Calcium in PDB 1dvi: Calpain Domain VI with Calcium Bound

The structure of Calpain Domain VI with Calcium Bound, PDB code: 1dvi was solved by M.Cygler, H.Blanchard, P.Grochulski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	75.000, 87.400, 118.300, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 29.4

The binding sites of Calcium atom in the Calpain Domain VI with Calcium Bound (pdb code 1dvi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Calpain Domain VI with Calcium Bound, PDB code: 1dvi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Calpain Domain VI with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calpain Domain VI with Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca271 b:14.5 occ:1.00 O A:ALA111 2.2 15.9 1.0 O A:GLU116 2.3 6.2 1.0 O A:HOH296 2.4 18.4 1.0 O A:HOH284 2.5 3.5 1.0 OE2 A:GLU121 2.5 13.1 1.0 OE1 A:GLU121 2.5 11.2 1.0 OD1 A:ASP114 2.5 22.0 1.0 CD A:GLU121 2.8 12.6 1.0 C A:ALA111 3.4 14.0 1.0 CG A:ASP114 3.5 18.9 1.0 C A:GLU116 3.5 10.9 1.0 OD2 A:ASP114 3.9 18.1 1.0 CA A:ALA111 4.0 13.8 1.0 N A:GLU116 4.3 15.6 1.0 CG A:GLU121 4.3 11.7 1.0 N A:SER118 4.4 5.0 1.0 N A:GLY112 4.4 13.8 1.0 N A:VAL117 4.4 9.1 1.0 O A:LEU110 4.4 12.4 1.0 CA A:GLU116 4.5 12.3 1.0 CA A:VAL117 4.5 7.2 1.0 O A:HOH360 4.5 23.8 1.0 O A:HOH351 4.6 37.4 1.0 O A:HOH330 4.6 33.8 1.0 N A:ASP114 4.7 17.6 1.0 CA A:GLY112 4.7 15.6 1.0 O A:HOH285 4.7 24.6 1.0 CB A:ASP114 4.8 18.0 1.0 OG A:SER118 4.9 5.4 1.0 CB A:SER118 4.9 3.1 1.0 C A:GLY112 4.9 16.4 1.0 C A:VAL117 4.9 5.7 1.0 CB A:ALA111 4.9 14.1 1.0

Calcium binding site 2 out of 8 in the Calpain Domain VI with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calpain Domain VI with Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca272 b:17.2 occ:1.00 O A:LYS160 2.2 9.6 1.0 OD1 A:ASP154 2.4 16.9 1.0 OG1 A:THR158 2.4 23.8 1.0 OD1 A:ASP156 2.4 21.6 1.0 O A:HOH275 2.5 19.2 1.0 OE1 A:GLU165 2.5 12.9 1.0 OE2 A:GLU165 2.9 15.0 1.0 CD A:GLU165 3.1 12.4 1.0 CG A:ASP156 3.3 22.9 1.0 C A:LYS160 3.4 10.8 1.0 CG A:ASP154 3.6 16.6 1.0 OD2 A:ASP156 3.6 24.0 1.0 CB A:THR158 3.7 21.7 1.0 N A:THR158 3.8 21.4 1.0 N A:GLY162 4.2 12.0 1.0 CA A:LEU161 4.2 11.2 1.0 CG2 A:THR158 4.2 19.9 1.0 N A:LYS160 4.2 11.4 1.0 CA A:ASP154 4.2 16.3 1.0 OE2 A:GLU116 4.2 22.9 1.0 N A:LEU161 4.3 10.4 1.0 CA A:THR158 4.3 18.7 1.0 CB A:ASP154 4.3 15.6 1.0 N A:ASP156 4.4 23.0 1.0 OD2 A:ASP154 4.4 14.8 1.0 CA A:LYS160 4.5 9.2 1.0 CG A:GLU165 4.6 12.0 1.0 C A:ASP154 4.6 20.4 1.0 CB A:ASP156 4.6 22.9 1.0 N A:THR157 4.6 25.8 1.0 N A:GLY159 4.6 16.2 1.0 C A:LEU161 4.7 11.6 1.0 C A:THR158 4.7 18.1 1.0 C A:ASP156 4.7 25.7 1.0 OE1 A:GLU116 4.8 25.3 1.0 CA A:ASP156 4.8 23.5 1.0 CD A:GLU116 4.8 20.7 1.0 N A:SER155 4.8 21.6 1.0 C A:THR157 4.9 24.2 1.0

