP1178 4.1 74.5 1.0 CG D:ASP1178 4.1 0.8 1.0 CG A:ASP1178 4.1 76.3 1.0 CB D:ASP1178 4.1 80.6 1.0 CB B:ASP1178 4.1 66.4 1.0 CG B:ASP1178 4.3 86.4 1.0 CB C:ASP1178 4.3 64.5 1.0 CA A:ASP1178 4.4 57.0 1.0 OD1 B:ASP1178 4.4 85.4 1.0 OD1 C:ASP1178 4.5 58.5 1.0 CG C:ASP1178 4.6 70.1 1.0 CA D:ASP1178 4.7 69.6 1.0 CA B:ASP1178 4.7 52.7 1.0 CA C:ASP1178 4.7 49.9 1.0 N A:ASP1178 4.8 57.4 1.0 OD2 A:ASP1178 4.9 70.4 1.0 N C:ASP1178 4.9 43.2 1.0 OD2 B:ASP1178 4.9 96.2 1.0 N B:ASP1178 5.0 43.4 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