Calcium in PDB 5d69: Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Iodoindol-3-Yl)Acrylic Acid) Bound

The structure of Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Iodoindol-3-Yl)Acrylic Acid) Bound, PDB code: 5d69 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)	34.47 / 1.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.030, 79.650, 57.160, 90.00, 91.81, 90.00
R / Rfree (%)	19.9 / 23.4

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

Iodine

(I)

8 atoms

The binding sites of Calcium atom in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Iodoindol-3-Yl)Acrylic Acid) Bound (pdb code 5d69). 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- Iodoindol-3-Yl)Acrylic Acid) Bound, PDB code: 5d69:
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- Iodoindol-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- Iodoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:51.2 occ:1.00 O A:HOH414 2.3 45.4 1.0 O A:ALA109 2.3 56.2 1.0 OD1 A:ASP112 2.3 52.2 1.0 O A:GLU114 2.3 48.9 1.0 OE1 A:GLU119 2.4 48.5 1.0 O A:HOH409 2.4 51.1 1.0 OE2 A:GLU119 2.5 50.8 1.0 CD A:GLU119 2.9 49.5 1.0 C A:ALA109 3.4 56.9 1.0 CG A:ASP112 3.4 52.8 1.0 C A:GLU114 3.6 50.2 1.0 OD2 A:ASP112 3.7 51.6 1.0 CA A:ALA109 4.0 55.7 1.0 N A:GLU114 4.2 53.4 1.0 CG A:GLU119 4.4 49.1 1.0 N A:SER116 4.5 46.2 1.0 N A:GLY110 4.5 58.0 1.0 O A:HOH432 4.5 59.2 1.0 N A:VAL115 4.5 49.2 1.0 CA A:VAL115 4.5 47.8 1.0 CA A:GLU114 4.5 53.0 1.0 CB A:ALA109 4.7 56.4 1.0 N A:ASP112 4.7 57.9 1.0 O A:LEU108 4.7 57.6 1.0 CB A:ASP112 4.8 54.3 1.0 CA A:GLY110 4.8 59.7 1.0 C A:GLY110 4.8 60.8 1.0 N A:MET113 4.9 55.3 1.0 C A:VAL115 4.9 46.3 1.0 N A:ASP111 5.0 62.0 1.0

Calcium binding site 2 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Iodoindol-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- Iodoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:51.1 occ:1.00 O A:HOH403 2.1 57.5 1.0 OD1 A:ASP154 2.3 63.3 1.0 OD1 A:ASP152 2.3 47.2 1.0 O A:LYS158 2.3 46.0 1.0 OG1 A:THR156 2.4 53.0 1.0 OE1 A:GLU163 2.4 51.9 1.0 OE2 A:GLU163 2.9 53.5 1.0 CD A:GLU163 3.1 52.3 1.0 CG A:ASP154 3.2 62.0 1.0 OD2 A:ASP154 3.5 62.4 1.0 C A:LYS158 3.5 45.6 1.0 CG A:ASP152 3.5 48.5 1.0 CB A:THR156 3.7 54.8 1.0 N A:THR156 3.9 54.0 1.0 OE1 A:GLU114 4.0 60.0 1.0 N A:GLY160 4.1 45.9 1.0 CG2 A:THR156 4.2 56.9 1.0 N A:LYS158 4.2 46.6 1.0 OE2 A:GLU114 4.3 61.6 1.0 CA A:LEU159 4.3 44.7 1.0 N A:LEU159 4.3 44.3 1.0 CA A:THR156 4.3 53.3 1.0 OD2 A:ASP152 4.4 47.5 1.0 CB A:ASP152 4.4 46.3 1.0 CA A:ASP152 4.4 48.3 1.0 CA A:LYS158 4.5 47.2 1.0 CD A:GLU114 4.5 59.3 1.0 CG A:GLU163 4.6 51.0 1.0 CB A:ASP154 4.6 61.1 1.0 N A:ASP154 4.6 58.2 1.0 C A:LEU159 4.6 45.2 1.0 N A:THR155 4.6 57.5 1.0 N A:GLY157 4.7 50.1 1.0 C A:ASP152 4.7 50.8 1.0 C A:ASP154 4.8 59.6 1.0 C A:THR156 4.9 51.7 1.0 CA A:ASP154 4.9 60.4 1.0

