Calcium in PDB 4wq3: Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound

The structure of Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound, PDB code: 4wq3 was solved by S.E.Adams, E.J.Robinson, 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)	39.65 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.560, 79.310, 57.020, 90.00, 91.47, 90.00
R / Rfree (%)	17.8 / 21.5

The structure of Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound also contains other interesting chemical elements:

Bromine

(Br)

8 atoms

The binding sites of Calcium atom in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound (pdb code 4wq3). 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 (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound, PDB code: 4wq3:
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 (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic 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 (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:29.9 occ:1.00 O A:HOH433 2.3 25.1 1.0 O A:GLU114 2.3 27.1 1.0 O A:HOH474 2.4 33.9 1.0 O A:ALA109 2.4 30.3 1.0 OD1 A:ASP112 2.4 33.6 1.0 OE1 A:GLU119 2.4 29.0 1.0 OE2 A:GLU119 2.4 29.6 1.0 CD A:GLU119 2.8 28.5 1.0 CG A:ASP112 3.4 30.6 1.0 C A:ALA109 3.4 30.9 1.0 C A:GLU114 3.5 25.5 1.0 OD2 A:ASP112 3.7 31.9 1.0 CA A:ALA109 4.0 29.5 1.0 N A:GLU114 4.3 27.1 1.0 CG A:GLU119 4.3 29.6 1.0 N A:SER116 4.4 26.8 1.0 O A:HOH406 4.4 41.9 1.0 N A:VAL115 4.5 28.4 1.0 O A:HOH435 4.5 48.6 1.0 CA A:VAL115 4.5 27.8 1.0 CA A:GLU114 4.5 27.8 1.0 N A:GLY110 4.5 32.6 1.0 O A:HOH493 4.6 38.4 1.0 N A:ASP112 4.6 30.5 1.0 CB A:ASP112 4.7 32.4 1.0 CB A:ALA109 4.8 29.2 1.0 O A:LEU108 4.8 34.2 1.0 C A:GLY110 4.9 34.4 1.0 N A:MET113 4.9 31.1 1.0 C A:VAL115 4.9 26.1 1.0 CA A:GLY110 4.9 34.4 1.0 N A:ASP111 4.9 34.4 1.0 OG A:SER116 4.9 27.2 1.0 CA A:ASP112 5.0 31.7 1.0

Calcium binding site 2 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic 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 (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:29.4 occ:1.00 O A:LYS158 2.2 25.1 1.0 OD1 A:ASP154 2.3 30.8 1.0 OD1 A:ASP152 2.3 24.7 1.0 OE1 A:GLU163 2.3 30.0 1.0 OG1 A:THR156 2.4 26.9 1.0 O A:HOH416 2.5 26.4 1.0 OE2 A:GLU163 2.9 31.9 1.0 CD A:GLU163 3.0 30.7 1.0 CG A:ASP154 3.3 36.2 1.0 C A:LYS158 3.5 25.7 1.0 CG A:ASP152 3.5 28.7 1.0 OD2 A:ASP154 3.6 32.3 1.0 CB A:THR156 3.6 30.6 1.0 N A:THR156 4.0 28.8 1.0 N A:GLY160 4.0 25.5 1.0 CG2 A:THR156 4.0 31.2 1.0 CA A:LEU159 4.1 24.4 1.0 CA A:ASP152 4.1 26.3 1.0 OE1 A:GLU114 4.2 28.8 1.0 N A:LYS158 4.2 26.3 1.0 N A:LEU159 4.3 24.2 1.0 CB A:ASP152 4.3 25.6 1.0 CA A:THR156 4.3 29.3 1.0 OD2 A:ASP152 4.3 25.3 1.0 OE2 A:GLU114 4.4 33.4 1.0 CG A:GLU163 4.4 30.1 1.0 CA A:LYS158 4.5 26.0 1.0 N A:ASP154 4.5 34.5 1.0 C A:LEU159 4.6 24.5 1.0 C A:ASP152 4.6 29.4 1.0 CD A:GLU114 4.6 31.0 1.0 N A:GLY157 4.6 26.8 1.0 CB A:ASP154 4.6 34.9 1.0 N A:THR155 4.7 32.3 1.0 C A:THR156 4.8 29.0 1.0 C A:ASP154 4.8 33.9 1.0 N A:SER153 4.8 31.5 1.0 CD2 A:LEU159 4.8 23.1 1.0 CA A:ASP154 4.9 35.8 1.0 CA A:GLY160 5.0 26.1 1.0

