Calcium in PDB 1alv: Calcium Bound Domain VI of Porcine Calpain

The structure of Calcium Bound Domain VI of Porcine Calpain, PDB code: 1alv was solved by S.V.L.Narayana, G.Lin, D.Chattopadhyay, M.Maki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.870, 80.460, 57.080, 90.00, 91.20, 90.00
R / Rfree (%)	19 / 23

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calcium Bound Domain VI of Porcine Calpain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:28.0 occ:1.00 H1 A:HOH521 1.4 0.0 1.0 H1 A:HOH531 2.1 0.0 1.0 O A:HOH521 2.2 24.3 1.0 OD1 A:ASP110 2.2 29.4 1.0 O A:GLU112 2.2 26.5 1.0 O A:ALA107 2.2 28.3 1.0 OE1 A:GLU117 2.4 27.6 1.0 OE2 A:GLU117 2.4 29.8 1.0 H2 A:HOH531 2.5 0.0 1.0 O A:HOH531 2.7 31.6 1.0 CD A:GLU117 2.8 26.0 1.0 H2 A:HOH521 2.9 0.0 1.0 CG A:ASP110 3.2 29.3 1.0 H A:GLU112 3.3 0.0 1.0 C A:ALA107 3.3 29.6 1.0 C A:GLU112 3.4 24.9 1.0 OD2 A:ASP110 3.5 32.0 1.0 H A:ASP110 3.8 0.0 1.0 H A:SER114 3.8 0.0 1.0 HZ3 A:LYS156 3.9 0.0 1.0 CA A:ALA107 4.0 29.8 1.0 N A:GLU112 4.1 30.9 1.0 CG A:GLU117 4.3 24.8 1.0 N A:VAL113 4.3 22.5 1.0 CA A:VAL113 4.3 23.3 1.0 CA A:GLU112 4.4 28.0 1.0 N A:SER114 4.4 21.5 1.0 N A:GLY108 4.4 29.0 1.0 H A:MET111 4.5 0.0 1.0 H2 A:HOH577 4.5 0.0 1.0 CB A:ASP110 4.5 31.6 1.0 N A:ASP110 4.6 30.4 1.0 H1 A:HOH577 4.6 0.0 1.0 O A:LEU106 4.7 33.6 1.0 CA A:GLY108 4.7 31.0 1.0 CB A:ALA107 4.7 29.0 1.0 N A:MET111 4.7 29.2 1.0 C A:VAL113 4.8 20.7 1.0 CA A:ASP110 4.8 28.2 1.0 C A:GLY108 4.8 30.5 1.0 NZ A:LYS156 4.9 50.0 1.0 C A:ASP110 4.9 27.5 1.0 CB A:GLU112 5.0 30.8 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calcium Bound Domain VI of Porcine Calpain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:25.4 occ:1.00 OD1 A:ASP152 2.1 39.3 1.0 OD1 A:ASP150 2.2 23.5 1.0 OE1 A:GLU161 2.3 26.9 1.0 O A:LYS156 2.4 26.7 1.0 O A:HOH526 2.4 30.8 1.0 HG1 A:THR154 2.4 0.0 1.0 OG1 A:THR154 2.5 29.7 1.0 H2 A:HOH526 2.7 0.0 1.0 H1 A:HOH526 2.7 0.0 1.0 OE2 A:GLU161 2.7 30.1 1.0 CD A:GLU161 2.8 25.8 1.0 H A:THR154 3.0 0.0 1.0 CG A:ASP152 3.2 38.5 1.0 CG A:ASP150 3.4 24.1 1.0 H A:GLY158 3.4 0.0 1.0 H A:ASP152 3.5 0.0 1.0 OD2 A:ASP152 3.5 38.7 1.0 C A:LYS156 3.6 21.9 1.0 H A:LYS156 3.7 0.0 1.0 CB A:THR154 3.7 30.6 1.0 N A:THR154 3.9 33.8 1.0 OE2 A:GLU112 3.9 37.5 1.0 CG2 A:THR154 4.0 28.0 1.0 H