Calcium binding site 3 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Iodoindol-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- Iodoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:57.0 occ:1.00 O A:HOH433 2.2 64.9 1.0 OD1 A:ASP184 2.2 69.0 1.0 OD1 A:ASP182 2.3 60.0 1.0 O A:THR188 2.5 55.1 1.0 OE1 A:GLU193 2.5 58.4 1.0 OE2 A:GLU193 2.5 61.7 1.0 OG A:SER186 2.6 61.0 1.0 CD A:GLU193 2.9 60.6 1.0 CG A:ASP184 3.3 71.0 1.0 CG A:ASP182 3.4 60.2 1.0 C A:THR188 3.6 53.0 1.0 CB A:SER186 3.7 62.4 1.0 OD2 A:ASP184 3.8 70.0 1.0 CA A:ASP182 3.9 61.1 1.0 N A:SER186 4.1 64.5 1.0 CB A:ASP182 4.1 59.7 1.0 C A:ASP182 4.3 65.5 1.0 OG1 A:THR188 4.3 55.6 1.0 N A:CYS190 4.4 56.2 1.0 N A:THR188 4.4 54.3 1.0 OD2 A:ASP182 4.4 59.1 1.0 CA A:ILE189 4.4 52.7 1.0 CG A:GLU193 4.4 59.4 1.0 N A:ASP184 4.4 72.0 1.0 N A:ILE189 4.5 52.9 1.0 CA A:SER186 4.5 63.4 1.0 CA A:THR188 4.6 53.1 1.0 N A:THR183 4.6 68.1 1.0 CB A:ASP184 4.6 73.0 1.0 N A:ARG185 4.7 71.2 1.0 O A:ASP182 4.8 66.7 1.0 C A:ILE189 4.8 52.6 1.0 ND2 A:ASN223 4.9 63.2 1.0 CA A:ASP184 4.9 73.6 1.0 C A:ASP184 4.9 72.9 1.0 SG A:CYS190 5.0 63.4 1.0 N A:GLY187 5.0 59.3 1.0

Calcium binding site 4 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Iodoindol-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- Iodoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:47.4 occ:1.00 OD1 A:ASP227 2.4 42.2 1.0 OD2 A:ASP227 2.4 41.0 1.0 O A:HOH438 2.4 41.7 1.0 OD1 A:ASN228 2.4 43.8 1.0 OD1 A:ASP137 2.5 57.3 1.0 O A:HOH436 2.5 47.0 1.0 OD2 A:ASP225 2.5 47.6 1.0 OD1 A:ASP225 2.7 44.1 1.0 CG A:ASP227 2.7 41.3 1.0 CG A:ASP225 3.0 45.7 1.0 CG A:ASN228 3.3 42.2 1.0 CG A:ASP137 3.4 57.5 1.0 OD2 A:ASP137 3.8 59.4 1.0 N A:ASN228 4.1 39.6 1.0 ND2 A:ASN228 4.1 42.9 1.0 CB A:ASP227 4.2 40.4 1.0 CB A:ASN228 4.3 40.7 1.0 O B:HOH461 4.5 53.5 1.0 N A:ASP137 4.5 53.9 1.0 CB A:ASP225 4.6 45.8 1.0 O A:GLY138 4.7 47.4 1.0 CA A:ASN228 4.7 39.0 1.0 CB A:ASP137 4.7 57.3 1.0 C A:ASP227 4.8 39.3 1.0 CG2 A:THR136 4.9 51.7 1.0 CA A:ASP227 4.9 40.1 1.0 N A:ASP227 4.9 40.8 1.0

