Calcium in PDB 1nx2: Calpain Domain VI

The structure of Calpain Domain VI, PDB code: 1nx2 was solved by B.Todd, D.Moore, C.C.S.Deivanayagam, G.-D.Lin, D.Chattopadhyay, M.Maki, K.K.W.Wang, S.V.L.Narayana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.673, 78.673, 77.776, 90.00, 90.00, 120.00
R / Rfree (%)	22.1 / 26.4

The binding sites of Calcium atom in the Calpain Domain VI (pdb code 1nx2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Calpain Domain VI, PDB code: 1nx2:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Calpain Domain VI


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:27.0 occ:1.00 OD2 A:ASP223 2.2 29.2 1.0 OD1 A:ASP135 2.3 34.0 1.0 OD1 A:ASP225 2.4 25.6 1.0 ND2 A:ASN226 2.5 26.7 1.0 OD2 A:ASP225 2.5 24.4 1.0 OD1 A:ASP223 2.7 29.6 1.0 CG A:ASP225 2.8 25.2 1.0 CG A:ASP223 2.8 29.3 1.0 CG A:ASN226 3.3 26.8 1.0 CG A:ASP135 3.3 34.4 1.0 OD2 A:ASP135 3.7 34.4 1.0 OD1 A:ASN226 3.8 27.8 1.0 N A:ASN226 4.1 25.6 1.0 CB A:ASP225 4.2 25.3 1.0 CB A:ASP223 4.3 29.4 1.0 CB A:ASN226 4.3 26.3 1.0 O A:HOH284 4.5 29.2 1.0 N A:ASP135 4.5 35.0 1.0 CB A:ASP135 4.6 34.3 1.0 O A:HOH289 4.6 30.9 1.0 CA A:ASN226 4.7 25.7 1.0 O A:GLY136 4.7 31.0 1.0 C A:ASP225 4.8 25.7 1.0 O A:HOH278 4.8 27.3 1.0 OG1 A:THR134 4.8 35.9 1.0 CA A:ASP225 4.8 25.8 1.0 N A:ASP225 4.8 26.1 1.0

Calcium binding site 2 out of 4 in the Calpain Domain VI


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:27.6 occ:1.00 OD1 A:ASP152 2.2 32.2 1.0 OD1 A:ASP150 2.3 27.3 1.0 O A:LYS156 2.3 26.7 1.0 OE1 A:GLU161 2.4 28.0 1.0 OG1 A:THR154 2.4 29.5 1.0 O A:HOH273 2.4 25.9 1.0 OE2 A:GLU161 2.7 27.8 1.0 CD A:GLU161 2.9 27.9 1.0 CG A:ASP152 3.1 32.4 1.0 OD2 A:ASP152 3.4 32.3 1.0 CG A:ASP150 3.5 28.1 1.0 C A:LYS156 3.6 26.6 1.0 CB A:THR154 3.6 29.9 1.0 CG2 A:THR154 3.9 29.9 1.0 N A:THR154 3.9 30.9 1.0 N A:GLY158 4.1 26.4 1.0 CA A:ASP150 4.1 29.3 1.0 OE1 A:GLU112 4.1 28.6 1.0 CB A:ASP150 4.2 28.6 1.0 CA A:LEU157 4.3 26.3 1.0 OE2 A:GLU112 4.3 29.1 1.0 CA A:THR154 4.3 30.0 1.0 CG A:GLU161 4.3 27.9 1.0 N A:LEU157 4.3 26.5 1.0 OD2 A:ASP150 4.4 27.5 1.0 N A:LYS156 4.4 27.3 1.0 N A:ASP152 4.4 32.1 1.0 CB A:ASP152 4.5 32.5 1.0 C A:ASP150 4.5 30.1 1.0 N A:THR153 4.6 32.2 1.0 CD A:GLU112 4.6 28.7 1.0 C A:LEU157 4.6 26.4 1.0 CA A:LYS156 4.6 27.0 1.0 N A:GLY155 4.7 28.7 1.0 N A:SER151 4.8 30.8 1.0 C A:ASP152 4.8 32.4 1.0 CA A:ASP152 4.8 32.4 1.0 C A:THR154 4.9 29.7 1.0 C A:THR153 5.0 31.6 1.0 CA A:GLY158 5.0 26.4 1.0