A:GLY155 4.1 0.0 1.0 N A:GLY158 4.1 25.2 1.0 CA A:ASP150 4.2 26.7 1.0 CB A:ASP150 4.2 21.3 1.0 OD2 A:ASP150 4.3 24.5 1.0 N A:ASP152 4.3 35.7 1.0 CA A:THR154 4.3 31.2 1.0 CG A:GLU161 4.3 25.3 1.0 N A:LYS156 4.4 27.9 1.0 CA A:LEU157 4.4 23.2 1.0 N A:LEU157 4.4 22.9 1.0 CB A:ASP152 4.5 37.7 1.0 C A:ASP150 4.5 30.5 1.0 H A:THR153 4.5 0.0 1.0 H A:SER151 4.6 0.0 1.0 N A:THR153 4.6 36.7 1.0 CA A:LYS156 4.6 26.3 1.0 N A:GLY155 4.6 31.3 1.0 C A:LEU157 4.7 24.9 1.0 N A:SER151 4.7 32.1 1.0 C A:ASP152 4.7 36.1 1.0 CD A:GLU112 4.7 36.9 1.0 CA A:ASP152 4.7 35.6 1.0 C A:THR154 4.8 31.5 1.0 OE1 A:GLU112 4.8 40.4 1.0 CA A:GLY158 5.0 26.4 1.0 C A:THR153 5.0 35.0 1.0 O A:ASP150 5.0 31.1 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calcium Bound Domain VI of Porcine Calpain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:30.4 occ:1.00 HG A:SER184 1.8 0.0 1.0 OD1 A:ASP180 2.2 26.1 1.0 O A:HOH502 2.2 34.8 1.0 OD1 A:ASP182 2.2 44.3 1.0 OE1 A:GLU191 2.4 37.7 1.0 O A:THR186 2.4 27.2 1.0 OG A:SER184 2.5 36.8 1.0 H2 A:HOH502 2.6 0.0 1.0 OE2 A:GLU191 2.7 36.4 1.0 H1 A:HOH502 2.7 0.0 1.0 CD A:GLU191 2.9 37.0 1.0 H A:SER184 3.1 0.0 1.0 CG A:ASP182 3.1 43.3 1.0 CG A:ASP180 3.4 28.6 1.0 HG1 A:THR186 3.5 0.0 1.0 H A:GLY188 3.5 0.0 1.0 OD2 A:ASP182 3.5 42.1 1.0 H A:THR186 3.6 0.0 1.0 C A:THR186 3.6 26.7 1.0 H A:ASP182 3.6 0.0 1.0 CB A:SER184 3.7 32.5 1.0 N A:SER184 4.0 33.8 1.0 CA A:ASP180 4.1 33.6 1.0 H1 A:HOH539 4.1 0.0 1.0 CB A:ASP180 4.2 28.9 1.0 N A:GLY188 4.2 26.0 1.0 OD2 A:ASP180 4.3 29.4 1.0 OG1 A:THR186 4.3 31.9 1.0 CG A:GLU191 4.4 33.5 1.0 CA A:SER184 4.4 32.9 1.0 N A:THR186 4.4 28.9 1.0 N A:ASP182 4.4 39.2 1.0 C A:ASP180 4.4 36.6 1.0 N A:ILE187 4.5 27.6 1.0 CB A:ASP182 4.5 40.3 1.0 CA A:ILE187 4.5 25.1 1.0 H A:GLY185 4.5 0.0 1.0 CA A:THR186 4.6 27.8 1.0 H A:ARG183 4.6 0.0 1.0 N A:ARG183 4.7 40.0 1.0 H2 A:HOH539 4.8 0.0 1.0 CA A:ASP182 4.8 39.4 1.0 C A:ASP182 4.8 40.1 1.0 O A:ASP180 4.8 39.0 1.0 C A:ILE187 4.8 25.5 1.0 N A:VAL181 4.9 37.2 1.0 N A:GLY185 4.9 29.3 1.0 H A:VAL181 4.9 0.0 1.0 C A:SER184 4.9 32.6 1.0 O A:HOH539 4.9 38.8 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calcium Bound Domain VI of Porcine Calpain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4 b:23.1 occ:1.00 OD1 A:ASP135 2.3 29.8 1.0 OD1 A:ASP225 