Calcium in PDB 4wq2: Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound

The structure of Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound, PDB code: 4wq2 was solved by S.E.Adams, P.J.Rizkallah, D.J.Miller, M.B.Hallett, R.K.Allemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.99 / 1.64
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.720, 78.430, 56.300, 90.00, 91.12, 90.00
R / Rfree (%)	17 / 19.7

The structure of Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Calcium atom in the Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound (pdb code 4wq2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound, PDB code: 4wq2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:25.7 occ:1.00 O A:HOH423 2.3 23.1 1.0 O A:ALA109 2.3 25.9 1.0 O A:GLU114 2.4 22.1 1.0 O A:HOH479 2.4 27.6 1.0 OD1 A:ASP112 2.5 28.2 1.0 OE1 A:GLU119 2.5 22.4 1.0 OE2 A:GLU119 2.5 27.3 1.0 CD A:GLU119 2.9 24.5 1.0 CG A:ASP112 3.3 30.7 1.0 C A:ALA109 3.4 26.9 1.0 C A:GLU114 3.6 21.6 1.0 OD2 A:ASP112 3.7 29.8 1.0 CA A:ALA109 3.9 24.3 1.0 N A:GLU114 4.2 25.8 1.0 CG A:GLU119 4.4 22.7 1.0 N A:SER116 4.4 19.3 1.0 N A:GLY110 4.5 29.5 1.0 O A:LEU108 4.5 28.4 1.0 N A:VAL115 4.5 21.1 1.0 N A:ASP112 4.5 26.3 1.0 CA A:VAL115 4.5 21.5 1.0 CA A:GLU114 4.6 24.6 1.0 CB A:ASP112 4.6 28.7 1.0 CB A:ALA109 4.6 24.4 1.0 O A:HOH476 4.7 38.6 1.0 O A:HOH445 4.7 47.1 1.0 CA A:GLY110 4.7 30.0 1.0 N A:MET113 4.8 26.6 0.5 C A:GLY110 4.8 30.8 1.0 N A:MET113 4.9 26.0 0.5 CA A:ASP112 4.9 26.8 1.0 CB A:SER116 4.9 20.4 1.0 C A:VAL115 4.9 19.4 1.0 N A:ASP111 5.0 31.1 1.0 OG A:SER116 5.0 21.5 1.0

Calcium binding site 2 out of 8 in the Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:28.3 occ:1.00 OD1 A:ASP152 2.3 24.6 1.0 OD1 A:ASP154 2.3 32.1 1.0 O A:HOH442 2.3 29.4 1.0 OE1 A:GLU163 2.3 25.6 1.0 OG1 A:THR156 2.4 29.1 1.0 O A:LYS158 2.4 24.5 1.0 OE2 A:GLU163 2.8 31.9 1.0 CD A:GLU163 3.0 27.9 1.0 CG A:ASP154 3.3 40.0 1.0 CG A:ASP152 3.5 25.4 1.0 C A:LYS158 3.6 24.2 1.0 OD2 A:ASP154 3.6 41.0 1.0 CB A:THR156 3.6 33.6 1.0 CG2 A:THR156 3.9 34.7 1.0 N A:THR156 4.0 33.8 1.0 N A:GLY160 4.0 23.2 1.0 OE1 A:GLU114 4.1 31.6 1.0 CA A:LEU159 4.3 22.8 1.0 CA A:ASP152 4.3 24.9 1.0 OD2 A:ASP152 4.3 26.6 1.0 CB A:ASP152 4.3 25.7 1.0 N A:LYS158 4.3 24.5 1.0 CA A:THR156 4.3 32.7 1.0 N A:LEU159 4.4 22.4 1.0 OE2 A:GLU114 4.4 38.6 1.0 CG A:GLU163 4.5 28.3 1.0 CD A:GLU114 4.5 34.9 1.0 N A:ASP154 4.6 40.2 1.0 CA A:LYS158 4.6 22.4 1.0 C A:LEU159 4.6 23.1 1.0 CB A:ASP154 4.6 39.6 1.0 C A:ASP152 4.6 29.3 1.0 N A:THR155 4.7 42.5 1.0 N A:GLY157 4.8 26.9 1.0 C A:ASP154 4.8 43.7 1.0 C A:THR156 4.9 33.9 1.0 CA A:ASP154 4.9 38.6 1.0 N A:SER153 4.9 33.3 1.0

