Calcium in PDB 3nsj: The X-Ray Crystal Structure of Lymphocyte Perforin

The structure of The X-Ray Crystal Structure of Lymphocyte Perforin, PDB code: 3nsj was solved by R.H.Law, J.C.Whisstock, T.T.Caradoc-Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.36 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	78.640, 109.800, 141.030, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 21.5

The structure of The X-Ray Crystal Structure of Lymphocyte Perforin also contains other interesting chemical elements:

Iodine	(I)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the The X-Ray Crystal Structure of Lymphocyte Perforin (pdb code 3nsj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The X-Ray Crystal Structure of Lymphocyte Perforin, PDB code: 3nsj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The X-Ray Crystal Structure 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 X-Ray Crystal Structure of Lymphocyte Perforin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:82.8 occ:0.60 OD1 A:ASP490 2.2 83.3 1.0 O A:ASP485 2.2 78.3 1.0 O A:HOH1053 2.5 76.9 1.0 O A:TRP488 2.7 82.0 1.0 O A:HOH1059 3.1 81.6 1.0 CG A:ASP490 3.3 81.7 1.0 C A:ASP485 3.4 77.9 1.0 O A:TYR486 3.5 84.1 1.0 N A:ASP490 3.9 73.0 1.0 C A:TRP488 3.9 82.9 1.0 OD2 A:ASP490 4.0 85.8 1.0 N A:ASP485 4.1 69.4 1.0 C A:TYR486 4.2 83.7 1.0 CA A:ASP485 4.2 70.6 1.0 N A:TYR486 4.4 76.4 1.0 CB A:ASP490 4.4 72.3 1.0 C A:ASP489 4.4 79.0 1.0 CA A:ASP490 4.5 70.9 1.0 CA A:ASP489 4.5 78.2 1.0 CB A:ASP485 4.5 72.9 1.0 O3 A:GOL652 4.6 93.3 1.0 CA A:TYR486 4.6 77.8 1.0 N A:ASP489 4.7 78.9 1.0 N A:TRP488 4.9 80.9 1.0

Calcium binding site 2 out of 2 in the The X-Ray Crystal Structure 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 X-Ray Crystal Structure of Lymphocyte Perforin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:95.7 occ:1.00 OD1 A:ASP435 2.4 63.2 1.0 OD2 A:ASP483 2.5 65.7 1.0 O A:ALA484 2.5 70.1 1.0 O A:HOH955 2.7 59.5 1.0 CG A:ASP435 3.3 62.8 1.0 CG A:ASP483 3.3 60.7 1.0 CB A:ASP435 3.5 55.3 1.0 C A:ALA484 3.5 70.2 1.0 OD1 A:ASP483 3.8 61.9 1.0 N A:ASP435 4.0 52.9 1.0 N A:ALA484 4.0 61.2 1.0 C A:ASP483 4.1 61.6 1.0 O A:ALA433 4.3 54.0 1.0 CB A:ASP483 4.3 55.5 1.0 CA A:ASP435 4.3 53.1 1.0 CA A:ALA484 4.3 62.8 1.0 OD2 A:ASP435 4.4 67.9 1.0 N A:ASP485 4.4 69.4 1.0 O A:ASP483 4.4 61.2 1.0 CA A:ASP483 4.6 54.4 1.0 CA A:ASP485 4.6 70.6 1.0 O A:ASP435 4.7 57.1 1.0 C A:ASP435 4.9 57.2 1.0 C A:THR434 4.9 56.4 1.0

R.H.Law, N.Lukoyanova, I.Voskoboinik, T.T.Caradoc-Davies, K.Baran, M.A.Dunstone, M.E.D'angelo, E.V.Orlova, F.Coulibaly, S.Verschoor, K.A.Browne, A.Ciccone, M.J.Kuiper, P.I.Bird, J.A.Trapani, H.R.Saibil, J.C.Whisstock. The Structural Basis For Membrane Binding and Pore Formation By Lymphocyte Perforin. Nature V. 468 447 2010.
ISSN: ISSN 0028-0836
PubMed: 21037563
DOI: 10.1038/NATURE09518