2.3 17.2 1.0 OD1 A:ASN226 2.4 21.2 1.0 OD2 A:ASP225 2.5 17.2 1.0 O A:HOH545 2.5 28.0 1.0 OD2 A:ASP223 2.5 22.8 1.0 O B:HOH543 2.6 23.6 1.0 H2 B:HOH543 2.6 0.0 1.0 OD1 A:ASP223 2.6 23.5 1.0 CG A:ASP225 2.7 14.3 1.0 H2 A:HOH545 2.9 0.0 1.0 CG A:ASP223 2.9 21.0 1.0 H1 A:HOH545 3.1 0.0 1.0 H A:ASP135 3.3 0.0 1.0 CG A:ASP135 3.3 29.6 1.0 CG A:ASN226 3.4 17.2 1.0 H1 B:HOH543 3.5 0.0 1.0 H A:ASN226 3.5 0.0 1.0 HH12 B:ARG143 3.8 0.0 1.0 OD2 A:ASP135 3.8 31.9 1.0 H1 A:HOH517 4.0 0.0 1.0 HD21 A:ASN226 4.0 0.0 1.0 N A:ASN226 4.1 16.2 1.0 ND2 A:ASN226 4.1 20.6 1.0 H2 A:HOH580 4.2 0.0 1.0 CB A:ASP225 4.2 13.1 1.0 N A:ASP135 4.3 26.2 1.0 O A:HOH580 4.3 30.7 1.0 CB A:ASN226 4.3 15.3 1.0 H A:ASP225 4.4 0.0 1.0 H2 A:HOH535 4.4 0.0 1.0 CB A:ASP223 4.5 18.6 1.0 CB A:ASP135 4.6 25.7 1.0 O A:HOH529 4.7 26.9 1.0 CA A:ASN226 4.7 16.2 1.0 NH1 B:ARG143 4.7 38.6 1.0 O A:GLY136 4.7 26.4 1.0 HH22 B:ARG143 4.8 0.0 1.0 C A:ASP225 4.8 18.2 1.0 O A:HOH517 4.8 28.0 1.0 O A:HOH535 4.8 30.8 1.0 CA A:ASP225 4.8 18.2 1.0 H A:ASP223 4.9 0.0 1.0 N A:ASP225 4.9 18.2 1.0 CA A:ASP135 4.9 28.5 1.0 H2 A:HOH529 5.0 0.0 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Calcium Bound Domain VI of Porcine Calpain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca5 b:20.2 occ:1.00 O B:GLU112 2.2 15.5 1.0 O B:ALA107 2.2 22.6 1.0 O B:HOH522 2.3 22.1 1.0 OD1 B:ASP110 2.4 26.7 1.0 OE1 B:GLU117 2.4 19.2 1.0 O B:HOH513 2.5 28.3 1.0 OE2 B:GLU117 2.5 23.9 1.0 H1 B:HOH513 2.5 0.0 1.0 H1 B:HOH522 2.7 0.0 1.0 CD B:GLU117 2.8 18.8 1.0 H2 B:HOH522 3.2 0.0 1.0 C B:ALA107 3.4 21.0 1.0 CG B:ASP110 3.4 24.4 1.0 H2 B:HOH513 3.4 0.0 1.0 H B:GLU112 3.4 0.0 1.0 C B:GLU112 3.5 15.6 1.0 H B:ASP110 3.7 0.0 1.0 OD2 B:ASP110 3.7 25.2 1.0 H B:SER114 3.7 0.0 1.0 H1 B:HOH572 3.9 0.0 1.0 CA B:ALA107 4.0 20.7 1.0 H1 B:HOH585 4.0 0.0 1.0 N B:GLU112 4.2 20.1 1.0 CG B:GLU117 4.3 16.4 1.0 N B:VAL113 4.4 18.6 1.0 CA B:VAL113 4.4 18.1 1.0 N B:SER114 4.4 15.9 1.0 CA B:GLU112 4.4 19.5 1.0 N B:GLY108 4.4 22.4 1.0 N B:ASP110 4.6 26.7 1.0 O B:LEU106 4.6 25.3 1.0 H2 B:HOH585 4.6 0.0 1.0 O B:HOH572 4.6 47.6 1.0 CA B:GLY108 4.7 25.4 1.0 H B:MET111 4.7 0.0 1.0 CB B:ASP110 4.7 25.0 1.0 O B:HOH585 4.7 46.9 1.0 C B:VAL113 4.9 16.4 1.0 C B:GLY108 4.9 26.5 1.0 CB B:ALA107 4.9 20.1 1.0 N B:MET111 4.9 23.4 1.0 CA