Calcium in PDB 2ary: Catalytic Domain of Human Calpain-1

All present enzymatic activity of Catalytic Domain of Human Calpain-1:
3.4.22.52;

The structure of Catalytic Domain of Human Calpain-1, PDB code: 2ary was solved by J.R.Walker, T.Davis, V.Lunin, E.M.Newman, F.Mackenzie, J.Weigelt, M.Sundstrom, C.Arrowsmith, 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)	44.32 / 2.40
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.534, 90.534, 433.102, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 26.4

The binding sites of Calcium atom in the Catalytic Domain of Human Calpain-1 (pdb code 2ary). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Catalytic Domain of Human Calpain-1, PDB code: 2ary:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Catalytic Domain of Human Calpain-1


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-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:32.4 occ:1.00 O A:VAL99 2.3 36.9 1.0 O A:GLY101 2.3 27.7 1.0 O A:HOH403 2.4 31.1 1.0 OD2 A:ASP106 2.4 32.3 1.0 O A:HOH406 2.4 36.2 1.0 OD1 A:ASP106 2.6 30.6 1.0 OE2 A:GLU185 2.6 32.8 1.0 OE1 A:GLU185 2.7 30.8 1.0 CG A:ASP106 2.8 32.5 1.0 CD A:GLU185 3.0 31.5 1.0 C A:VAL99 3.5 36.5 1.0 C A:GLY101 3.6 31.6 1.0 O A:ASP100 3.9 35.3 1.0 C A:ASP100 4.1 35.8 1.0 N A:VAL99 4.1 36.1 1.0 O A:HOH425 4.2 41.2 1.0 CB A:ASP106 4.2 32.4 1.0 CA A:VAL99 4.3 36.6 1.0 N A:GLY101 4.3 34.2 1.0 OG1 A:THR103 4.3 25.9 1.0 N A:THR103 4.4 26.9 1.0 N A:ASP100 4.5 36.7 1.0 CG A:GLU185 4.5 28.5 1.0 NE1 A:TRP187 4.5 32.3 1.0 N A:ALA102 4.5 31.0 1.0 CB A:VAL99 4.5 36.3 1.0 CA A:GLY101 4.5 32.5 1.0 CA A:ALA102 4.6 29.3 1.0 CA A:ASP100 4.7 36.3 1.0 OG A:SER180 4.7 30.6 1.0 CB A:ASP100 4.9 37.6 1.0 O A:HOH502 4.9 38.5 1.0 OG1 A:THR105 4.9 35.0 1.0 C A:ALA102 5.0 27.6 1.0

Calcium binding site 2 out of 4 in the Catalytic Domain of Human Calpain-1


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-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:31.6 occ:1.00 O A:GLU333 2.3 32.2 1.0 O A:HOH414 2.3 30.5 1.0 O A:MET329 2.3 46.4 1.0 OE1 A:GLU302 2.5 32.0 1.0 OD1 A:ASP331 2.5 42.4 1.0 OD2 A:ASP309 2.6 40.6 1.0 OE2 A:GLU302 2.8 39.0 1.0 CD A:GLU302 2.9 35.8 1.0 OD1 A:ASP309 3.1 36.1 1.0 CG A:ASP309 3.2 38.0 1.0 C A:GLU333 3.5 31.0 1.0 CG A:ASP331 3.5 37.6 1.0 C A:MET329 3.6 47.6 1.0 OD2 A:ASP331 3.9 36.5 1.0 O A:VAL327 4.0 42.8 1.0 N A:ASP331 4.0 40.5 1.0 N A:GLU333 4.1 31.3 1.0 N A:MET329 4.2 48.6 1.0 CA A:GLU333 4.3 31.1 1.0 CG A:GLU302 4.4 33.0 1.0 CA A:MET329 4.4 50.3 1.0 N A:PHE334 4.5 30.5 1.0 N A:GLU330 4.5 47.1 1.0 O A:HOH441 4.6 33.7 1.0 CA A:GLU330 4.6 46.1 1.0 CB A:ASP331 4.7 36.8 1.0 CB A:ASP309 4.7 37.9 1.0 CA A:PHE334 4.7 30.0 1.0 CB A:GLU333 4.7 30.4 1.0 O A:HOH407 4.7 28.7 1.0 N A:GLY332 4.7 34.7 1.0 CA A:ASP331 4.7 37.7 1.0 CB A:PHE334 4.9 28.7 1.0 C A:GLU330 4.9 43.9 1.0 CB A:MET329 4.9 50.3 1.0 O A:HOH415 4.9 33.0 1.0 C A:ASP331 5.0 35.3 1.0

