Calcium in PDB 1kxr: Crystal Structure of Calcium-Bound Protease Core of Calpain I

All present enzymatic activity of Crystal Structure of Calcium-Bound Protease Core of Calpain I:
3.4.22.17;

The structure of Crystal Structure of Calcium-Bound Protease Core of Calpain I, PDB code: 1kxr was solved by T.Moldoveanu, C.M.Hosfield, D.Lim, J.S.Elce, Z.Jia, P.L.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.07
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.443, 40.492, 132.328, 90.00, 105.96, 90.00
R / Rfree (%)	21.3 / 25.6

The binding sites of Calcium atom in the Crystal Structure of Calcium-Bound Protease Core of Calpain I (pdb code 1kxr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Calcium-Bound Protease Core of Calpain I, PDB code: 1kxr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Calcium-Bound Protease Core of Calpain I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Calcium-Bound Protease Core of Calpain I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:21.1 occ:1.00 O A:HOH450 2.2 22.6 1.0 O A:VAL99 2.4 24.1 1.0 O A:GLY101 2.5 21.2 1.0 OD1 A:ASP106 2.5 19.5 1.0 OD2 A:ASP106 2.5 19.7 1.0 OE2 A:GLU185 2.5 18.1 1.0 O A:HOH451 2.6 15.3 1.0 OE1 A:GLU185 2.6 20.0 1.0 CG A:ASP106 2.8 20.2 1.0 CD A:GLU185 2.9 19.6 1.0 C A:VAL99 3.5 24.4 1.0 C A:GLY101 3.7 20.7 1.0 O A:HOH452 3.9 32.9 1.0 N A:VAL99 4.1 24.2 1.0 O A:ASP100 4.1 21.3 1.0 CB A:ASP106 4.2 19.6 1.0 C A:ASP100 4.2 22.8 1.0 CA A:VAL99 4.3 24.4 1.0 OG1 A:THR103 4.3 20.4 1.0 N A:THR103 4.4 19.2 1.0 O A:HOH435 4.4 28.2 1.0 CG A:GLU185 4.4 18.4 1.0 N A:GLY101 4.4 22.4 1.0 CA A:ALA102 4.5 19.1 1.0 NE1 A:TRP187 4.5 17.1 1.0 N A:ALA102 4.6 18.8 1.0 CB A:VAL99 4.6 24.8 1.0 N A:ASP100 4.6 23.4 1.0 OG A:SER180 4.6 18.7 1.0 CA A:GLY101 4.7 21.4 1.0 CA A:ASP100 4.7 24.9 1.0 CB A:ASP100 4.8 25.4 1.0 CG A:GLN182 4.9 37.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Calcium-Bound Protease Core of Calpain I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Calcium-Bound Protease Core of Calpain I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:25.4 occ:1.00 OD1 A:ASP309 2.2 23.1 1.0 O A:GLU333 2.2 20.7 1.0 OE2 A:GLU302 2.4 26.3 1.0 O A:HOH380 2.4 16.9 1.0 OD1 A:ASP331 2.4 25.5 1.0 OE1 A:GLU302 2.5 24.4 1.0 O A:MET329 2.5 30.6 1.0 CD A:GLU302 2.8 26.2 1.0 CG A:ASP309 3.0 23.8 1.0 OD2 A:ASP309 3.1 23.7 1.0 C A:GLU333 3.4 20.9 1.0 CG A:ASP331 3.4 26.0 1.0 C A:MET329 3.8 32.8 1.0 OD2 A:ASP331 3.8 29.2 1.0 N A:GLU333 3.9 20.9 1.0 N A:ASP331 4.0 27.8 1.0 O A:VAL327 4.1 30.9 1.0 CA A:GLU333 4.2 21.4 1.0 O A:HOH434 4.2 30.1 1.0 CG A:GLU302 4.2 24.9 1.0 N A:MET329 4.4 35.5 1.0 CB A:ASP309 4.4 25.1 1.0 N A:PHE334 4.4 20.1 1.0 N A:GLY332 4.5 22.9 1.0 CA A:PHE334 4.6 20.6 1.0 CA A:MET329 4.6 34.7 1.0 CB A:GLU333 4.6 22.0 1.0 O A:HOH510 4.6 28.1 1.0 CB A:PHE334 4.6 19.2 1.0 CB A:ASP331 4.7 25.3 1.0 N A:GLU330 4.7 30.9 1.0 O A:HOH381 4.7 15.6 1.0 CA A:GLU330 4.7 30.5 1.0 CA A:ASP331 4.8 25.4 1.0 O A:HOH392 4.8 19.8 1.0 C A:GLY332 4.8 20.6 1.0 C A:ASP331 4.9 24.4 1.0 C A:GLU330 4.9 29.1 1.0 CB A:MET329 5.0 38.