B:ASP110 5.0 24.7 1.0 H B:ASP109 5.0 0.0 1.0 OG B:SER114 5.0 16.7 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Calcium Bound Domain VI of Porcine Calpain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca6 b:22.6 occ:1.00 H1 B:HOH503 1.9 0.0 1.0 OD1 B:ASP150 2.0 21.6 1.0 OD1 B:ASP152 2.2 33.6 1.0 OE1 B:GLU161 2.3 23.8 1.0 O B:HOH503 2.3 25.2 1.0 O B:LYS156 2.3 20.7 1.0 OG1 B:THR154 2.3 25.7 1.0 HG1 B:THR154 2.6 0.0 1.0 OE2 B:GLU161 2.7 24.1 1.0 H2 B:HOH503 2.8 0.0 1.0 CD B:GLU161 2.8 23.5 1.0 H B:THR154 3.0 0.0 1.0 CG B:ASP152 3.2 31.5 1.0 CG B:ASP150 3.2 21.6 1.0 H B:GLY158 3.3 0.0 1.0 C B:LYS156 3.5 19.6 1.0 OD2 B:ASP152 3.6 33.4 1.0 H B:ASP152 3.6 0.0 1.0 CB B:THR154 3.6 25.4 1.0 H B:LYS156 3.7 0.0 1.0 N B:THR154 3.9 26.1 1.0 N B:GLY158 4.1 19.4 1.0 CG2 B:THR154 4.1 23.0 1.0 CB B:ASP150 4.1 19.3 1.0 OD2 B:ASP150 4.1 20.9 1.0 CA B:ASP150 4.1 21.1 1.0 CA B:LEU157 4.2 18.2 1.0 H B:GLY155 4.2 0.0 1.0 CA B:THR154 4.3 25.6 1.0 N B:LEU157 4.3 17.2 1.0 N B:LYS156 4.3 21.2 1.0 OE1 B:GLU112 4.4 29.6 1.0 CG B:GLU161 4.4 22.1 1.0 OE2 B:GLU112 4.4 36.8 1.0 N B:ASP152 4.4 28.9 1.0 C B:ASP150 4.5 23.4 1.0 CB B:ASP152 4.5 29.2 1.0 C B:LEU157 4.6 18.6 1.0 CA B:LYS156 4.6 19.3 1.0 H B:THR153 4.6 0.0 1.0 N B:THR153 4.7 29.1 1.0 N B:GLY155 4.7 23.1 1.0 C B:ASP152 4.7 30.0 1.0 CD B:GLU112 4.7 30.3 1.0 CA B:ASP152 4.8 29.8 1.0 H B:SER151 4.8 0.0 1.0 N B:SER151 4.8 25.8 1.0 C B:THR154 4.8 24.9 1.0 O B:ASP150 4.9 22.4 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Calcium Bound Domain VI of Porcine Calpain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca7 b:22.7 occ:1.00 HG B:SER184 1.8 0.0 1.0 OD1 B:ASP180 2.2 17.2 1.0 OG B:SER184 2.3 24.9 1.0 OE1 B:GLU191 2.4 26.7 1.0 OD1 B:ASP182 2.4 34.2 1.0 O B:HOH501 2.4 32.6 1.0 O B:THR186 2.5 20.3 1.0 OE2 B:GLU191 2.6 27.0 1.0 CD B:GLU191 2.8 27.9 1.0 H1 B:HOH501 2.9 0.0 1.0 H B:SER184 3.1 0.0 1.0 H2 B:HOH501 3.2 0.0 1.0 H B:GLY188 3.3 0.0 1.0 CG B:ASP180 3.3 14.1 1.0 CG B:ASP182 3.4 34.0 1.0 CB B:SER184 3.6 19.9 1.0 H B:THR186 3.6 0.0 1.0 H B:ASP182 3.6 0.0 1.0 C B:THR186 3.7 20.8 1.0 HG1 B:THR186 3.8 0.0 1.0 OD2 B:ASP182 3.8 35.2 1.0 CA B:ASP180 4.0 19.8 1.0 N B:SER184 4.0 23.1 1.0 N B:GLY188 4.1 20.3 1.0 CB B:ASP180 4.1 16.3 1.0 OD2 B:ASP180 4.2 18.7 1.0 CG B:GLU191 4.3 22.5 