Iodine 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:

Calcium

(Ca)

8 atoms

The binding sites of Iodine 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 Iodine atom.
In total 8 binding sites of Iodine 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 Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine 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 Iodine with other atoms in the I 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:I305 b:0.3 occ:0.40 IAT A:57T305 0.0 0.3 0.4 CAB A:57T305 2.1 94.8 0.4 CAC A:57T305 3.0 91.9 0.4 CAA A:57T305 3.1 93.6 0.4 CD1 A:ILE123 3.4 55.9 1.0 NH1 A:ARG130 3.4 77.6 1.0 CD A:LYS126 3.9 65.9 1.0 CAD A:57T305 4.3 88.8 0.4 CAF A:57T305 4.4 90.6 0.4 CZ A:ARG130 4.5 78.4 1.0 CG1 A:ILE123 4.7 53.0 1.0 NH2 A:ARG130 4.8 78.1 1.0 CE A:LYS126 4.8 67.6 1.0 CG A:LYS126 4.9 63.4 1.0 CAE A:57T305 4.9 88.0 0.4

Iodine 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 Iodine with other atoms in the I 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:I305 b:81.0 occ:0.40 IAT A:57T305 0.0 81.0 0.4 CAB A:57T305 2.1 80.2 0.4 CAC A:57T305 3.1 80.2 0.4 CAA A:57T305 3.1 79.7 0.4 CB A:LEU104 3.5 63.0 1.0 C A:LEU104 3.9 58.5 1.0 O A:LEU104 4.1 57.4 1.0 CE2 A:PHE164 4.1 46.9 1.0 CZ A:PHE164 4.2 45.9 1.0 N A:PHE105 4.2 56.4 1.0 CA A:LEU104 4.3 61.7 1.0 CAD A:57T305 4.4 88.8 0.4 CAD A:57T305 4.4 79.7 0.4 CAF A:57T305 4.4 79.1 0.4 CAC A:57T305 4.4 91.9 0.4 CG A:LEU104 4.5 65.3 1.0 CG A:LEU108 4.6 56.8 1.0 CB A:LEU108 4.7 57.0 1.0 CZ2 A:TRP168 4.7 58.3 1.0 CE2 A:TRP168 4.8 55.9 1.0 CA A:PHE105 4.8 54.5 1.0 CG1 A:ILE123 4.8 53.0 1.0 CD1 A:LEU108 4.9 56.5 1.0 CE1 A:PHE101 4.9 58.8 1.0 CAE A:57T305 4.9 79.1 0.4

Iodine 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 Iodine with other atoms in the I 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:I305 b:54.4 occ:0.40 IAZ A:57T305 0.0 54.4 0.4 IAZ A:57T305 1.4 61.6 0.4 CAW A:57T305 2.1 57.3 0.4 CAV A:57T305 3.1 57.8 0.4 CAX A:57T305 3.1 57.4 0.4 CAW A:57T305 3.4 63.3 0.4 O A:LEU124 3.5 47.4 1.0 CG1 A:VAL128 3.6 58.3 1.0 CD1 A:LEU124 3.9 47.5 1.0 CE2 A:PHE226 4.0 43.6 1.0 N A:VAL128 4.1 58.4 1.0 CA A:LEU124 4.1 47.0 1.0 CB A:VAL127 4.1 56.8 1.0 CG1 A:VAL127 4.1 58.3 1.0 CG A:LEU124 4.2 46.1 1.0 CAX A:57T305 4.2 63.6 0.4 C A:LEU124 4.2 47.2 1.0 CAV A:57T305 4.3 64.0 0.4 CE1 A:PHE139 4.3 45.2 1.0 CAU A:57T305 4.4 59.0 0.4 CB A:LEU124 4.4 46.2 1.0 CAY A:57T305 4.4 58.6 0.4 CB A:VAL128 4.5 59.6 1.0 CA A:VAL128 4.5 60.0 1.0 CZ A:PHE139 4.6 44.5 1.0 CG2 A:ILE171 4.7 43.6 1.0 CZ A:PHE226 4.7 43.5 1.0 C A:VAL127 4.7 58.2 1.0 CAS A:57T305 4.9 59.9 0.4 CG2 A:VAL128 4.9 58.8 1.0 CA A:VAL127 5.0 57.4 1.0