Calcium binding site 3 out of 4 in the Calpain Domain VI


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:27.4 occ:1.00 O A:ALA107 2.2 27.5 1.0 OE1 A:GLU117 2.4 27.3 1.0 O A:HOH267 2.4 24.0 1.0 OD2 A:ASP110 2.4 29.3 1.0 O A:GLU112 2.5 26.9 1.0 OE2 A:GLU117 2.5 26.6 1.0 CD A:GLU117 2.8 26.9 1.0 CG A:ASP110 3.3 29.7 1.0 C A:ALA107 3.3 27.6 1.0 OD1 A:ASP110 3.6 30.0 1.0 C A:GLU112 3.7 27.2 1.0 CA A:ALA107 3.9 27.7 1.0 N A:GLU112 4.2 28.2 1.0 CG A:GLU117 4.3 26.6 1.0 N A:SER114 4.4 25.3 1.0 N A:GLY108 4.4 28.0 1.0 N A:ASP110 4.5 29.6 1.0 CA A:VAL113 4.6 26.1 1.0 N A:VAL113 4.6 26.7 1.0 CA A:GLU112 4.6 27.9 1.0 CB A:ASP110 4.6 29.6 1.0 O A:HOH281 4.6 27.9 1.0 CB A:ALA107 4.6 27.1 1.0 N A:MET111 4.7 29.3 1.0 CA A:GLY108 4.7 28.3 1.0 O A:LEU106 4.7 27.9 1.0 CD A:LYS156 4.8 27.4 1.0 O A:HOH335 4.8 31.7 1.0 O A:HOH292 4.8 32.1 1.0 C A:GLY108 4.8 28.7 1.0 C A:ASP110 4.9 29.5 1.0 CA A:ASP110 4.9 29.4 1.0 C A:VAL113 4.9 25.6 1.0 OG A:SER114 4.9 24.4 1.0 CB A:SER114 5.0 24.8 1.0 N A:ASP109 5.0 29.2 1.0

Calcium binding site 4 out of 4 in the Calpain Domain VI


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4 b:43.0 occ:1.00 OD1 A:ASP182 2.3 46.8 1.0 OD1 A:ASP180 2.3 44.1 1.0 OE1 A:GLU191 2.4 41.6 1.0 O A:THR186 2.5 42.3 1.0 OG A:SER184 2.5 45.0 1.0 OE2 A:GLU191 2.6 41.7 1.0 CD A:GLU191 2.8 41.6 1.0 CG A:ASP182 3.2 46.8 1.0 CG A:ASP180 3.5 44.3 1.0 OD2 A:ASP182 3.5 46.6 1.0 CB A:SER184 3.5 45.3 1.0 C A:THR186 3.7 42.4 1.0 N A:GLY188 3.9 41.7 1.0 CA A:ASP180 4.1 44.5 1.0 N A:SER184 4.1 45.7 1.0 CB A:ASP180 4.2 44.2 1.0 CG A:GLU191 4.2 41.5 1.0 CA A:ILE187 4.4 41.7 1.0 CA A:SER184 4.4 45.2 1.0 C A:ASP180 4.5 44.8 1.0 OG1 A:THR186 4.5 42.5 1.0 OD2 A:ASP180 4.5 44.1 1.0 N A:ILE187 4.5 42.0 1.0 N A:ASP182 4.6 46.3 1.0 N A:THR186 4.6 43.1 1.0 C A:ILE187 4.6 41.7 1.0 CB A:ASP182 4.6 46.6 1.0 CA A:GLY188 4.7 41.7 1.0 CA A:THR186 4.7 42.6 1.0 N A:VAL181 4.8 45.3 1.0 N A:ARG183 4.8 46.8 1.0 O A:ASP180 4.9 44.9 1.0 CA A:ASP182 5.0 46.5 1.0 N A:GLY185 5.0 44.5 1.0 O A:HOH291 5.0 43.3 1.0

B.Todd, D.Moore, C.C.S.Deivanayagam, G.-D.Lin, D.Chattopadhyay, M.Maki, K.K.W.Wang, S.V.L.Narayana. A Structural Model For the Inhibition of Calpain By Calpastatin: Crystal Structures of the Native Domain VI of Calpain and Its Complexes with Calpastatin Peptide and A Small Molecule Inhibitor. J.Mol.Biol. V. 328 131 2003.
ISSN: ISSN 0022-2836
PubMed: 12684003
DOI: 10.1016/S0022-2836(03)00274-2