Calcium binding site 3 out of 8 in the Calpain Domain VI with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calpain Domain VI with Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca273 b:21.4 occ:1.00 O A:HOH278 2.2 26.3 1.0 OG A:SER188 2.3 19.3 1.0 OD1 A:ASP184 2.4 22.5 1.0 OE1 A:GLU195 2.4 23.7 1.0 OD1 A:ASP186 2.5 29.6 1.0 O A:THR190 2.6 20.5 1.0 OE2 A:GLU195 2.8 23.6 1.0 CD A:GLU195 3.0 23.5 1.0 CG A:ASP186 3.5 28.7 1.0 CG A:ASP184 3.5 20.2 1.0 CB A:SER188 3.7 18.9 1.0 C A:THR190 3.7 17.4 1.0 OD2 A:ASP186 3.9 30.4 1.0 N A:SER188 4.0 21.3 1.0 CA A:ASP184 4.1 18.9 1.0 N A:GLY192 4.2 18.4 1.0 OG1 A:THR190 4.2 21.4 1.0 CB A:ASP184 4.3 19.3 1.0 OD2 A:ASP184 4.4 21.1 1.0 CA A:SER188 4.4 20.2 1.0 CA A:ILE191 4.4 14.4 1.0 N A:THR190 4.4 17.7 1.0 C A:ASP184 4.5 20.9 1.0 O A:HOH297 4.5 40.6 1.0 N A:ILE191 4.5 14.6 1.0 CG A:GLU195 4.5 20.6 1.0 N A:ASP186 4.6 22.5 1.0 OD1 A:ASN225 4.6 20.9 1.0 CA A:THR190 4.6 17.4 1.0 N A:THR185 4.8 24.4 1.0 CB A:ASP186 4.8 25.6 1.0 N A:ARG187 4.8 25.8 1.0 C A:ILE191 4.8 17.3 1.0 N A:GLY189 4.9 21.0 1.0 O A:ASP184 4.9 18.3 1.0 C A:SER188 4.9 20.4 1.0 C A:ASP186 5.0 25.2 1.0

Calcium binding site 4 out of 8 in the Calpain Domain VI with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calpain Domain VI with Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca274 b:15.2 occ:1.00 O B:HOH282 2.3 6.9 1.0 OD1 A:ASN230 2.3 13.2 1.0 OD1 A:ASP139 2.3 20.8 1.0 OD2 A:ASP227 2.5 5.5 1.0 OD1 A:ASP227 2.6 7.1 1.0 OD2 A:ASP229 2.6 10.6 1.0 O B:HOH285 2.6 11.2 1.0 OD1 A:ASP229 2.7 13.7 1.0 CG A:ASP227 2.9 7.9 1.0 CG A:ASP229 3.0 11.4 1.0 CG A:ASP139 3.4 23.0 1.0 CG A:ASN230 3.4 13.0 1.0 OD2 A:ASP139 3.8 22.2 1.0 O B:HOH367 3.8 29.3 1.0 O B:HOH354 3.9 34.9 1.0 N A:ASN230 4.2 12.8 1.0 ND2 A:ASN230 4.2 16.7 1.0 CB A:ASN230 4.3 10.2 1.0 O B:HOH286 4.3 20.1 1.0 CB A:ASP229 4.4 9.7 1.0 N A:ASP139 4.4 17.3 1.0 CB A:ASP227 4.4 8.6 1.0 O A:HOH282 4.5 16.2 1.0 OD1 B:ASP144 4.5 12.1 1.0 O A:GLY140 4.6 7.5 1.0 OG1 A:THR138 4.6 11.4 1.0 CB A:ASP139 4.6 20.8 1.0 CA A:ASN230 4.7 9.7 1.0 O A:HOH295 4.7 17.1 1.0 C A:ASP229 4.8 10.3 1.0 N A:ASP229 4.9 9.0 1.0 CA A:ASP229 5.0 10.6 1.0 NH2 B:ARG147 5.0 41.9 1.0