Calcium binding site 3 out of 8 in the Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:32.0 occ:1.00 OD1 A:ASP182 2.3 32.4 1.0 O A:HOH480 2.3 40.5 1.0 O A:THR188 2.4 26.7 1.0 OG A:SER186 2.4 34.9 1.0 OD1 A:ASP184 2.4 35.3 1.0 OE1 A:GLU193 2.4 27.6 1.0 OE2 A:GLU193 2.6 31.1 1.0 CD A:GLU193 2.9 28.6 1.0 CG A:ASP182 3.4 31.3 1.0 CG A:ASP184 3.4 42.4 1.0 C A:THR188 3.5 28.2 1.0 CB A:SER186 3.6 37.3 1.0 OD2 A:ASP184 3.8 42.3 1.0 CA A:ASP182 4.0 30.6 1.0 CB A:ASP182 4.1 29.6 1.0 N A:SER186 4.2 33.1 1.0 OG1 A:THR188 4.2 33.9 1.0 OD2 A:ASP182 4.2 29.2 1.0 N A:CYS190 4.3 28.2 1.0 N A:THR188 4.3 26.5 1.0 N A:ILE189 4.4 25.8 1.0 CA A:ILE189 4.4 25.0 1.0 C A:ASP182 4.4 32.4 1.0 CG A:GLU193 4.5 29.5 1.0 CA A:SER186 4.5 38.2 1.0 CA A:THR188 4.5 26.6 1.0 N A:THR183 4.6 33.5 1.0 N A:ASP184 4.6 38.8 1.0 CB A:ASP184 4.8 41.3 1.0 N A:ARG185 4.8 43.7 1.0 O A:ASP182 4.8 35.9 1.0 SG A:CYS190 4.8 37.3 1.0 C A:ILE189 4.8 28.1 1.0 N A:GLY187 4.9 32.4 1.0 O A:HOH416 4.9 43.2 1.0

Calcium binding site 4 out of 8 in the Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:27.1 occ:1.00 O A:HOH465 2.3 29.4 1.0 OD1 A:ASN228 2.3 23.7 1.0 O A:HOH481 2.4 32.0 1.0 OD1 A:ASP137 2.5 35.4 1.0 OD1 A:ASP227 2.5 26.4 1.0 OD1 A:ASP225 2.5 24.8 1.0 OD2 A:ASP225 2.5 28.4 1.0 OD2 A:ASP227 2.6 25.8 1.0 CG A:ASP227 2.9 23.4 1.0 CG A:ASP225 2.9 27.4 1.0 CG A:ASP137 3.2 41.2 1.0 CG A:ASN228 3.3 24.8 1.0 OD2 A:ASP137 3.5 44.8 1.0 ND2 A:ASN228 4.0 28.8 1.0 N A:ASN228 4.1 18.6 1.0 CB A:ASP227 4.4 21.9 1.0 CB A:ASN228 4.4 19.4 1.0 CB A:ASP225 4.4 23.3 1.0 O A:HOH454 4.5 44.1 1.0 OG1 A:THR136 4.6 22.4 0.5 N A:ASP137 4.6 27.2 1.0 O A:HOH466 4.6 35.9 1.0 CB A:ASP137 4.7 33.4 1.0 O A:GLY138 4.7 23.9 1.0 CA A:ASN228 4.7 18.5 1.0 C A:ASP227 4.8 18.9 1.0 N A:ASP227 4.9 18.8 1.0 O A:HOH460 4.9 28.3 1.0 CA A:ASP227 4.9 20.2 1.0

