Iodine in PDB 3wgw: Structure of Pcna Bound to A Small Molecule Inhibitor

The structure of Structure of Pcna Bound to A Small Molecule Inhibitor, PDB code: 3wgw was solved by H.Hashimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	P 41 3 2
Cell size a, b, c (Å), α, β, γ (°)	192.173, 192.173, 192.173, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.1

The binding sites of Iodine atom in the Structure of Pcna Bound to A Small Molecule Inhibitor (pdb code 3wgw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Structure of Pcna Bound to A Small Molecule Inhibitor, PDB code: 3wgw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Structure of Pcna Bound to A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Pcna Bound to A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:38.1 occ:1.00 I3 A:T2B301 0.0 38.1 1.0 C9 A:T2B301 2.1 29.3 1.0 C11 A:T2B301 3.0 34.4 1.0 O A:GLY127 3.1 41.0 1.0 C7 A:T2B301 3.1 32.4 1.0 O2 A:T2B301 3.2 32.0 1.0 C A:GLY127 3.7 36.0 1.0 C2 A:T2B301 3.7 31.0 1.0 C4 A:T2B301 3.9 28.9 1.0 CB B:PRO129 4.0 39.6 1.0 CA A:ILE128 4.1 33.5 1.0 N A:ILE128 4.2 33.8 1.0 N A:GLY127 4.2 36.5 1.0 CA B:PRO129 4.2 42.3 1.0 CD A:PRO129 4.3 32.8 1.0 C1 A:T2B301 4.3 38.4 1.0 CB A:LEU126 4.4 44.0 1.0 N B:GLU130 4.4 51.2 1.0 CD1 A:LEU47 4.4 33.2 1.0 C5 A:T2B301 4.5 36.4 1.0 CA A:GLY127 4.6 36.0 1.0 CD2 A:LEU126 4.6 46.4 1.0 C12 A:T2B301 4.6 30.3 1.0 C B:PRO129 4.8 45.1 1.0 C A:LEU126 4.9 39.5 1.0 C3 A:T2B301 4.9 35.1 1.0 O B:GLU130 4.9 51.6 1.0 CG1 A:ILE128 4.9 28.8 1.0 C6 A:T2B301 5.0 30.6 1.0 CG A:LEU126 5.0 45.2 1.0

Iodine binding site 2 out of 6 in the Structure of Pcna Bound to A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Pcna Bound to A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:52.4 occ:1.00 I1 A:T2B301 0.0 52.4 1.0 C5 A:T2B301 2.2 36.4 1.0 C3 A:T2B301 3.2 35.1 1.0 O A:HOH441 3.3 32.9 1.0 C7 A:T2B301 3.3 32.4 1.0 O2 A:T2B301 3.5 32.0 1.0 O A:TYR250 3.7 24.8 1.0 C2 A:T2B301 3.9 31.0 1.0 O A:VAL45 4.0 31.9 1.0 CB A:TYR250 4.1 23.7 1.0 C A:TYR250 4.2 23.4 1.0 N A:LEU47 4.2 28.3 1.0 CG A:PRO234 4.2 30.4 1.0 CB A:LEU47 4.3 29.3 1.0 C4 A:T2B301 4.3 28.9 1.0 CB A:PRO234 4.5 32.4 1.0 C1 A:T2B301 4.5 38.4 1.0 N A:LEU251 4.6 23.0 1.0 CA A:SER46 4.6 30.1 1.0 CA A:LEU251 4.6 24.8 1.0 N A:ALA252 4.6 27.2 1.0 C A:SER46 4.7 29.7 1.0 C9 A:T2B301 4.7 29.3 1.0 C12 A:T2B301 4.7 30.3 1.0 CA A:TYR250 4.9 23.5 1.0 CA A:LEU47 4.9 28.9 1.0 C A:LEU251 4.9 26.8 1.0

