Calcium in PDB 5ug7: Calcium Bound Perforin C2 Domain - T431D

The structure of Calcium Bound Perforin C2 Domain - T431D, PDB code: 5ug7 was solved by R.H.P.Law, P.J.Conroy, I.Voskoboinik, J.C.Whisstock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.34 / 1.80
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	50.996, 31.312, 86.364, 90.00, 101.35, 90.00
R / Rfree (%)	21.1 / 23.3

The binding sites of Calcium atom in the Calcium Bound Perforin C2 Domain - T431D (pdb code 5ug7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Calcium Bound Perforin C2 Domain - T431D, PDB code: 5ug7:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Calcium Bound Perforin C2 Domain - T431D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calcium Bound Perforin C2 Domain - T431D within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:18.7 occ:1.00 O A:ALA433 2.3 19.9 1.0 OD1 A:ASN454 2.3 24.6 1.0 OD2 A:ASP429 2.4 17.9 1.0 OG1 A:THR432 2.4 19.9 1.0 OD1 A:ASP435 2.5 18.7 1.0 OD2 A:ASP435 2.6 20.2 1.0 CG A:ASP435 2.9 20.3 1.0 CG A:ASN454 3.4 31.3 1.0 CB A:THR432 3.5 22.9 1.0 C A:ALA433 3.5 20.2 1.0 CG A:ASP429 3.6 21.6 1.0 ND2 A:ASN454 4.0 27.8 1.0 N A:ALA433 4.0 17.2 1.0 CA A:CA602 4.0 18.9 1.0 C A:THR432 4.1 22.1 1.0 CB A:ASP429 4.2 19.9 1.0 CB A:ASP435 4.4 18.1 1.0 CA A:ALA433 4.4 17.6 1.0 C A:THR434 4.4 18.4 1.0 CA A:ASN454 4.4 16.8 1.0 CA A:THR432 4.4 18.4 1.0 N A:ASP435 4.4 15.3 1.0 CB A:ASN454 4.5 18.3 1.0 N A:THR434 4.5 16.6 1.0 OD1 A:ASP429 4.5 19.2 1.0 CG2 A:THR432 4.6 25.7 1.0 O A:THR432 4.6 21.6 1.0 N A:ASN454 4.6 17.5 1.0 O A:HOH747 4.6 28.5 1.0 CA A:THR434 4.7 15.6 1.0 O A:THR434 4.7 17.2 1.0 OD1 A:ASP483 4.9 19.9 1.0 CA A:ASP435 4.9 16.7 1.0

Calcium binding site 2 out of 3 in the Calcium Bound Perforin C2 Domain - T431D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calcium Bound Perforin C2 Domain - T431D within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:18.9 occ:1.00 O A:ALA484 2.3 21.3 1.0 OD2 A:ASP435 2.3 20.2 1.0 OD1 A:ASP429 2.4 19.2 1.0 OD1 A:ASP485 2.5 19.9 1.0 OD2 A:ASP429 2.6 17.9 1.0 OD2 A:ASP483 2.6 21.2 1.0 OD1 A:ASP483 2.7 19.9 1.0 CG A:ASP429 2.8 21.6 1.0 CG A:ASP483 3.0 19.4 1.0 C A:ALA484 3.4 24.2 1.0 CG A:ASP435 3.4 20.3 1.0 CA A:CA603 3.6 19.4 1.0 CG A:ASP485 3.6 23.3 1.0 CB A:ASP435 3.9 18.1 1.0 CA A:CA601 4.0 18.7 1.0 CA A:ASP485 4.1 23.3 1.0 N A:ASP485 4.1 21.6 1.0 O A:HOH772 4.3 45.1 1.0 N A:ALA484 4.3 18.0 1.0 OD2 A:ASP485 4.4 21.5 1.0 CB A:ASP429 4.4 19.9 1.0 CA A:ALA484 4.4 19.7 1.0 OD1 A:ASP435 4.5 18.7 1.0 CB A:ASP485 4.5 24.4 1.0 CB A:ASP483 4.5 16.6 1.0 N A:ASP435 4.5 15.3 1.0 C A:ASP483 4.6 19.6 1.0 O A:GLY428 4.7 18.8 1.0 O A:HOH735 4.7 32.9 1.0 CA A:ASP435 4.8 16.7 1.0

Calcium binding site 3 out of 3 in the Calcium Bound Perforin C2 Domain - T431D


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calcium Bound Perforin C2 Domain - T431D within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:19.4 occ:1.00 OD2 A:ASP483 2.3 21.2 1.0 OD2 A:ASP491 2.3 22.7 1.0 OD1 A:ASP429 2.4 19.2 1.0 O A:GLY428 2.4 18.8 1.0 OD2 A:ASP485 2.4 21.5 1.0 OD1 A:ASP485 2.6 19.9 1.0 CG A:ASP485 2.9 23.3 1.0 CG A:ASP483 3.3 19.4 1.0 CG A:ASP491 3.5 24.9 1.0 C A:GLY428 3.5 20.1 1.0 CA A:CA602 3.6 18.9 1.0 CG A:ASP429 3.6 21.6 1.0 OD1 A:ASP483 4.0 19.9 1.0 CA A:ASP429 4.0 17.7 1.0 CB A:ASP491 4.1 20.4 1.0 CB A:ASP483 4.2 16.6 1.0 N A:ASP429 4.2 17.5 1.0 CB A:ASP429 4.4 19.9 1.0 CB A:ASP485 4.4 24.4 1.0 OD1 A:ASP491 4.5 23.0 1.0 OD2 A:ASP429 4.5 17.9 1.0 CA A:GLY428 4.6 15.8 1.0 O A:ASP483 4.8 19.5 1.0 O A:ALA484 4.9 21.3 1.0 N A:ASP491 4.9 21.1 1.0

A.J.Brennan, R.H.P.Law, P.J.Conroy, T.Noori, N.Lukoyanova, H.Saibil, H.Yagita, A.Ciccone, S.Verschoor, J.C.Whisstock, J.A.Trapani, I.Voskoboinik. Perforin Proteostasis Is Regulated Through Its C2 Domain: Supra-Physiological Cell Death Mediated By T431D-Perforin. Cell Death Differ. V. 25 1517 2018.
ISSN: ISSN 1476-5403
PubMed: 29416110
DOI: 10.1038/S41418-018-0057-Z