Calcium in PDB 4y1t: Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes

The structure of Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes, PDB code: 4y1t was solved by P.J.Conroy, H.Yagi, J.C.Whisstock, R.S.Norton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.38 / 2.67
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	45.009, 59.828, 125.919, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 21.5

The binding sites of Calcium atom in the Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes (pdb code 4y1t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes, PDB code: 4y1t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:14.0 occ:1.00 OD1 A:ASP429 2.4 12.9 1.0 OD1 A:ASP485 2.5 14.3 1.0 OD2 A:ASP435 2.6 17.5 1.0 OD2 A:ASP429 2.6 14.8 1.0 OD2 A:ASP483 2.6 14.1 1.0 O A:ALA484 2.6 22.6 1.0 OD1 A:ASP483 2.6 12.9 1.0 CG A:ASP429 2.8 12.6 1.0 CG A:ASP483 3.0 15.7 1.0 C A:ALA484 3.4 14.5 1.0 CG A:ASP435 3.5 14.7 1.0 CA A:CA604 3.6 10.7 1.0 CG A:ASP485 3.7 21.7 1.0 CB A:ASP435 3.9 11.1 1.0 N A:ASP485 3.9 15.2 1.0 CA A:ASP485 4.0 19.6 1.0 CA A:CA603 4.1 12.6 1.0 N A:ALA484 4.2 19.5 1.0 CB A:ASP429 4.3 9.1 1.0 CA A:ALA484 4.4 11.7 1.0 N A:ASP435 4.4 13.5 1.0 CB A:ASP485 4.4 10.3 1.0 CB A:ASP483 4.5 12.4 1.0 OD2 A:ASP485 4.5 24.3 1.0 OD1 A:ASP435 4.6 12.4 1.0 C A:ASP483 4.6 19.4 1.0 CA A:ASP435 4.8 9.7 1.0 O A:GLY428 4.8 20.6 1.0 O A:HOH723 4.9 31.1 1.0 C A:GLY428 5.0 14.5 1.0

Calcium binding site 2 out of 5 in the Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:23.1 occ:1.00 OD2 A:ASP485 2.4 24.3 1.0 OD1 A:ASP491 2.4 32.3 1.0 O A:HOH718 2.4 23.8 1.0 O A:ASP489 2.9 25.2 1.0 CG A:ASP491 3.3 24.5 1.0 OD2 A:ASP491 3.4 26.5 1.0 CG A:ASP485 3.4 21.7 1.0 CB A:ASP485 3.9 10.3 1.0 C A:ASP489 4.0 34.7 1.0 C A:ASP490 4.3 22.4 1.0 CA A:CA604 4.3 10.7 1.0 O A:ASP490 4.4 23.9 1.0 O A:HOH752 4.5 20.3 1.0 OD1 A:ASP485 4.5 14.3 1.0 CA A:ASP490 4.6 21.4 1.0 N A:ASP491 4.6 19.2 1.0 CB A:ASP491 4.7 15.2 1.0 N A:ASP490 4.7 32.0 1.0 O A:HOH723 4.9 31.1 1.0 CB A:ASP489 4.9 49.6 1.0