Calcium binding site 3 out of 4 in the Catalytic Domain of Human Calpain-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catalytic Domain of Human Calpain-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:40.4 occ:1.00 O B:GLY101 2.3 40.1 1.0 O B:VAL99 2.4 48.5 1.0 O B:HOH442 2.4 47.3 1.0 OD2 B:ASP106 2.6 40.3 1.0 OD1 B:ASP106 2.6 41.5 1.0 OE2 B:GLU185 2.6 47.6 1.0 OE1 B:GLU185 2.7 48.2 1.0 CG B:ASP106 2.9 39.4 1.0 CD B:GLU185 3.0 47.1 1.0 C B:VAL99 3.6 49.0 1.0 C B:GLY101 3.6 41.6 1.0 O B:ASP100 3.8 48.2 1.0 C B:ASP100 4.0 47.3 1.0 OG1 B:THR103 4.1 44.7 1.0 N B:VAL99 4.2 49.2 1.0 N B:THR103 4.3 42.0 1.0 CB B:ASP106 4.3 40.1 1.0 N B:GLY101 4.4 45.0 1.0 CA B:VAL99 4.4 48.9 1.0 CA B:ALA102 4.4 40.6 1.0 N B:ALA102 4.4 40.6 1.0 CG B:GLU185 4.5 43.2 1.0 NE1 B:TRP187 4.5 34.4 1.0 N B:ASP100 4.5 48.9 1.0 CA B:GLY101 4.5 42.6 1.0 CA B:ASP100 4.7 48.9 1.0 OG B:SER180 4.8 42.1 1.0 CB B:ASP100 4.9 50.3 1.0 OG1 B:THR105 4.9 45.2 1.0 C B:ALA102 4.9 41.8 1.0

Calcium binding site 4 out of 4 in the Catalytic Domain of Human Calpain-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Catalytic Domain of Human Calpain-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:36.0 occ:1.00 O B:HOH420 2.1 30.1 1.0 O B:GLU333 2.2 31.3 1.0 O B:MET329 2.3 40.9 1.0 OE2 B:GLU302 2.4 35.2 1.0 OE1 B:GLU302 2.5 38.2 1.0 OD1 B:ASP331 2.5 42.7 1.0 OD2 B:ASP309 2.5 40.5 1.0 CD B:GLU302 2.7 34.0 1.0 OD1 B:ASP309 3.3 36.8 1.0 CG B:ASP309 3.3 40.0 1.0 C B:GLU333 3.4 31.9 1.0 CG B:ASP331 3.4 37.6 1.0 C B:MET329 3.6 41.8 1.0 OD2 B:ASP331 3.8 38.6 1.0 N B:ASP331 3.9 35.6 1.0 N B:GLU333 3.9 30.1 1.0 CA B:GLU333 4.1 31.7 1.0 O B:VAL327 4.2 40.9 1.0 CG B:GLU302 4.2 32.2 1.0 N B:MET329 4.4 44.8 1.0 O B:HOH499 4.4 32.6 1.0 N B:PHE334 4.4 29.9 1.0 N B:GLU330 4.5 39.3 1.0 CA B:GLU330 4.5 39.3 1.0 CA B:MET329 4.5 44.1 1.0 CB B:ASP331 4.6 36.4 1.0 O B:HOH473 4.6 34.7 1.0 CB B:GLU333 4.6 33.1 1.0 N B:GLY332 4.6 32.2 1.0 CA B:ASP331 4.6 35.3 1.0 CA B:PHE334 4.7 29.7 1.0 C B:GLU330 4.7 37.5 1.0 O B:HOH424 4.7 36.3 1.0 CB B:ASP309 4.7 39.5 1.0 C B:GLY332 4.8 29.9 1.0 C B:ASP331 4.9 34.9 1.0 CB B:MET329 4.9 47.2 1.0 CB B:PHE334 4.9 27.6 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