Calcium binding site 5 out of 8 in the Calpain Domain VI with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Calpain Domain VI with Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca275 b:15.5 occ:1.00 O B:ALA111 2.2 14.0 1.0 O B:GLU116 2.2 9.8 1.0 O B:HOH302 2.4 14.6 1.0 OD1 B:ASP114 2.4 21.8 1.0 O B:HOH314 2.5 30.5 1.0 OE2 B:GLU121 2.6 15.8 1.0 OE1 B:GLU121 2.6 13.9 1.0 CD B:GLU121 3.0 16.1 1.0 C B:ALA111 3.4 14.2 1.0 CG B:ASP114 3.4 21.0 1.0 C B:GLU116 3.5 12.5 1.0 OD2 B:ASP114 3.7 23.4 1.0 CA B:ALA111 4.0 15.1 1.0 N B:GLU116 4.2 16.8 1.0 N B:VAL117 4.4 13.1 1.0 N B:GLY112 4.4 13.6 1.0 CA B:GLU116 4.4 13.6 1.0 N B:SER118 4.4 10.4 1.0 CA B:VAL117 4.5 10.6 1.0 CG B:GLU121 4.5 15.7 1.0 O B:LEU110 4.5 16.5 1.0 N B:ASP114 4.6 17.2 1.0 O B:HOH303 4.6 23.7 1.0 CB B:ASP114 4.7 19.6 1.0 CA B:GLY112 4.7 14.1 1.0 OG B:SER118 4.8 8.6 1.0 C B:GLY112 4.8 16.5 1.0 CB B:ALA111 4.8 14.5 1.0 C B:VAL117 4.9 10.2 1.0 CA B:ASP114 4.9 15.8 1.0

Calcium binding site 6 out of 8 in the Calpain Domain VI with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Calpain Domain VI with Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca276 b:18.8 occ:1.00 O B:LYS160 2.2 12.9 1.0 OE1 B:GLU165 2.4 15.2 1.0 OD1 B:ASP156 2.4 30.3 1.0 OG1 B:THR158 2.5 26.9 1.0 OD1 B:ASP154 2.5 18.3 1.0 O B:HOH292 2.5 28.6 1.0 OE2 B:GLU165 2.8 15.8 1.0 CD B:GLU165 2.9 13.8 1.0 CG B:ASP156 3.3 30.1 1.0 C B:LYS160 3.5 14.5 1.0 OD2 B:ASP156 3.5 31.3 1.0 CG B:ASP154 3.7 18.6 1.0 CB B:THR158 3.8 25.9 1.0 N B:THR158 4.0 26.6 1.0 OE2 B:GLU116 4.1 18.5 1.0 N B:GLY162 4.1 16.7 1.0 CG2 B:THR158 4.2 24.9 1.0 CA B:LEU161 4.2 15.5 1.0 N B:LEU161 4.3 12.9 1.0 N B:LYS160 4.3 12.7 1.0 CA B:ASP154 4.3 18.4 1.0 CG B:GLU165 4.4 14.1 1.0 CA B:THR158 4.4 24.0 1.0 N B:ASP156 4.5 28.5 1.0 CB B:ASP154 4.5 17.7 1.0 CA B:LYS160 4.5 12.3 1.0 OD2 B:ASP154 4.6 16.9 1.0 CB B:ASP156 4.6 29.3 1.0 C B:LEU161 4.6 15.5 1.0 C B:ASP154 4.7 20.6 1.0 CD B:GLU116 4.7 19.8 1.0 N B:THR157 4.8 30.2 1.0 C B:ASP156 4.8 31.0 1.0 N B:GLY159 4.8 20.5 1.0 CA B:ASP156 4.8 29.9 1.0 OE1 B:GLU116 4.9 25.0 1.0 N B:SER155 4.9 24.2 1.0 C B:THR158 4.9 23.5 1.0 CD1 B:LEU161 4.9 10.5 1.0

