Calcium in PDB 1nx3: Calpain Domain VI in Complex with the Inhibitor PD150606

The structure of Calpain Domain VI in Complex with the Inhibitor PD150606, PDB code: 1nx3 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 / 2.45
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.578, 78.578, 77.891, 90.00, 90.00, 120.00
R / Rfree (%)	21 / 25.3

The structure of Calpain Domain VI in Complex with the Inhibitor PD150606 also contains other interesting chemical elements:

Iodine

(I)

1 atom

The binding sites of Calcium atom in the Calpain Domain VI in Complex with the Inhibitor PD150606 (pdb code 1nx3). 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 in Complex with the Inhibitor PD150606, PDB code: 1nx3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Calpain Domain VI in Complex with the Inhibitor PD150606


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 in Complex with the Inhibitor PD150606 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1 b:31.4 occ:1.00 OD1 A:ASP152 2.2 31.5 1.0 OD1 A:ASP150 2.3 29.2 1.0 O A:LYS156 2.3 26.0 1.0 OG1 A:THR154 2.4 32.9 1.0 O A:HOH277 2.5 24.2 1.0 OE1 A:GLU161 2.6 34.9 1.0 OE2 A:GLU161 2.6 32.4 1.0 CD A:GLU161 2.9 32.4 1.0 CG A:ASP152 3.2 35.1 1.0 OD2 A:ASP152 3.5 35.4 1.0 CG A:ASP150 3.5 29.8 1.0 C A:LYS156 3.5 27.4 1.0 CB A:THR154 3.7 34.1 1.0 N A:THR154 3.9 36.7 1.0 CG2 A:THR154 4.0 31.0 1.0 N A:GLY158 4.1 29.4 1.0 CA A:ASP150 4.1 33.7 1.0 OE1 A:GLU112 4.1 32.9 1.0 CA A:LEU157 4.2 28.3 1.0 OE2 A:GLU112 4.3 35.4 1.0 CB A:ASP150 4.3 33.2 1.0 CA A:THR154 4.3 34.4 1.0 N A:LEU157 4.3 26.9 1.0 N A:LYS156 4.4 28.1 1.0 OD2 A:ASP150 4.4 26.3 1.0 CG A:GLU161 4.4 29.3 1.0 N A:ASP152 4.5 36.6 1.0 CB A:ASP152 4.5 35.5 1.0 CD A:GLU112 4.5 35.9 1.0 C A:LEU157 4.6 29.4 1.0 CA A:LYS156 4.6 28.2 1.0 N A:THR153 4.6 37.3 1.0 C A:ASP150 4.6 34.7 1.0 N A:GLY155 4.7 32.4 1.0 C A:ASP152 4.7 36.3 1.0 N A:SER151 4.7 35.0 1.0 CA A:ASP152 4.8 36.9 1.0 C A:THR154 4.8 34.9 1.0 C A:THR153 5.0 38.4 1.0 CA A:GLY158 5.0 27.4 1.0

Calcium binding site 2 out of 4 in the Calpain Domain VI in Complex with the Inhibitor PD150606


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 in Complex with the Inhibitor PD150606 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2 b:36.2 occ:1.00 O A:ALA107 2.2 31.9 1.0 OE1 A:GLU117 2.3 33.5 1.0 O A:HOH290 2.4 34.1 1.0 OD1 A:ASP110 2.5 41.0 1.0 O A:GLU112 2.5 32.8 1.0 OE2 A:GLU117 2.6 34.2 1.0 CD A:GLU117 2.8 33.6 1.0 CG A:ASP110 3.4 44.0 1.0 C A:ALA107 3.4 32.3 1.0 OD2 A:ASP110 3.6 45.1 1.0 C A:GLU112 3.7 34.7 1.0 CA A:ALA107 4.0 31.6 1.0 N A:GLU112 4.2 37.2 1.0 CG A:GLU117 4.3 32.7 1.0 N A:SER114 4.4 29.7 1.0 N A:GLY108 4.4 33.8 1.0 N A:ASP110 4.5 44.4 1.0 CA A:VAL113 4.5 30.3 1.0 N A:VAL113 4.6 33.0 1.0 N A:MET111 4.7 43.2 1.0 CA A:GLU112 4.7 36.1 1.0 CB A:ASP110 4.7 44.4 1.0 O A:LEU106 4.7 35.6 1.0 CA A:GLY108 4.7 34.8 1.0 CB A:ALA107 4.7 25.4 1.0 C A:GLY108 4.8 38.0 1.0 CD A:LYS156 4.8 32.1 1.0 C A:VAL113 4.9 30.8 1.0 CB A:SER114 4.9 29.1 1.0 OG A:SER114 4.9 28.6 1.0 N A:ASP109 5.0 40.4 1.0 CA A:ASP110 5.0 44.2 1.0