Calcium binding site 3 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic 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 (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:35.3 occ:1.00 OD1 A:ASP182 2.3 32.4 1.0 O A:HOH494 2.3 42.6 1.0 OD1 A:ASP184 2.4 42.0 1.0 OE1 A:GLU193 2.5 32.6 1.0 O A:THR188 2.5 28.2 1.0 OG A:SER186 2.6 33.9 1.0 OE2 A:GLU193 2.6 36.2 1.0 CD A:GLU193 2.9 32.9 1.0 CG A:ASP182 3.4 35.3 1.0 CG A:ASP184 3.4 46.9 1.0 C A:THR188 3.6 27.7 1.0 CB A:SER186 3.7 36.0 1.0 OD2 A:ASP184 3.8 45.8 1.0 CA A:ASP182 4.0 32.5 1.0 N A:SER186 4.1 37.1 1.0 CB A:ASP182 4.1 33.2 1.0 N A:CYS190 4.2 32.4 1.0 OD2 A:ASP182 4.2 37.3 1.0 C A:ASP182 4.2 38.5 1.0 OG1 A:THR188 4.3 27.2 1.0 N A:ASP184 4.4 49.3 1.0 CA A:ILE189 4.4 29.0 1.0 N A:THR188 4.4 29.0 1.0 CG A:GLU193 4.4 33.1 1.0 N A:ILE189 4.5 27.6 1.0 CA A:SER186 4.5 34.0 1.0 CA A:THR188 4.6 27.0 1.0 N A:THR183 4.6 42.9 1.0 N A:ARG185 4.6 43.5 1.0 CB A:ASP184 4.6 49.7 1.0 O A:ASP182 4.7 38.8 1.0 O A:HOH520 4.8 46.2 1.0 C A:ILE189 4.8 29.4 1.0 CA A:ASP184 4.8 47.9 1.0 O A:HOH467 4.9 41.7 1.0 CB A:CYS190 4.9 39.6 1.0 C A:ASP184 4.9 46.1 1.0 N A:GLY187 5.0 31.9 1.0 CD1 A:ILE189 5.0 32.2 1.0

Calcium binding site 4 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic 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 (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:25.1 occ:1.00 OD1 A:ASP227 2.4 23.5 1.0 O A:HOH452 2.4 24.6 1.0 OD1 A:ASP137 2.4 26.8 1.0 OD1 A:ASN228 2.4 23.3 1.0 O A:HOH516 2.5 25.3 1.0 OD2 A:ASP227 2.5 26.9 1.0 OD2 A:ASP225 2.5 23.5 1.0 OD1 A:ASP225 2.7 21.9 1.0 CG A:ASP227 2.8 22.3 1.0 CG A:ASP225 3.0 24.3 1.0 CG A:ASP137 3.3 31.2 1.0 CG A:ASN228 3.3 24.2 1.0 OD2 A:ASP137 3.6 34.0 1.0 ND2 A:ASN228 3.9 23.0 1.0 N A:ASN228 4.1 22.4 1.0 CB A:ASP227 4.3 22.2 1.0 CB A:ASN228 4.3 21.4 1.0 O B:HOH515 4.4 23.9 1.0 O A:HOH439 4.4 36.0 1.0 N A:ASP137 4.5 26.8 1.0 CB A:ASP225 4.5 25.4 1.0 O B:HOH402 4.5 33.4 1.0 CB A:ASP137 4.6 30.2 1.0 CA A:ASN228 4.7 20.8 1.0 OG1 A:THR136 4.7 26.5 1.0 O A:HOH485 4.7 28.2 1.0 O A:GLY138 4.8 25.8 1.0 C A:ASP227 4.8 22.7 1.0 O A:HOH425 4.8 27.5 1.0 CA A:ASP227 4.9 23.5 1.0 N A:ASP227 5.0 23.1 1.0