Iodine 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 Iodine with other atoms in the I 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:I305 b:61.6 occ:0.40 IAZ A:57T305 0.0 61.6 0.4 CAW A:57T305 0.9 57.3 0.4 IAZ A:57T305 1.4 54.4 0.4 CAV A:57T305 1.8 57.8 0.4 CAW A:57T305 2.1 63.3 0.4 CAX A:57T305 2.2 57.4 0.4 CAV A:57T305 3.0 64.0 0.4 CAX A:57T305 3.0 63.6 0.4 CAU A:57T305 3.1 59.0 0.4 CAY A:57T305 3.3 58.6 0.4 CAS A:57T305 3.7 59.9 0.4 CE2 A:PHE226 3.9 43.6 1.0 CG1 A:VAL127 3.9 58.3 1.0 CG1 A:VAL128 4.0 58.3 1.0 CZ A:PHE226 4.2 43.5 1.0 CG2 A:ILE171 4.2 43.6 1.0 CAU A:57T305 4.3 64.8 0.4 CAY A:57T305 4.3 64.8 0.4 CB A:VAL127 4.4 56.8 1.0 N A:VAL128 4.6 58.4 1.0 O A:LEU124 4.7 47.4 1.0 CA A:VAL128 4.9 60.0 1.0 CAS A:57T305 4.9 65.8 0.4 CD1 A:LEU124 4.9 47.5 1.0 CD1 A:LEU134 4.9 58.3 1.0 C A:VAL127 5.0 58.2 1.0

Iodine 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 Iodine with other atoms in the I 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:I305 b:60.2 occ:0.40 IAT B:57T305 0.0 60.2 0.4 IAT B:57T305 0.9 55.9 0.4 CAB B:57T305 1.3 54.1 0.4 CAB B:57T305 2.1 60.4 0.4 CAC B:57T305 2.2 55.1 0.4 CAA B:57T305 2.5 53.4 0.4 CAC B:57T305 3.0 62.1 0.4 CAA B:57T305 3.0 60.3 0.4 CAD B:57T305 3.5 56.2 0.4 CAF B:57T305 3.7 54.8 0.4 CG1 B:VAL127 3.8 41.8 1.0 CE2 B:PHE226 3.9 33.4 1.0 CG1 B:VAL128 4.0 49.2 1.0 CAE B:57T305 4.1 56.7 0.4 CB B:VAL127 4.2 40.8 1.0 CZ B:PHE226 4.2 32.9 1.0 CG2 B:ILE171 4.3 35.4 1.0 CAD B:57T305 4.3 64.0 0.4 CAF B:57T305 4.3 62.9 0.4 O B:LEU124 4.4 33.5 1.0 N B:VAL128 4.4 42.3 1.0 CD1 B:LEU124 4.7 37.9 1.0 CA B:VAL128 4.8 44.7 1.0 CAE B:57T305 4.8 65.9 0.4 C B:VAL127 4.8 41.3 1.0 CB B:VAL128 4.9 45.8 1.0

