Calcium in PDB 1ziv: Catalytic Domain of Human Calpain-9

The structure of Catalytic Domain of Human Calpain-9, PDB code: 1ziv was solved by J.R.Walker, T.Davis, E.M.Newman, F.Mackenzie, A.Dong, J.Choe, C.Arrowsmith, M.Sundstrom, A.Edwards, A.Bochkarev, S.Dhe-Paganon, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.38 / 2.31
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	45.308, 80.900, 100.545, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 27.2

The binding sites of Calcium atom in the Catalytic Domain of Human Calpain-9 (pdb code 1ziv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Catalytic Domain of Human Calpain-9, PDB code: 1ziv:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Catalytic Domain of Human Calpain-9


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytic Domain of Human Calpain-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:35.4 occ:1.00 OE2 A:GLU284 2.2 37.0 1.0 O A:LEU312 2.3 42.9 1.0 O A:GLU316 2.4 34.9 1.0 OD2 A:ASP291 2.5 44.5 1.0 OD1 A:ASP314 2.5 35.8 1.0 OE1 A:GLU284 2.5 37.6 1.0 CD A:GLU284 2.7 36.6 1.0 OD1 A:ASP291 3.1 40.6 1.0 CG A:ASP291 3.2 44.0 1.0 C A:LEU312 3.6 46.5 1.0 CG A:ASP314 3.6 40.2 1.0 C A:GLU316 3.6 37.1 1.0 N A:GLU316 3.9 35.1 1.0 N A:ASP314 4.0 44.0 1.0 OD2 A:ASP314 4.0 31.3 1.0 N A:LEU312 4.1 51.9 1.0 CG A:GLU284 4.2 36.9 1.0 CA A:GLU316 4.3 37.5 1.0 CA A:LEU312 4.4 49.2 1.0 N A:GLY315 4.4 39.5 1.0 N A:ASP313 4.5 46.6 1.0 CB A:ASP291 4.6 42.3 1.0 CA A:ASP313 4.6 49.0 1.0 N A:PHE317 4.6 33.4 1.0 CA A:ASP314 4.7 42.1 1.0 CB A:ASP314 4.7 38.9 1.0 O A:HOH357 4.8 28.2 1.0 C A:ASP313 4.8 47.2 1.0 CA A:PHE317 4.8 32.6 1.0 C A:GLY315 4.8 35.9 1.0 CB A:LEU312 4.9 50.7 1.0 CB A:PHE317 4.9 29.9 1.0 C A:ASP314 4.9 41.9 1.0 O A:THR310 4.9 56.9 1.0 CB A:GLU316 4.9 37.9 1.0

Calcium binding site 2 out of 2 in the Catalytic Domain of Human Calpain-9


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catalytic Domain of Human Calpain-9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:40.4 occ:1.00 O A:GLY83 2.3 37.3 1.0 O A:LEU81 2.3 42.9 1.0 O A:HOH389 2.3 36.1 1.0 OE2 A:GLU167 2.4 36.2 1.0 OD2 A:ASP88 2.5 37.5 1.0 OD1 A:ASP88 2.6 38.2 1.0 OE1 A:GLU167 2.6 36.0 1.0 CG A:ASP88 2.8 37.1 1.0 CD A:GLU167 2.9 36.4 1.0 C A:LEU81 3.5 44.9 1.0 C A:GLY83 3.6 39.2 1.0 O A:GLY82 4.0 43.9 1.0 C A:GLY82 4.2 44.9 1.0 N A:LEU81 4.2 41.0 1.0 CB A:ASP88 4.2 36.9 1.0 CA A:LEU81 4.3 44.3 1.0 CG A:GLU167 4.4 35.4 1.0 N A:GLY83 4.4 41.1 1.0 N A:ALA84 4.5 35.8 1.0 N A:THR85 4.5 36.5 1.0 NE1 A:TRP169 4.5 36.9 1.0 CA A:GLY83 4.5 39.1 1.0 CB A:LEU81 4.5 45.3 1.0 N A:GLY82 4.5 44.3 1.0 CA A:ALA84 4.6 35.4 1.0 OG1 A:THR85 4.7 35.2 1.0 OG A:SER162 4.7 35.7 1.0 CA A:GLY82 4.7 45.2 1.0

T.L.Davis, J.R.Walker, P.J.Finerty, F.Mackenzie, E.M.Newman, S.Dhe-Paganon. The Crystal Structures of Human Calpains 1 and 9 Imply Diverse Mechanisms of Action and Auto-Inhibition. J.Mol.Biol. V. 366 216 2007.
ISSN: ISSN 0022-2836
PubMed: 17157313
DOI: 10.1016/J.JMB.2006.11.037