1.0 CA B:SER184 4.4 20.4 1.0 OG1 B:THR186 4.4 24.6 1.0 H B:GLY185 4.4 0.0 1.0 C B:ASP180 4.4 25.7 1.0 N B:THR186 4.4 19.9 1.0 CA B:ILE187 4.5 20.2 1.0 N B:ILE187 4.5 20.9 1.0 N B:ASP182 4.6 28.1 1.0 H B:VAL181 4.6 0.0 1.0 H B:ARG183 4.6 0.0 1.0 CA B:THR186 4.6 20.0 1.0 N B:VAL181 4.7 27.0 1.0 CB B:ASP182 4.7 30.6 1.0 O B:HOH578 4.7 36.4 1.0 C B:ILE187 4.8 21.3 1.0 N B:GLY185 4.8 20.4 1.0 N B:ARG183 4.8 25.3 1.0 C B:SER184 4.9 19.8 1.0 O B:ASP180 4.9 25.1 1.0 H2 B:HOH578 5.0 0.0 1.0 CA B:GLY188 5.0 20.2 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Calcium Bound Domain VI of Porcine Calpain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca8 b:17.3 occ:1.00 H2 B:HOH512 1.7 0.0 1.0 H1 B:HOH530 1.7 0.0 1.0 OD1 B:ASP135 2.3 21.6 1.0 OD1 B:ASN226 2.3 18.1 1.0 OD2 B:ASP225 2.4 15.1 1.0 O B:HOH530 2.4 16.3 1.0 OD1 B:ASP225 2.4 17.8 1.0 O B:HOH512 2.4 22.3 1.0 OD1 B:ASP223 2.5 20.0 1.0 H1 B:HOH512 2.5 0.0 1.0 OD2 B:ASP223 2.5 16.6 1.0 CG B:ASP225 2.7 17.4 1.0 CG B:ASP223 2.9 16.5 1.0 H2 B:HOH530 3.2 0.0 1.0 CG B:ASP135 3.3 21.7 1.0 CG B:ASN226 3.4 15.4 1.0 H B:ASP135 3.4 0.0 1.0 H B:ASN226 3.5 0.0 1.0 OD2 B:ASP135 3.6 27.8 1.0 H2 B:HOH528 4.0 0.0 1.0 H2 A:HOH592 4.1 0.0 1.0 N B:ASN226 4.1 13.2 1.0 HD21 B:ASN226 4.1 0.0 1.0 CB B:ASP225 4.2 13.1 1.0 ND2 B:ASN226 4.2 18.2 1.0 H2 B:HOH516 4.3 0.0 1.0 CB B:ASN226 4.3 12.7 1.0 N B:ASP135 4.3 18.8 1.0 H B:ASP225 4.4 0.0 1.0 CB B:ASP223 4.4 14.8 1.0 H1 B:HOH538 4.4 0.0 1.0 O A:HOH507 4.5 27.2 1.0 CB B:ASP135 4.5 20.5 1.0 H1 A:HOH592 4.6 0.0 1.0 OG1 B:THR134 4.6 16.5 1.0 H1 B:HOH528 4.7 0.0 1.0 CA B:ASN226 4.7 14.8 1.0 OD1 A:ASP140 4.8 21.4 1.0 C B:ASP225 4.8 12.3 1.0 O B:HOH528 4.8 34.4 1.0 O B:GLY136 4.8 16.3 1.0 O A:HOH592 4.8 44.8 1.0 H B:ASP223 4.8 0.0 1.0 CA B:ASP225 4.8 13.7 1.0 N B:ASP225 4.8 16.5 1.0 H1 A:HOH507 4.8 0.0 1.0 H2 B:HOH505 4.9 0.0 1.0 CA B:ASP135 4.9 18.8 1.0 H B:GLY136 5.0 0.0 1.0 O B:HOH505 5.0 20.5 1.0

G.D.Lin, D.Chattopadhyay, M.Maki, K.K.Wang, M.Carson, L.Jin, P.W.Yuen, E.Takano, M.Hatanaka, L.J.Delucas, S.V.Narayana. Crystal Structure of Calcium Bound Domain VI of Calpain at 1.9 A Resolution and Its Role in Enzyme Assembly, Regulation, and Inhibitor Binding. Nat.Struct.Biol. V. 4 539 1997.
ISSN: ISSN 1072-8368
PubMed: 9228946
DOI: 10.1038/NSB0797-539