Calcium in PDB 7pag: The Pore Conformation of Lymphocyte Perforin

The binding sites of Calcium atom in the The Pore Conformation of Lymphocyte Perforin (pdb code 7pag). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the The Pore Conformation of Lymphocyte Perforin, PDB code: 7pag:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the The Pore Conformation of Lymphocyte Perforin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Pore Conformation of Lymphocyte Perforin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:166.8 occ:1.00 OD1 A:ASN454 2.4 163.9 1.0 O A:ALA433 2.4 166.9 1.0 OD2 A:ASP429 2.5 166.7 1.0 OD2 A:ASP435 2.5 166.4 1.0 OG1 A:THR432 2.7 169.0 1.0 CG A:ASP435 3.0 166.4 1.0 OD1 A:ASP435 3.1 166.4 1.0 CG A:ASN454 3.4 163.9 1.0 CB A:THR432 3.4 169.0 1.0 CG A:ASP429 3.5 166.7 1.0 C A:ALA433 3.6 166.9 1.0 N A:ALA433 3.8 166.9 1.0 CB A:ASP429 4.0 166.7 1.0 CB A:ASP435 4.2 166.4 1.0 CA A:ASN454 4.2 163.9 1.0 ND2 A:ASN454 4.2 163.9 1.0 CA A:ALA433 4.2 166.9 1.0 C A:THR432 4.3 169.0 1.0 CB A:ASN454 4.3 163.9 1.0 N A:ASN454 4.3 163.9 1.0 CG2 A:THR432 4.4 169.0 1.0 N A:ASP435 4.5 166.4 1.0 CA A:THR432 4.5 169.0 1.0 C A:THR434 4.6 166.6 1.0 OD1 A:ASP429 4.6 166.7 1.0 N A:THR434 4.7 166.6 1.0 CB A:ALA433 4.8 166.9 1.0 O A:THR434 4.8 166.6 1.0 CA A:ASP435 4.9 166.4 1.0

Calcium binding site 2 out of 3 in the The Pore Conformation of Lymphocyte Perforin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Pore Conformation of Lymphocyte Perforin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:170.4 occ:1.00 OD1 A:ASP483 2.4 167.0 1.0 O A:ALA484 2.4 167.3 1.0 OD1 A:ASP429 2.5 166.7 1.0 O A:ASP435 2.6 166.4 1.0 CB A:ASP435 2.8 166.4 1.0 CG A:ASP483 2.8 167.0 1.0 C A:ALA484 2.9 167.3 1.0 N A:ALA484 3.0 167.3 1.0 OD2 A:ASP483 3.1 167.0 1.0 CG A:ASP429 3.2 166.7 1.0 OD2 A:ASP429 3.3 166.7 1.0 C A:ASP435 3.3 166.4 1.0 CA A:ASP435 3.3 166.4 1.0 N A:ASP435 3.4 166.4 1.0 CA A:ALA484 3.4 167.3 1.0 C A:ASP483 3.4 167.0 1.0 OD1 A:ASP485 3.6 167.1 1.0 N A:ASP485 3.8 167.1 1.0 CG A:ASP435 3.9 166.4 1.0 CA A:ASP483 3.9 167.0 1.0 CB A:ASP483 3.9 167.0 1.0 OD2 A:ASP435 4.0 166.4 1.0 CB A:ALA484 4.1 167.3 1.0 O A:ASP483 4.1 167.0 1.0 CG A:ASP485 4.2 167.1 1.0 CA A:ASP485 4.3 167.1 1.0 N A:ALA436 4.6 160.1 1.0 CB A:ASP429 4.6 166.7 1.0 C A:THR434 4.7 166.6 1.0 N A:ASP429 4.8 166.7 1.0 CB A:ASP485 4.8 167.1 1.0 OD2 A:ASP485 4.9 167.1 1.0 OD1 A:ASP435 4.9 166.4 1.0 CA A:ASP429 5.0 166.7 1.0

Calcium binding site 3 out of 3 in the The Pore Conformation of Lymphocyte Perforin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Pore Conformation of Lymphocyte Perforin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:170.0 occ:1.00 OD2 A:ASP485 2.5 167.1 1.0 O A:GLY428 2.6 165.2 1.0 CE2 A:TYR430 2.8 165.2 1.0 CZ A:TYR430 3.0 165.2 1.0 OD2 A:ASP483 3.1 167.0 1.0 OD2 A:ASP491 3.3 163.7 1.0 OH A:TYR430 3.4 165.2 1.0 CD2 A:TYR430 3.4 165.2 1.0 CG A:ASP491 3.6 163.7 1.0 CG A:ASP485 3.6 167.1 1.0 CE1 A:TYR430 3.7 165.2 1.0 C A:GLY428 3.7 165.2 1.0 CB A:ASP491 3.9 163.7 1.0 CG A:TYR430 4.0 165.2 1.0 OD1 A:ASP485 4.0 167.1 1.0 CD1 A:TYR430 4.1 165.2 1.0 CG A:ASP483 4.1 167.0 1.0 CA A:ASP429 4.2 166.7 1.0 OD1 A:ASP491 4.3 163.7 1.0 N A:TYR430 4.3 165.2 1.0 N A:ASP429 4.4 166.7 1.0 OD1 A:ASP429 4.5 166.7 1.0 C A:ASP429 4.7 166.7 1.0 CA A:GLY428 4.8 165.2 1.0 CB A:ASP483 4.8 167.0 1.0 CB A:ASP485 4.9 167.1 1.0 OD1 A:ASP483 5.0 167.0 1.0

M.E.Ivanova, N.Lukoyanova, S.Malhotra, M.Topf, J.A.Trapani, I.Voskoboinik, H.R.Saibil. The Pore Conformation of Lymphocyte Perforin. Sci Adv V. 8 K3147 2022.
ISSN: ESSN 2375-2548
PubMed: 35148176
DOI: 10.1126/SCIADV.ABK3147