Calcium binding site 7 out of 8 in the Calpain Domain VI with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Calpain Domain VI with Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca277 b:21.1 occ:1.00 O B:HOH295 2.3 25.0 1.0 OD1 B:ASP184 2.3 23.5 1.0 OG B:SER188 2.4 19.6 1.0 OE1 B:GLU195 2.4 22.8 1.0 OD1 B:ASP186 2.4 32.7 1.0 O B:THR190 2.5 18.0 1.0 OE2 B:GLU195 2.7 19.0 1.0 CD B:GLU195 2.9 20.2 1.0 CG B:ASP184 3.5 23.1 1.0 CG B:ASP186 3.5 31.3 1.0 C B:THR190 3.7 16.4 1.0 CB B:SER188 3.7 18.8 1.0 OD2 B:ASP186 3.9 32.7 1.0 N B:SER188 3.9 23.1 1.0 CA B:ASP184 4.0 23.0 1.0 CB B:ASP184 4.2 22.5 1.0 N B:GLY192 4.2 15.3 1.0 OG1 B:THR190 4.3 16.2 1.0 C B:ASP184 4.3 25.1 1.0 OD2 B:ASP184 4.3 23.9 1.0 CA B:SER188 4.3 19.7 1.0 CA B:ILE191 4.4 14.0 1.0 CG B:GLU195 4.4 19.2 1.0 N B:THR190 4.4 17.0 1.0 N B:ILE191 4.5 14.9 1.0 N B:ASP186 4.5 26.7 1.0 CA B:THR190 4.6 15.3 1.0 N B:ARG187 4.7 26.2 1.0 N B:THR185 4.7 27.2 1.0 O B:HOH316 4.7 34.0 1.0 O B:ASP184 4.7 22.7 1.0 OD1 B:ASN225 4.7 22.5 1.0 CB B:ASP186 4.8 29.4 1.0 C B:ILE191 4.8 14.5 1.0 N B:GLY189 4.8 18.6 1.0 C B:ASP186 4.9 26.6 1.0 C B:SER188 4.9 19.6 1.0 CA B:ASP186 4.9 27.2 1.0

Calcium binding site 8 out of 8 in the Calpain Domain VI with Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Calpain Domain VI with Calcium Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca278 b:13.6 occ:1.00 OD1 B:ASN230 2.3 9.8 1.0 OD1 B:ASP139 2.4 16.4 1.0 O B:HOH301 2.5 14.9 1.0 O B:HOH315 2.6 21.7 1.0 OD2 B:ASP229 2.6 8.4 1.0 OD2 B:ASP227 2.6 14.4 1.0 OD1 B:ASP229 2.6 8.8 1.0 OD1 B:ASP227 2.7 15.1 1.0 CG B:ASP229 2.9 8.1 1.0 CG B:ASP227 3.0 13.9 1.0 CG B:ASN230 3.4 11.2 1.0 CG B:ASP139 3.4 14.1 1.0 OD2 B:ASP139 3.8 15.8 1.0 N B:ASN230 4.1 10.5 1.0 O B:HOH318 4.2 15.6 1.0 ND2 B:ASN230 4.2 12.8 1.0 CB B:ASN230 4.3 9.4 1.0 CB B:ASP229 4.4 8.9 1.0 N B:ASP139 4.4 10.2 1.0 CB B:ASP227 4.5 13.0 1.0 O B:HOH299 4.6 15.9 1.0 OG1 B:THR138 4.7 7.9 1.0 O B:GLY140 4.7 5.6 1.0 CB B:ASP139 4.7 13.3 1.0 CA B:ASN230 4.7 7.4 1.0 C B:ASP229 4.8 9.3 1.0 O B:HOH313 4.8 10.6 1.0 N B:ASP229 4.8 8.8 1.0 OD1 A:ASP144 4.9 17.4 1.0 CA B:ASP229 4.9 8.9 1.0 O B:HOH306 4.9 31.7 1.0

H.Blanchard, P.Grochulski, Y.Li, J.S.Arthur, P.L.Davies, J.S.Elce, M.Cygler. Structure of A Calpain Ca(2+)-Binding Domain Reveals A Novel Ef-Hand and Ca(2+)-Induced Conformational Changes. Nat.Struct.Biol. V. 4 532 1997.
ISSN: ISSN 1072-8368
PubMed: 9228945
DOI: 10.1038/NSB0797-532