Iodine 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 Iodine with other atoms in the I 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:I305 b:55.9 occ:0.40 IAT B:57T305 0.0 55.9 0.4 IAT B:57T305 0.9 60.2 0.4 CAB B:57T305 2.1 54.1 0.4 CAB B:57T305 2.8 60.4 0.4 CAA B:57T305 3.0 53.4 0.4 CAC B:57T305 3.0 55.1 0.4 CAA B:57T305 3.6 60.3 0.4 CAC B:57T305 3.8 62.1 0.4 O B:LEU124 3.8 33.5 1.0 CG1 B:VAL128 3.9 49.2 1.0 CD1 B:LEU124 4.0 37.9 1.0 CE2 B:PHE226 4.0 33.4 1.0 CG1 B:VAL127 4.1 41.8 1.0 CB B:VAL127 4.2 40.8 1.0 CG2 B:ILE171 4.3 35.4 1.0 CA B:LEU124 4.3 34.4 1.0 CG B:LEU124 4.3 36.6 1.0 CAF B:57T305 4.3 54.8 0.4 CAD B:57T305 4.4 56.2 0.4 N B:VAL128 4.4 42.3 1.0 CZ B:PHE226 4.5 32.9 1.0 C B:LEU124 4.5 34.2 1.0 CE1 B:PHE139 4.5 33.5 1.0 CB B:LEU124 4.5 35.1 1.0 CZ B:PHE139 4.7 33.1 1.0 CAE B:57T305 4.9 56.7 0.4 CA B:VAL128 4.9 44.7 1.0 CB B:VAL128 4.9 45.8 1.0 CAF B:57T305 4.9 62.9 0.4 C B:VAL127 5.0 41.3 1.0

Iodine 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 Iodine with other atoms in the I 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:I305 b:0.4 occ:0.40 IAZ B:57T305 0.0 0.4 0.4 CAW B:57T305 2.1 98.8 0.4 NH2 B:ARG130 2.5 51.5 0.5 CAX B:57T305 3.0 94.7 0.4 CAV B:57T305 3.0 0.1 0.4 CZ B:ARG130 3.8 51.7 0.5 CAU B:57T305 3.8 69.3 0.4 NH1 B:ARG130 3.9 55.4 0.5 CD1 B:ILE123 4.2 40.5 1.0 CG2 B:VAL127 4.3 41.1 1.0 CAY B:57T305 4.3 94.0 0.4 CAU B:57T305 4.4 98.4 0.4 CD B:LYS126 4.4 52.1 1.0 NE B:ARG130 4.4 53.9 0.5 CZ B:ARG130 4.5 55.1 0.5 CAV B:57T305 4.5 69.8 0.4 NE B:ARG130 4.5 52.1 0.5 NH1 B:ARG130 4.6 52.3 0.5 CAM B:57T305 4.6 71.1 0.4 CAS B:57T305 4.7 70.5 0.4 CG B:LYS126 4.9 47.9 1.0 CAS B:57T305 4.9 95.0 0.4

Iodine 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 Iodine with other atoms in the I 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:I305 b:77.0 occ:0.40 IAZ B:57T305 0.0 77.0 0.4 CAW B:57T305 2.1 72.0 0.4 CAV B:57T305 3.1 69.8 0.4 CAX B:57T305 3.1 73.3 0.4 CB B:LEU104 3.4 59.0 1.0 C B:LEU104 3.7 52.2 1.0 O B:LEU104 3.8 50.5 1.0 CE2 B:PHE164 4.0 40.6 1.0 N B:PHE105 4.0 50.2 1.0 CA B:LEU104 4.1 57.1 1.0 CZ B:PHE164 4.1 40.5 1.0 CAU B:57T305 4.4 69.3 0.4 CAY B:57T305 4.4 72.8 0.4 CG B:LEU104 4.4 62.9 1.0 CA B:PHE105 4.6 48.2 1.0 CE1 B:PHE101 4.6 56.4 1.0 CG B:LEU108 4.7 50.0 1.0 CB B:LEU108 4.7 48.7 1.0 CE2 B:TRP168 4.7 46.3 1.0 CZ2 B:TRP168 4.8 48.2 1.0 NE1 B:TRP168 4.9 47.5 1.0 CD1 B:LEU108 4.9 49.7 1.0 CAS B:57T305 4.9 70.5 0.4

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