Calcium binding site 3 out of 5 in the Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:12.6 occ:1.00 O A:ALA433 2.4 16.7 1.0 OD2 A:ASP429 2.4 14.8 1.0 OD1 A:ASN454 2.4 14.2 1.0 OG1 A:THR432 2.5 13.1 1.0 OD2 A:ASP435 2.5 17.5 1.0 OD1 A:ASP435 2.6 12.4 1.0 CG A:ASP435 2.9 14.7 1.0 CB A:THR432 3.5 12.6 1.0 CG A:ASN454 3.5 13.5 1.0 CG A:ASP429 3.6 12.6 1.0 C A:ALA433 3.6 16.1 1.0 N A:ALA433 4.1 14.3 1.0 CA A:CA601 4.1 14.0 1.0 C A:THR432 4.2 11.1 1.0 CB A:ASP429 4.2 9.1 1.0 ND2 A:ASN454 4.2 20.9 1.0 CB A:ASP435 4.3 11.1 1.0 CA A:ASN454 4.3 12.3 1.0 N A:ASP435 4.3 13.5 1.0 C A:THR434 4.4 12.7 1.0 CA A:THR432 4.4 10.7 1.0 CA A:ALA433 4.5 14.3 1.0 N A:ASN454 4.5 15.3 1.0 CB A:ASN454 4.5 8.7 1.0 CG2 A:THR432 4.5 12.7 1.0 N A:THR434 4.5 9.8 1.0 OD1 A:ASP429 4.6 12.9 1.0 O A:THR432 4.6 10.0 1.0 CA A:THR434 4.6 9.8 1.0 O A:THR434 4.7 11.0 1.0 CA A:ASP435 4.9 9.7 1.0 O A:HOH704 4.9 17.8 1.0

Calcium binding site 4 out of 5 in the Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:10.7 occ:1.00 OD2 A:ASP491 2.4 26.5 1.0 OD1 A:ASP429 2.4 12.9 1.0 O A:GLY428 2.4 20.6 1.0 O A:HOH752 2.5 20.3 1.0 OD2 A:ASP483 2.5 14.1 1.0 OD1 A:ASP485 2.6 14.3 1.0 OD2 A:ASP485 2.6 24.3 1.0 O A:HOH723 2.7 31.1 1.0 CG A:ASP485 2.9 21.7 1.0 C A:GLY428 3.4 14.5 1.0 CG A:ASP491 3.5 24.5 1.0 CA A:CA601 3.6 14.0 1.0 CG A:ASP483 3.6 15.7 1.0 CG A:ASP429 3.6 12.6 1.0 O A:HOH718 3.6 23.8 1.0 CA A:ASP429 4.0 13.2 1.0 N A:ASP429 4.1 14.3 1.0 OD1 A:ASP491 4.3 32.3 1.0 OD1 A:ASP483 4.3 12.9 1.0 CA A:CA602 4.3 23.1 1.0 CB A:ASP429 4.4 9.1 1.0 CB A:ASP485 4.4 10.3 1.0 CB A:ASP491 4.5 15.2 1.0 CA A:GLY428 4.5 11.9 1.0 OD2 A:ASP429 4.5 14.8 1.0 CB A:ASP483 4.5 12.4 1.0 O A:HOH755 4.9 21.2 1.0

Calcium binding site 5 out of 5 in the Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:51.4 occ:1.00 O A:ALA488 2.4 44.7 1.0 O A:HOH761 2.5 37.6 1.0 OD1 A:ASP490 2.7 21.5 1.0 O A:HOH714 3.0 27.6 1.0 O A:ASP485 3.2 29.8 1.0 CG A:ASP490 3.5 18.2 1.0 OD2 A:ASP490 3.5 15.6 1.0 C A:ALA488 3.5 61.8 1.0 CA A:ALA488 4.0 71.5 1.0 C A:ASP485 4.1 30.9 1.0 N A:ALA488 4.3 62.1 1.0 CA A:ALA486 4.5 53.8 1.0 N A:ALA486 4.6 42.6 1.0 N A:ASP489 4.7 50.3 1.0 C A:ALA486 4.7 53.9 1.0 N A:ASP485 4.7 15.2 1.0 O A:ALA486 4.8 61.7 1.0 N A:ASP490 4.8 32.0 1.0 CB A:ASP490 4.8 12.3 1.0

H.Yagi, P.J.Conroy, E.W.Leung, R.H.Law, J.A.Trapani, I.Voskoboinik, J.C.Whisstock, R.S.Norton. Structural Basis For CA2+-Mediated Interaction of the Perforin C2 Domain with Lipid Membranes. J.Biol.Chem. V. 290 25213 2015.
ISSN: ESSN 1083-351X
PubMed: 26306037
DOI: 10.1074/JBC.M115.668384