Calcium in PDB 4phn: The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids

The structure of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids, PDB code: 4phn was solved by R.K.Allemann, P.J.Rizkallah, S.E.Adams, D.J.Miller, M.B.Hallett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.05 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.530, 70.560, 58.670, 90.00, 108.79, 90.00
R / Rfree (%)	18.3 / 22.8

The binding sites of Calcium atom in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids (pdb code 4phn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids, PDB code: 4phn:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:37.7 occ:1.00 O A:HOH474 2.4 35.5 1.0 O A:GLU112 2.4 28.6 1.0 OD1 A:ASP110 2.4 36.6 1.0 O A:ALA107 2.4 38.1 1.0 O A:HOH452 2.5 31.9 1.0 OE1 A:GLU117 2.5 33.0 1.0 OE2 A:GLU117 2.6 32.3 1.0 CD A:GLU117 2.9 32.5 1.0 CG A:ASP110 3.3 36.4 1.0 OD2 A:ASP110 3.5 35.2 1.0 C A:ALA107 3.5 39.4 1.0 C A:GLU112 3.7 28.8 1.0 CA A:ALA107 4.1 36.7 1.0 N A:GLU112 4.4 31.5 1.0 CG A:GLU117 4.4 31.1 1.0 N A:SER114 4.5 24.2 1.0 N A:VAL113 4.6 26.1 1.0 CA A:VAL113 4.6 25.8 1.0 N A:GLY108 4.6 42.9 1.0 CA A:GLU112 4.6 29.4 1.0 CB A:ASP110 4.7 37.5 1.0 O A:HOH543 4.7 52.5 1.0 CB A:ALA107 4.7 34.8 1.0 CA A:GLY108 4.8 45.5 1.0 N A:ASP110 4.8 42.4 1.0 C A:GLY108 4.9 47.0 1.0 N A:MET111 5.0 36.2 1.0 C A:VAL113 5.0 23.8 1.0

Calcium binding site 2 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:32.0 occ:1.00 OD1 A:ASP152 2.3 20.6 1.0 O A:LYS156 2.3 19.5 1.0 OD1 A:ASP150 2.3 18.0 1.0 OE1 A:GLU161 2.4 21.4 1.0 O A:HOH412 2.5 20.8 1.0 OG1 A:THR154 2.5 19.6 1.0 OE2 A:GLU161 2.9 23.4 1.0 CD A:GLU161 3.0 21.2 1.0 CG A:ASP152 3.2 21.9 1.0 C A:LYS156 3.5 20.9 1.0 CG A:ASP150 3.6 22.7 1.0 OD2 A:ASP152 3.6 22.8 1.0 CB A:THR154 3.8 22.2 1.0 OE2 A:GLU112 3.8 28.6 1.0 N A:THR154 3.9 20.5 1.0 N A:GLY158 4.1 22.0 1.0 CG2 A:THR154 4.2 24.2 1.0 CA A:ASP150 4.2 20.7 1.0 N A:LYS156 4.3 21.6 1.0 CA A:LEU157 4.3 20.3 1.0 CB A:ASP150 4.4 19.6 1.0 CA A:THR154 4.4 21.9 1.0 N A:LEU157 4.4 20.5 1.0 OD2 A:ASP150 4.4 20.7 1.0 CG A:GLU161 4.5 19.9 1.0 N A:ASP152 4.5 23.4 1.0 CB A:ASP152 4.6 22.7 1.0 CA A:LYS156 4.6 21.9 1.0 N A:GLY155 4.6 21.7 1.0 C A:ASP150 4.6 21.3 1.0 N A:THR153 4.6 21.5 1.0 C A:LEU157 4.7 21.6 1.0 C A:ASP152 4.8 21.9 1.0 C A:THR154 4.8 22.3 1.0 CA A:ASP152 4.8 22.2 1.0 N A:SER151 4.9 22.4 1.0 O A:HOH406 5.0 30.4 1.0 C A:THR153 5.0 22.5 1.0 CD A:GLU112 5.0 30.1 1.0