Calcium binding site 5 out of 8 in the Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:30.3 occ:1.00 O B:ALA109 2.3 27.5 1.0 O B:GLU114 2.4 26.0 1.0 OD1 B:ASP112 2.4 35.2 1.0 O B:HOH424 2.4 29.3 1.0 O B:HOH439 2.4 33.5 1.0 OE1 B:GLU119 2.4 28.1 1.0 OE2 B:GLU119 2.5 30.5 1.0 CD B:GLU119 2.8 28.5 1.0 CG B:ASP112 3.3 35.0 1.0 C B:ALA109 3.3 30.7 1.0 C B:GLU114 3.6 28.3 1.0 OD2 B:ASP112 3.7 37.0 1.0 CA B:ALA109 3.9 29.6 1.0 N B:GLU114 4.3 29.3 1.0 CG B:GLU119 4.3 28.9 1.0 N B:SER116 4.4 26.6 1.0 O B:HOH409 4.4 47.4 1.0 CA B:VAL115 4.4 28.0 1.0 N B:GLY110 4.4 31.4 1.0 N B:VAL115 4.5 27.1 1.0 O2 B:EDO306 4.5 51.3 1.0 N B:ASP112 4.5 32.5 1.0 CA B:GLU114 4.5 28.1 1.0 O B:LEU108 4.6 34.6 1.0 CB B:ASP112 4.6 33.7 1.0 O B:HOH415 4.6 43.3 1.0 CB B:ALA109 4.6 31.0 1.0 CA B:GLY110 4.8 34.9 1.0 N B:MET113 4.8 30.9 1.0 C B:GLY110 4.8 35.8 1.0 CA B:ASP112 4.9 30.7 1.0 C B:VAL115 4.9 26.2 1.0 OG B:SER116 4.9 27.8 1.0 N B:ASP111 4.9 34.4 1.0 C B:ASP112 4.9 31.2 1.0 CB B:SER116 5.0 27.4 1.0

Calcium binding site 6 out of 8 in the Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:30.5 occ:1.00 OD1 B:ASP152 2.3 26.7 1.0 OD1 B:ASP154 2.3 37.1 1.0 OE1 B:GLU163 2.3 29.0 1.0 O B:HOH419 2.3 32.0 1.0 O B:LYS158 2.4 29.2 1.0 OG1 B:THR156 2.5 31.1 1.0 OE2 B:GLU163 2.7 33.2 1.0 CD B:GLU163 2.9 31.9 1.0 CG B:ASP154 3.3 41.9 1.0 CG B:ASP152 3.4 28.6 1.0 C B:LYS158 3.6 25.5 1.0 OD2 B:ASP154 3.7 39.3 1.0 CB B:THR156 3.7 35.3 1.0 CG2 B:THR156 4.0 36.5 1.0 N B:THR156 4.0 40.5 1.0 N B:GLY160 4.1 26.0 1.0 OE1 B:GLU114 4.1 40.6 1.0 CA B:ASP152 4.2 26.9 1.0 OD2 B:ASP152 4.3 29.3 1.0 CB B:ASP152 4.3 26.8 1.0 CA B:LEU159 4.3 24.8 1.0 N B:LYS158 4.3 26.9 1.0 CA B:THR156 4.3 36.9 1.0 N B:LEU159 4.4 24.2 1.0 OE2 B:GLU114 4.4 42.6 1.0 CG B:GLU163 4.4 28.0 1.0 N B:ASP154 4.5 36.4 1.0 C B:ASP152 4.5 29.8 1.0 CD B:GLU114 4.6 41.5 1.0 CA B:LYS158 4.6 26.8 1.0 C B:LEU159 4.6 25.9 1.0 CB B:ASP154 4.7 39.5 1.0 N B:THR155 4.7 38.2 1.0 N B:GLY157 4.7 34.9 1.0 C B:ASP154 4.8 41.2 1.0 C B:THR156 4.8 37.6 1.0 N B:SER153 4.9 30.4 1.0 CA B:ASP154 4.9 40.0 1.0