Calcium binding site 5 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Iodoindol-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- Iodoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:43.4 occ:1.00 OD1 B:ASP112 2.3 43.4 1.0 O B:ALA109 2.3 47.9 1.0 O B:HOH430 2.4 42.9 1.0 OE1 B:GLU119 2.4 38.2 1.0 O B:HOH425 2.4 42.0 1.0 O B:GLU114 2.4 41.2 1.0 OE2 B:GLU119 2.5 40.4 1.0 CD B:GLU119 2.8 39.4 1.0 CG B:ASP112 3.3 44.7 1.0 C B:ALA109 3.4 48.3 1.0 C B:GLU114 3.6 41.9 1.0 OD2 B:ASP112 3.6 45.7 1.0 CA B:ALA109 4.0 47.2 1.0 N B:GLU114 4.2 46.1 1.0 CG B:GLU119 4.3 37.7 1.0 N B:SER116 4.4 35.8 1.0 N B:GLY110 4.5 50.2 1.0 N B:VAL115 4.5 39.0 1.0 CA B:VAL115 4.5 37.9 1.0 O B:HOH433 4.5 49.3 1.0 CA B:GLU114 4.5 44.5 1.0 N B:ASP112 4.6 49.4 1.0 CB B:ASP112 4.7 46.9 1.0 O B:LEU108 4.7 46.1 1.0 CB B:ALA109 4.7 47.5 1.0 CA B:GLY110 4.8 51.7 1.0 N B:MET113 4.8 47.7 1.0 C B:GLY110 4.8 54.1 1.0 C B:VAL115 4.9 36.0 1.0 OG B:SER116 5.0 36.3 1.0 CA B:ASP112 5.0 48.5 1.0

Calcium binding site 6 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Iodoindol-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- Iodoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:44.8 occ:1.00 OD1 B:ASP152 2.2 43.9 1.0 O B:HOH413 2.3 44.2 1.0 OD1 B:ASP154 2.3 57.0 1.0 O B:LYS158 2.3 40.4 1.0 OE1 B:GLU163 2.4 48.7 1.0 OG1 B:THR156 2.5 49.4 1.0 OE2 B:GLU163 2.9 51.8 1.0 CD B:GLU163 3.0 48.5 1.0 CG B:ASP154 3.3 59.0 1.0 CG B:ASP152 3.4 45.1 1.0 C B:LYS158 3.5 40.4 1.0 OD2 B:ASP154 3.6 58.9 1.0 CB B:THR156 3.8 52.4 1.0 N B:THR156 3.9 54.4 1.0 OE1 B:GLU114 4.1 53.6 1.0 N B:GLY160 4.1 40.1 1.0 N B:LYS158 4.2 42.5 1.0 CG2 B:THR156 4.2 53.7 1.0 CB B:ASP152 4.3 43.4 1.0 CA B:LEU159 4.3 38.9 1.0 OD2 B:ASP152 4.3 43.7 1.0 CA B:ASP152 4.3 44.4 1.0 N B:LEU159 4.3 39.6 1.0 CA B:THR156 4.4 52.6 1.0 OE2 B:GLU114 4.4 55.7 1.0 CA B:LYS158 4.5 41.7 1.0 CG B:GLU163 4.5 47.0 1.0 N B:ASP154 4.6 56.2 1.0 CB B:ASP154 4.6 59.5 1.0 CD B:GLU114 4.6 53.2 1.0 N B:THR155 4.6 61.8 1.0 C B:LEU159 4.7 39.2 1.0 C B:ASP152 4.7 46.5 1.0 N B:GLY157 4.7 47.9 1.0 C B:ASP154 4.8 61.3 1.0 C B:THR156 4.9 50.0 1.0 CA B:ASP154 4.9 59.5 1.0 C B:THR155 5.0 58.8 1.0