Calcium binding site 3 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:40.4 occ:1.00 O A:HOH476 2.0 34.6 1.0 OD1 A:ASP180 2.3 26.4 1.0 O A:THR186 2.3 23.9 1.0 OD1 A:ASP182 2.3 30.7 1.0 OE2 A:GLU191 2.5 29.4 1.0 OE1 A:GLU191 2.6 25.4 1.0 OG A:SER184 2.6 32.5 1.0 CD A:GLU191 2.9 27.0 1.0 CG A:ASP182 3.4 33.6 1.0 CG A:ASP180 3.4 27.2 1.0 C A:THR186 3.6 24.5 1.0 CB A:SER184 3.7 32.5 1.0 OD2 A:ASP182 3.7 35.9 1.0 CA A:ASP180 4.0 26.0 1.0 CB A:ASP180 4.1 26.9 1.0 N A:SER184 4.1 31.7 1.0 N A:GLY188 4.1 29.2 1.0 OG1 A:THR186 4.3 24.9 1.0 C A:ASP180 4.3 28.6 1.0 OD2 A:ASP180 4.3 28.1 1.0 CG A:GLU191 4.4 27.1 1.0 N A:ILE187 4.4 25.7 1.0 N A:ASP182 4.4 31.9 1.0 CA A:ILE187 4.5 25.2 1.0 N A:THR186 4.5 24.8 1.0 CA A:SER184 4.5 31.7 1.0 N A:VAL181 4.5 30.1 1.0 CA A:THR186 4.6 24.0 1.0 O A:HOH422 4.6 32.1 1.0 CB A:ASP182 4.7 34.0 1.0 N A:ARG183 4.8 31.1 1.0 C A:ILE187 4.8 26.3 1.0 CA A:ASP182 4.9 32.6 1.0 O A:ASP180 4.9 28.0 1.0 N A:GLY185 4.9 27.6 1.0

Calcium binding site 4 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:27.0 occ:1.00 O A:HOH431 2.2 25.1 1.0 OD1 A:ASP135 2.4 23.5 1.0 OD1 A:ASN226 2.4 21.8 1.0 O B:HOH407 2.5 22.7 1.0 OD1 A:ASP223 2.5 21.4 1.0 OD1 A:ASP225 2.5 22.9 1.0 OD2 A:ASP223 2.6 23.9 1.0 OD2 A:ASP225 2.7 21.6 1.0 CG A:ASP223 2.9 21.8 1.0 CG A:ASP225 2.9 24.6 1.0 CG A:ASN226 3.3 23.2 1.0 CG A:ASP135 3.4 27.3 1.0 OD2 A:ASP135 3.7 29.1 1.0 N A:ASN226 4.0 21.1 1.0 ND2 A:ASN226 4.1 25.2 1.0 CB A:ASN226 4.2 21.8 1.0 O A:HOH411 4.3 34.3 1.0 O A:HOH492 4.3 27.0 1.0 CB A:ASP223 4.3 22.8 1.0 CB A:ASP225 4.4 23.4 1.0 N A:ASP135 4.4 27.2 1.0 O B:HOH434 4.6 29.2 1.0 CA A:ASN226 4.6 21.1 1.0 OD1 B:ASP140 4.7 37.0 1.0 CB A:ASP135 4.7 27.9 1.0 O A:GLY136 4.7 23.9 1.0 OG1 A:THR134 4.8 22.3 1.0 C A:ASP225 4.8 19.9 1.0 O A:HOH405 4.8 28.9 1.0 N A:ASP225 4.9 22.4 1.0 CA A:ASP225 4.9 22.4 1.0 CA A:ASP135 5.0 29.7 1.0