Calcium binding site 7 out of 8 in the Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:44.0 occ:1.00 O B:HOH445 2.2 51.9 1.0 OD1 B:ASP184 2.3 48.1 1.0 OD1 B:ASP182 2.3 44.7 1.0 O B:THR188 2.4 36.6 1.0 OG B:SER186 2.4 42.7 1.0 OE1 B:GLU193 2.5 37.9 1.0 OE2 B:GLU193 2.6 43.1 1.0 CD B:GLU193 2.9 43.8 1.0 CG B:ASP184 3.4 55.6 1.0 CG B:ASP182 3.5 42.3 1.0 C B:THR188 3.5 36.4 1.0 CB B:SER186 3.5 43.4 1.0 OD2 B:ASP184 3.7 52.3 1.0 OG1 B:THR188 4.0 41.4 1.0 CA B:ASP182 4.0 41.8 1.0 N B:SER186 4.1 45.4 1.0 CB B:ASP182 4.2 41.1 1.0 CA B:ILE189 4.3 33.1 1.0 N B:CYS190 4.3 34.1 1.0 N B:THR188 4.3 39.4 1.0 N B:ILE189 4.3 36.6 1.0 CA B:SER186 4.4 43.9 1.0 OD2 B:ASP182 4.4 41.8 1.0 C B:ASP182 4.4 45.6 1.0 CG B:GLU193 4.5 38.8 1.0 CA B:THR188 4.5 39.5 1.0 N B:ASP184 4.6 53.1 1.0 N B:THR183 4.7 47.8 1.0 CB B:ASP184 4.7 54.4 1.0 C B:ILE189 4.7 36.0 1.0 N B:GLY187 4.8 45.5 1.0 SG B:CYS190 4.8 46.2 1.0 N B:ARG185 4.9 50.9 1.0 C B:SER186 4.9 44.8 1.0 CB B:THR188 4.9 39.8 1.0 O B:ASP182 4.9 46.9 1.0

Calcium binding site 8 out of 8 in the Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Human Calpain Pef(S) with (Z)-3-(6-Bromondol-3-Yl)-2-Mercaptoacrylic Acid Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca305 b:38.4 occ:1.00 O B:HOH450 2.2 42.6 1.0 O B:HOH453 2.3 50.6 1.0 OD1 B:ASN228 2.3 33.4 1.0 OD1 B:ASP137 2.4 44.1 1.0 OD2 B:ASP227 2.4 35.5 1.0 OD1 B:ASP227 2.5 34.8 1.0 OD2 B:ASP225 2.6 43.5 1.0 CG B:ASP227 2.8 30.3 1.0 OD1 B:ASP225 2.9 35.2 1.0 CG B:ASP225 3.2 36.6 1.0 CG B:ASN228 3.3 32.4 1.0 CG B:ASP137 3.4 58.3 1.0 OD2 B:ASP137 3.8 57.4 1.0 ND2 B:ASN228 4.1 32.3 1.0 N B:ASN228 4.2 26.7 1.0 CB B:ASP227 4.3 31.2 1.0 CB B:ASN228 4.3 27.9 1.0 O A:HOH477 4.4 40.5 1.0 O B:GLY138 4.6 34.9 1.0 N B:ASP137 4.6 42.5 1.0 CB B:ASP137 4.7 52.3 1.0 CB B:ASP225 4.7 35.2 1.0 CA B:ASN228 4.7 26.8 1.0 C B:ASP227 4.8 28.3 1.0 O B:HOH451 4.9 48.3 1.0 CG2 B:THR136 4.9 40.0 1.0 O B:HOH432 4.9 38.2 1.0 CA B:ASP227 5.0 28.6 1.0

S.E.Adams, E.J.Robinson, D.J.Miller, P.J.Rizkallah, M.B.Hallett, R.K.Allemann. Conformationally Restricted Calpain Inhibitors. Chem Sci V. 6 6865 2015.
ISSN: ISSN 2041-6520
PubMed: 28757975
DOI: 10.1039/C5SC01158B