Calcium binding site 7 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Iodoindol-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- Iodoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:47.8 occ:1.00 O B:HOH455 2.3 56.8 1.0 O B:THR188 2.3 41.5 1.0 OD1 B:ASP182 2.4 45.1 1.0 OD1 B:ASP184 2.4 59.8 1.0 OE1 B:GLU193 2.5 45.0 1.0 OG B:SER186 2.5 46.7 1.0 OE2 B:GLU193 2.6 47.2 1.0 CD B:GLU193 2.9 46.0 1.0 CG B:ASP184 3.5 61.2 1.0 CG B:ASP182 3.5 45.1 1.0 C B:THR188 3.5 41.4 1.0 CB B:SER186 3.6 48.8 1.0 OD2 B:ASP184 3.8 62.9 1.0 CA B:ASP182 4.1 46.1 1.0 OG1 B:THR188 4.1 45.8 1.0 N B:SER186 4.2 50.3 1.0 CB B:ASP182 4.2 44.5 1.0 N B:THR188 4.2 41.8 1.0 N B:CYS190 4.3 46.7 1.0 CA B:ILE189 4.3 42.4 1.0 OD2 B:ASP182 4.4 44.0 1.0 N B:ILE189 4.4 41.0 1.0 CA B:THR188 4.4 41.6 1.0 CG B:GLU193 4.4 46.4 1.0 C B:ASP182 4.4 49.1 1.0 CA B:SER186 4.5 49.2 1.0 N B:ASP184 4.6 57.6 1.0 N B:THR183 4.7 52.9 1.0 C B:ILE189 4.8 42.9 1.0 CB B:ASP184 4.8 61.5 1.0 N B:ARG185 4.9 54.2 1.0 N B:GLY187 4.9 45.2 1.0 CB B:THR188 4.9 43.5 1.0 SG B:CYS190 4.9 58.5 1.0 C B:SER186 5.0 46.9 1.0 O B:ASP182 5.0 48.1 1.0

Calcium binding site 8 out of 8 in the Human Calpain Pef(S) with (2Z,2Z')-2,2'-Disulfanediylbis(3-(6- Iodoindol-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- Iodoindol-3-Yl)Acrylic Acid) Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:39.1 occ:1.00 O B:HOH444 2.3 37.9 1.0 OD1 B:ASP227 2.4 34.7 1.0 O A:HOH412 2.4 36.1 1.0 OD1 B:ASN228 2.4 36.3 1.0 OD2 B:ASP227 2.4 33.4 1.0 OD1 B:ASP137 2.5 45.8 1.0 OD2 B:ASP225 2.5 41.1 1.0 OD1 B:ASP225 2.7 39.7 1.0 CG B:ASP227 2.7 33.2 1.0 CG B:ASP225 3.0 39.5 1.0 CG B:ASP137 3.4 45.5 1.0 CG B:ASN228 3.4 35.8 1.0 OD2 B:ASP137 3.7 47.5 1.0 N B:ASN228 4.1 33.1 1.0 CB B:ASP227 4.2 32.2 1.0 ND2 B:ASN228 4.2 36.6 1.0 CB B:ASN228 4.3 34.9 1.0 O B:HOH454 4.4 50.9 1.0 O B:HOH463 4.4 47.9 1.0 CB B:ASP225 4.5 39.4 1.0 O A:HOH430 4.5 56.1 1.0 N B:ASP137 4.5 40.6 1.0 OD1 A:ASP142 4.6 56.4 1.0 O B:GLY138 4.6 36.1 1.0 CB B:ASP137 4.7 44.5 1.0 CA B:ASN228 4.7 33.3 1.0 C B:ASP227 4.8 31.4 1.0 CA B:ASP227 4.8 31.7 1.0 N B:ASP227 4.8 31.5 1.0 CG2 B:THR136 4.9 39.5 1.0 O B:HOH469 4.9 61.8 1.0 O B:HOH446 4.9 40.0 1.0 O B:HOH434 5.0 47.7 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