Calcium binding site 5 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:29.8 occ:1.00 O B:ALA107 2.1 37.3 1.0 OD1 B:ASP110 2.2 35.0 1.0 O B:GLU112 2.4 29.3 1.0 O B:HOH509 2.4 32.9 1.0 O B:HOH469 2.4 28.7 1.0 OE1 B:GLU117 2.5 34.2 1.0 OE2 B:GLU117 2.6 38.9 1.0 CD B:GLU117 2.9 37.8 1.0 CG B:ASP110 3.2 36.1 1.0 C B:ALA107 3.3 37.2 1.0 OD2 B:ASP110 3.5 35.9 1.0 C B:GLU112 3.6 29.7 1.0 CA B:ALA107 4.0 36.4 1.0 N B:GLU112 4.3 31.6 1.0 N B:GLY108 4.4 38.4 1.0 N B:ASP110 4.4 39.8 1.0 CG B:GLU117 4.4 38.3 1.0 CB B:ASP110 4.4 37.0 1.0 N B:VAL113 4.5 28.4 1.0 N B:SER114 4.5 29.4 1.0 O B:HOH439 4.5 40.1 1.0 O B:HOH501 4.5 42.6 1.0 CA B:VAL113 4.6 27.7 1.0 CA B:GLU112 4.6 29.8 1.0 O B:LEU106 4.7 37.6 1.0 CB B:ALA107 4.7 36.1 1.0 N B:MET111 4.7 35.1 1.0 CA B:GLY108 4.7 40.7 1.0 CA B:ASP110 4.8 37.9 1.0 C B:GLY108 4.8 41.4 1.0 O B:HOH471 4.8 37.6 1.0 C B:ASP110 4.8 35.4 1.0 N B:ASP109 4.9 42.7 1.0 C B:VAL113 5.0 27.3 1.0

Calcium binding site 6 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:27.8 occ:1.00 OD1 B:ASP152 2.2 33.0 1.0 OD1 B:ASP150 2.4 24.8 1.0 O B:LYS156 2.4 30.1 1.0 OE1 B:GLU161 2.4 23.8 1.0 OG1 B:THR154 2.4 29.0 1.0 O B:HOH487 2.4 26.5 1.0 OE2 B:GLU161 2.8 24.2 1.0 CD B:GLU161 3.0 24.9 1.0 CG B:ASP152 3.2 35.0 1.0 CG B:ASP150 3.5 26.5 1.0 OD2 B:ASP152 3.6 31.7 1.0 C B:LYS156 3.6 27.8 1.0 CB B:THR154 3.7 31.0 1.0 N B:THR154 4.0 30.5 1.0 CG2 B:THR154 4.1 31.7 1.0 N B:GLY158 4.1 23.8 1.0 OE1 B:GLU112 4.1 35.0 1.0 CA B:ASP150 4.2 26.2 1.0 CA B:LEU157 4.3 25.5 1.0 N B:LYS156 4.3 30.5 1.0 CB B:ASP150 4.3 26.7 1.0 CA B:THR154 4.3 30.4 1.0 N B:ASP152 4.4 31.5 1.0 N B:LEU157 4.4 26.6 1.0 OD2 B:ASP150 4.4 27.7 1.0 CB B:ASP152 4.5 35.0 1.0 CG B:GLU161 4.5 23.8 1.0 OE2 B:GLU112 4.6 37.9 1.0 C B:ASP150 4.6 30.8 1.0 CA B:LYS156 4.6 30.7 1.0 C B:LEU157 4.7 24.9 1.0 N B:THR153 4.7 33.1 1.0 N B:GLY155 4.7 30.0 1.0 CA B:ASP152 4.7 33.5 1.0 C B:ASP152 4.7 33.7 1.0 CD B:GLU112 4.7 34.2 1.0 N B:SER151 4.8 31.6 1.0 C B:THR154 4.8 29.5 1.0 O B:HOH498 4.9 38.2 1.0 CD2 B:LEU157 5.0 27.2 1.0