Calcium binding site 3 out of 4 in the Calpain Domain VI in Complex with the Inhibitor PD150606


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 in Complex with the Inhibitor PD150606 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:48.5 occ:1.00 OD1 A:ASP182 2.1 62.2 1.0 OE1 A:GLU191 2.2 45.9 1.0 OD1 A:ASP180 2.3 53.2 1.0 OG A:SER184 2.5 53.2 1.0 O A:THR186 2.5 54.0 1.0 O A:HOH320 2.6 40.3 1.0 CD A:GLU191 2.9 48.5 1.0 OE2 A:GLU191 2.9 49.4 1.0 CG A:ASP182 3.1 61.3 1.0 OD2 A:ASP182 3.5 61.8 1.0 CG A:ASP180 3.5 54.8 1.0 CB A:SER184 3.6 54.9 1.0 C A:THR186 3.7 53.1 1.0 N A:GLY188 3.8 51.7 1.0 CA A:ASP180 4.1 56.2 1.0 N A:SER184 4.2 55.9 1.0 CB A:ASP180 4.2 55.0 1.0 CA A:ILE187 4.3 51.4 1.0 CG A:GLU191 4.3 47.4 1.0 OD2 A:ASP180 4.4 53.4 1.0 N A:ILE187 4.4 52.2 1.0 CB A:ASP182 4.4 60.1 1.0 CA A:SER184 4.5 54.3 1.0 C A:ILE187 4.5 52.3 1.0 C A:ASP180 4.5 58.2 1.0 OG1 A:THR186 4.5 53.7 1.0 N A:THR186 4.6 52.9 1.0 CA A:GLY188 4.6 50.8 1.0 N A:ASP182 4.6 60.5 1.0 CA A:THR186 4.7 53.0 1.0 O A:ASP180 4.8 58.8 1.0 CA A:ASP182 4.9 60.0 1.0 N A:ARG183 5.0 59.5 1.0 N A:GLY185 5.0 53.8 1.0 N A:VAL181 5.0 60.1 1.0 C A:ASP182 5.0 60.5 1.0

Calcium binding site 4 out of 4 in the Calpain Domain VI in Complex with the Inhibitor PD150606


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 in Complex with the Inhibitor PD150606 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4 b:35.3 occ:1.00 OD2 A:ASP223 2.1 42.5 1.0 OD1 A:ASP135 2.4 43.7 1.0 ND2 A:ASN226 2.4 31.3 1.0 OD1 A:ASP225 2.5 28.5 1.0 OD2 A:ASP225 2.5 26.6 1.0 CG A:ASP223 2.7 41.3 1.0 OD1 A:ASP223 2.7 43.4 1.0 O A:HOH316 2.8 31.6 1.0 CG A:ASP225 2.9 28.7 1.0 CG A:ASN226 3.2 33.5 1.0 CG A:ASP135 3.4 41.7 1.0 OD1 A:ASN226 3.5 36.1 1.0 OD2 A:ASP135 3.7 42.0 1.0 CB A:ASP223 4.2 38.6 1.0 N A:ASN226 4.2 30.4 1.0 CB A:ASP225 4.3 28.7 1.0 CB A:ASN226 4.3 31.4 1.0 N A:ASP135 4.5 39.2 1.0 O A:GLY136 4.6 34.2 1.0 CB A:ASP135 4.7 39.9 1.0 CA A:ASN226 4.8 31.2 1.0 OG1 A:THR134 4.8 40.8 1.0 C A:ASP225 4.9 30.4 1.0 O A:HOH298 4.9 51.1 1.0 O A:HOH273 4.9 27.4 1.0 CA A:ASP225 5.0 30.2 1.0 N A:ASP225 5.0 32.0 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