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Calcium-Bound Protease Core of Calpain I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Calcium-Bound Protease Core of Calpain I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3 b:16.8 occ:1.00 O B:HOH444 2.3 18.8 1.0 O B:VAL99 2.4 18.2 1.0 OD2 B:ASP106 2.4 15.6 1.0 O B:GLY101 2.4 18.6 1.0 OE2 B:GLU185 2.4 16.9 1.0 O B:HOH443 2.5 17.6 1.0 OD1 B:ASP106 2.6 15.2 1.0 OE1 B:GLU185 2.6 17.5 1.0 CG B:ASP106 2.8 16.4 1.0 CD B:GLU185 2.9 14.6 1.0 C B:VAL99 3.5 18.1 1.0 C B:GLY101 3.6 19.2 1.0 O B:ASP100 4.0 15.6 1.0 N B:VAL99 4.1 16.4 1.0 O B:HOH403 4.1 30.6 1.0 C B:ASP100 4.1 18.5 1.0 CB B:ASP106 4.2 15.8 1.0 OG1 B:THR103 4.2 19.8 1.0 N B:THR103 4.3 19.7 1.0 CA B:VAL99 4.3 18.2 1.0 CG B:GLU185 4.4 15.8 1.0 CA B:ALA102 4.4 20.4 1.0 N B:GLY101 4.4 16.1 1.0 O B:HOH445 4.4 23.4 1.0 N B:ALA102 4.5 18.8 1.0 NE1 B:TRP187 4.5 13.0 1.0 N B:ASP100 4.5 19.5 1.0 CB B:VAL99 4.6 18.8 1.0 CA B:GLY101 4.6 18.7 1.0 OG B:SER180 4.7 16.6 1.0 CA B:ASP100 4.7 18.8 1.0 CB B:ASP100 4.7 24.7 1.0 C B:ALA102 4.9 19.7 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Calcium-Bound Protease Core of Calpain I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Calcium-Bound Protease Core of Calpain I within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4 b:23.0 occ:1.00 OD1 B:ASP309 2.2 24.4 1.0 O B:GLU333 2.3 16.8 1.0 O B:HOH446 2.3 18.0 1.0 OE1 B:GLU302 2.4 16.7 1.0 O B:MET329 2.4 29.2 1.0 OE2 B:GLU302 2.5 18.1 1.0 OD1 B:ASP331 2.5 19.7 1.0 CD B:GLU302 2.7 19.0 1.0 CG B:ASP309 3.0 24.3 1.0 OD2 B:ASP309 3.2 21.5 1.0 C B:GLU333 3.5 16.6 1.0 CG B:ASP331 3.6 23.0 1.0 C B:MET329 3.6 31.5 1.0 N B:GLU333 4.0 19.2 1.0 O B:HOH507 4.0 30.4 1.0 OD2 B:ASP331 4.0 25.6 1.0 N B:ASP331 4.0 26.4 1.0 O B:VAL327 4.1 31.9 1.0 CG B:GLU302 4.2 18.1 1.0 CA B:GLU333 4.3 17.8 1.0 N B:MET329 4.4 33.4 1.0 CB B:ASP309 4.5 27.8 1.0 N B:PHE334 4.5 17.5 1.0 N B:GLY332 4.5 23.5 1.0 CA B:MET329 4.5 33.2 1.0 O B:HOH394 4.5 18.6 1.0 O B:HOH485 4.6 39.6 1.0 N B:GLU330 4.6 30.2 1.0 CA B:PHE334 4.6 20.1 1.0 CB B:PHE334 4.7 21.1 1.0 CA B:GLU330 4.7 29.3 1.0 CB B:ASP331 4.8 25.4 1.0 O B:HOH401 4.8 29.3 1.0 CB B:GLU333 4.8 16.2 1.0 CA B:ASP331 4.8 25.1 1.0 C B:GLY332 4.9 21.7 1.0 C B:GLU330 4.9 27.6 1.0 C B:ASP331 4.9 24.8 1.0 CB B:MET329 5.0 36.6 1.0 O B:HOH457 5.0 38.0 1.0

T.Moldoveanu, C.M.Hosfield, D.Lim, J.S.Elce, Z.Jia, P.L.Davies. A Ca(2+) Switch Aligns the Active Site of Calpain. Cell(Cambridge,Mass.) V. 108 649 2002.
ISSN: ISSN 0092-8674
PubMed: 11893336
DOI: 10.1016/S0092-8674(02)00659-1