Calcium binding site 5 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic 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 (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:24.0 occ:1.00 O B:GLU114 2.3 23.9 1.0 O B:HOH421 2.4 18.4 1.0 O B:HOH509 2.4 27.6 1.0 O B:ALA109 2.4 27.5 1.0 OD1 B:ASP112 2.4 24.1 1.0 OE1 B:GLU119 2.5 21.7 1.0 OE2 B:GLU119 2.5 24.0 1.0 CD B:GLU119 2.8 22.6 1.0 CG B:ASP112 3.3 22.9 1.0 C B:ALA109 3.4 26.7 1.0 C B:GLU114 3.5 23.1 1.0 OD2 B:ASP112 3.7 22.6 1.0 CA B:ALA109 4.0 26.8 1.0 N B:GLU114 4.2 26.7 1.0 CG B:GLU119 4.4 21.9 1.0 N B:SER116 4.4 17.7 1.0 N B:VAL115 4.4 22.9 1.0 N B:ASP112 4.5 24.2 1.0 CA B:GLU114 4.5 24.9 1.0 CA B:VAL115 4.5 21.0 1.0 N B:GLY110 4.5 26.1 1.0 O B:LEU108 4.6 25.8 1.0 O B:HOH543 4.6 36.4 1.0 O B:HOH437 4.6 33.4 1.0 CB B:ASP112 4.6 24.4 1.0 CB B:ALA109 4.7 26.4 1.0 O B:HOH539 4.7 35.4 1.0 O B:HOH504 4.7 32.5 1.0 N B:MET113 4.8 26.2 1.0 C B:GLY110 4.8 29.8 1.0 CA B:GLY110 4.8 28.2 1.0 CA B:ASP112 4.9 24.2 1.0 C B:VAL115 4.9 19.8 1.0 N B:ASP111 4.9 29.5 1.0 C B:ASP112 5.0 23.1 1.0 OG B:SER116 5.0 18.6 1.0

Calcium binding site 6 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic 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 (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:26.1 occ:1.00 OD1 B:ASP152 2.3 22.1 1.0 OD1 B:ASP154 2.3 31.4 1.0 OE1 B:GLU163 2.4 25.9 1.0 O B:LYS158 2.4 20.6 1.0 O B:HOH411 2.4 23.8 1.0 OG1 B:THR156 2.4 28.4 1.0 OE2 B:GLU163 2.7 28.0 1.0 CD B:GLU163 2.9 23.6 1.0 CG B:ASP154 3.3 33.7 1.0 CG B:ASP152 3.5 26.0 1.0 C B:LYS158 3.6 23.0 1.0 OD2 B:ASP154 3.6 32.6 1.0 CB B:THR156 3.6 32.0 1.0 N B:THR156 3.9 29.7 1.0 OE1 B:GLU114 4.0 26.5 1.0 N B:GLY160 4.0 24.4 1.0 CG2 B:THR156 4.1 32.4 1.0 CA B:ASP152 4.2 24.5 1.0 CA B:LEU159 4.2 21.6 1.0 CB B:ASP152 4.3 21.4 1.0 CA B:THR156 4.3 30.1 1.0 OE2 B:GLU114 4.3 28.3 1.0 N B:LYS158 4.3 21.3 1.0 OD2 B:ASP152 4.4 25.7 1.0 N B:LEU159 4.4 21.3 1.0 CG B:GLU163 4.5 24.4 1.0 CD B:GLU114 4.5 30.9 1.0 C B:LEU159 4.6 22.6 1.0 C B:ASP152 4.6 24.0 1.0 N B:ASP154 4.6 30.5 1.0 CB B:ASP154 4.7 34.2 1.0 CA B:LYS158 4.7 19.9 1.0 N B:THR155 4.7 33.7 1.0 N B:GLY157 4.7 24.8 1.0 C B:THR156 4.8 28.8 1.0 N B:SER153 4.9 26.0 0.5 C B:ASP154 4.9 35.9 1.0 CA B:ASP154 4.9 32.9 1.0 N B:SER153 4.9 27.6 0.5