Calcium binding site 7 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:31.4 occ:1.00 O B:HOH451 2.2 38.0 1.0 OD1 B:ASP182 2.2 33.1 1.0 OD1 B:ASP180 2.3 32.3 1.0 O B:THR186 2.4 28.2 1.0 OG B:SER184 2.4 31.1 1.0 OE1 B:GLU191 2.5 27.3 1.0 OE2 B:GLU191 2.7 27.3 1.0 CD B:GLU191 3.0 27.9 1.0 CG B:ASP182 3.3 36.6 1.0 CG B:ASP180 3.4 31.4 1.0 C B:THR186 3.6 26.1 1.0 CB B:SER184 3.6 36.2 1.0 OD2 B:ASP182 3.8 35.6 1.0 N B:SER184 4.1 36.0 1.0 CA B:ASP180 4.1 30.0 1.0 CB B:ASP180 4.2 30.9 1.0 N B:GLY188 4.3 25.4 1.0 OD2 B:ASP180 4.3 31.3 1.0 OG1 B:THR186 4.3 27.8 1.0 C B:ASP180 4.4 32.3 1.0 N B:THR186 4.4 29.5 1.0 N B:ILE187 4.4 23.3 1.0 N B:ASP182 4.4 36.8 1.0 CA B:SER184 4.4 36.6 1.0 CA B:ILE187 4.4 23.2 1.0 CG B:GLU191 4.5 27.6 1.0 CB B:ASP182 4.5 37.7 1.0 CA B:THR186 4.6 27.1 1.0 N B:VAL181 4.7 34.1 1.0 N B:ARG183 4.7 39.5 1.0 O B:HOH455 4.8 34.6 1.0 CA B:ASP182 4.8 38.9 1.0 C B:ILE187 4.8 23.4 1.0 O B:ASP180 4.8 32.5 1.0 N B:GLY185 4.8 34.5 1.0 C B:ASP182 4.9 39.2 1.0 C B:SER184 5.0 35.7 1.0

Calcium binding site 8 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:27.5 occ:1.00 OD1 B:ASN226 2.4 23.2 1.0 OD1 B:ASP135 2.4 28.6 1.0 OD2 B:ASP223 2.5 28.6 1.0 OD1 B:ASP225 2.5 26.5 1.0 O B:HOH472 2.5 25.8 1.0 OD2 B:ASP225 2.5 24.0 1.0 OD1 B:ASP223 2.5 23.4 1.0 O B:HOH418 2.6 25.6 1.0 CG B:ASP225 2.8 24.0 1.0 CG B:ASP223 2.8 26.2 1.0 CG B:ASN226 3.3 23.1 1.0 CG B:ASP135 3.4 33.4 1.0 OD2 B:ASP135 3.7 32.7 1.0 N B:ASN226 4.0 18.8 1.0 ND2 B:ASN226 4.1 22.6 1.0 CB B:ASP225 4.3 22.7 1.0 CB B:ASN226 4.3 20.1 1.0 N B:ASP135 4.3 35.1 1.0 CB B:ASP223 4.3 26.6 1.0 O B:HOH478 4.5 30.7 1.0 O A:HOH521 4.6 27.4 1.0 O B:HOH510 4.6 26.7 1.0 CA B:ASN226 4.6 19.1 1.0 CB B:ASP135 4.6 35.6 1.0 C B:ASP225 4.7 18.8 1.0 O B:HOH483 4.8 30.4 1.0 O B:GLY136 4.8 30.2 1.0 OG1 B:THR134 4.8 30.1 1.0 CA B:ASP225 4.8 20.7 1.0 N B:ASP225 4.9 20.2 1.0 CA B:ASP135 5.0 35.7 1.0

S.E.Adams, P.J.Rizkallah, D.J.Miller, E.J.Robinson, M.B.Hallett, R.K.Allemann. The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids. J.Struct.Biol. V. 187 236 2014.
ISSN: ESSN 1095-8657
PubMed: 25086406
DOI: 10.1016/J.JSB.2014.07.004