Calcium binding site 7 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic 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 (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:28.7 occ:1.00 O B:HOH469 2.2 34.3 1.0 OD1 B:ASP182 2.3 24.5 1.0 OG B:SER186 2.4 27.2 1.0 O B:THR188 2.4 23.2 1.0 OD1 B:ASP184 2.4 24.4 1.0 OE1 B:GLU193 2.4 22.2 1.0 OE2 B:GLU193 2.5 25.0 1.0 CD B:GLU193 2.8 23.5 1.0 CG B:ASP182 3.4 25.6 1.0 CG B:ASP184 3.4 31.1 1.0 C B:THR188 3.6 22.2 1.0 CB B:SER186 3.6 28.4 1.0 OD2 B:ASP184 3.7 29.4 1.0 CA B:ASP182 3.9 25.9 1.0 N B:SER186 4.0 31.3 1.0 CB B:ASP182 4.1 25.5 1.0 OG1 B:THR188 4.2 25.7 1.0 OD2 B:ASP182 4.3 26.6 1.0 N B:CYS190 4.3 25.5 1.0 N B:THR188 4.3 22.8 1.0 CG B:GLU193 4.3 23.9 1.0 C B:ASP182 4.3 28.3 1.0 CA B:ILE189 4.4 21.0 1.0 N B:ILE189 4.4 21.1 1.0 CA B:SER186 4.4 30.4 1.0 N B:ASP184 4.5 35.5 1.0 CA B:THR188 4.5 22.1 1.0 N B:THR183 4.6 30.7 1.0 CB B:ASP184 4.7 33.7 1.0 N B:ARG185 4.8 34.2 1.0 C B:ILE189 4.8 23.0 1.0 O B:HOH453 4.9 31.6 1.0 O B:ASP182 4.9 32.0 1.0 SG B:CYS190 4.9 34.7 1.0 CA B:ASP184 4.9 33.5 1.0 N B:GLY187 5.0 23.1 1.0

Calcium binding site 8 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic 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 (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Bromoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:20.8 occ:1.00 OD1 B:ASP137 2.3 19.5 1.0 OD1 B:ASN228 2.4 16.5 1.0 OD1 B:ASP227 2.4 17.5 1.0 O B:HOH518 2.4 23.3 1.0 O B:HOH502 2.5 21.6 1.0 OD1 B:ASP225 2.5 18.9 1.0 OD2 B:ASP225 2.6 18.7 1.0 OD2 B:ASP227 2.6 19.6 1.0 CG B:ASP227 2.8 17.5 1.0 CG B:ASP225 2.9 19.1 1.0 CG B:ASP137 3.4 24.9 1.0 CG B:ASN228 3.4 21.5 1.0 OD2 B:ASP137 3.8 28.0 1.0 N B:ASN228 4.0 16.8 1.0 ND2 B:ASN228 4.2 21.6 1.0 CB B:ASN228 4.3 17.5 1.0 CB B:ASP227 4.3 16.2 1.0 CB B:ASP225 4.4 19.0 1.0 O A:HOH471 4.4 26.0 1.0 O B:HOH506 4.4 30.5 1.0 O B:HOH511 4.5 26.9 1.0 N B:ASP137 4.5 19.5 1.0 OG1 B:THR136 4.7 19.2 1.0 O B:GLY138 4.7 19.6 1.0 CB B:ASP137 4.7 21.5 1.0 CA B:ASN228 4.7 15.7 1.0 C B:ASP227 4.8 16.8 1.0 N B:ASP227 4.8 15.4 1.0 CA B:ASP227 4.9 16.9 1.0 OD1 A:ASP142 4.9 35.2 1.0 O B:HOH434 4.9 24.9 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