Iodine binding site 3 out of 6 in the Structure of Pcna Bound to A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Pcna Bound to A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:0.4 occ:1.00 I3 A:T2B303 0.0 0.4 1.0 C9 A:T2B303 2.1 0.1 1.0 C7 A:T2B303 3.0 96.9 1.0 O2 A:T2B303 3.2 86.9 1.0 C11 A:T2B303 3.2 0.5 1.0 C2 A:T2B303 3.6 77.7 1.0 O A:ASP165 3.7 47.9 1.0 CG A:ASP165 3.9 77.6 1.0 CB A:ASP165 3.9 60.5 1.0 C A:ASP165 4.0 51.8 1.0 C12 A:T2B303 4.0 74.7 1.0 O A:HOH458 4.0 46.2 1.0 OD2 A:ASP165 4.1 83.5 1.0 OD1 A:ASP165 4.3 70.1 1.0 C4 A:T2B303 4.4 60.4 1.0 C5 A:T2B303 4.5 0.1 1.0 N A:GLY166 4.5 40.8 1.0 C1 A:T2B303 4.5 94.2 1.0 CA A:ASP165 4.6 54.7 1.0 CB A:SER183 4.6 43.3 1.0 CA A:GLY166 4.7 37.5 1.0 CA A:SER183 4.9 41.5 1.0

Iodine binding site 4 out of 6 in the Structure of Pcna Bound to A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Pcna Bound to A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:90.1 occ:1.00 I1 A:T2B303 0.0 90.1 1.0 C5 A:T2B303 2.1 0.1 1.0 C7 A:T2B303 3.1 96.9 1.0 C3 A:T2B303 3.2 94.8 1.0 O2 A:T2B303 3.2 86.9 1.0 O A:LYS181 3.5 28.6 1.0 C2 A:T2B303 3.8 77.7 1.0 C A:LYS181 3.9 30.2 1.0 N A:SER183 4.0 39.1 1.0 CB A:LYS181 4.0 28.9 1.0 CB A:SER183 4.0 43.3 1.0 C A:LEU182 4.3 36.8 1.0 C12 A:T2B303 4.3 74.7 1.0 N A:LEU182 4.4 31.4 1.0 CA A:LEU182 4.4 35.1 1.0 C9 A:T2B303 4.5 0.1 1.0 C1 A:T2B303 4.5 94.2 1.0 CA A:SER183 4.6 41.5 1.0 CA A:LYS181 4.6 29.4 1.0 C4 A:T2B303 4.6 60.4 1.0 C11 A:T2B303 5.0 0.5 1.0 O A:LEU182 5.0 41.5 1.0

Iodine binding site 5 out of 6 in the Structure of Pcna Bound to A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Pcna Bound to A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:54.3 occ:1.00 I3 B:T2B302 0.0 54.3 1.0 C9 B:T2B302 2.1 52.2 1.0 C7 B:T2B302 3.1 41.0 1.0 O2 B:T2B302 3.1 34.8 1.0 C11 B:T2B302 3.2 56.3 1.0 O B:VAL45 3.6 48.7 1.0 C2 B:T2B302 3.7 35.2 1.0 O B:TYR250 3.8 33.7 1.0 CB B:TYR250 4.0 29.5 1.0 C B:TYR250 4.0 32.5 1.0 N B:ALA252 4.1 42.7 1.0 CB B:PRO234 4.1 56.2 1.0 CG B:PRO234 4.2 57.8 1.0 C12 B:T2B302 4.3 36.0 1.0 CB B:LEU47 4.3 35.1 1.0 N B:LEU251 4.3 33.9 1.0 N B:LEU47 4.3 34.8 1.0 CA B:SER46 4.4 38.3 1.0 C4 B:T2B302 4.4 35.1 1.0 CA B:LEU251 4.4 33.8 1.0 C1 B:T2B302 4.5 60.2 1.0 C B:LEU251 4.5 36.4 1.0 C5 B:T2B302 4.5 53.0 1.0 C B:VAL45 4.5 45.5 1.0 C B:SER46 4.6 36.1 1.0 CA B:TYR250 4.7 30.5 1.0 CB B:ALA252 4.8 55.0 1.0 CA B:ALA252 4.8 49.7 1.0 N B:SER46 4.9 41.3 1.0

Iodine binding site 6 out of 6 in the Structure of Pcna Bound to A Small Molecule Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Pcna Bound to A Small Molecule Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:I302 b:61.5 occ:1.00 I1 B:T2B302 0.0 61.5 1.0 C5 B:T2B302 2.1 53.0 1.0 C7 B:T2B302 3.1 41.0 1.0 C3 B:T2B302 3.2 53.3 1.0 O2 B:T2B302 3.2 34.8 1.0 C2 B:T2B302 3.6 35.2 1.0 O B:GLY127 3.7 41.8 1.0 C12 B:T2B302 3.9 36.0 1.0 CD B:PRO129 4.0 36.6 1.0 CD1 B:LEU126 4.1 50.7 1.0 CD1 B:LEU47 4.4 43.4 1.0 C B:GLY127 4.4 42.9 1.0 C4 B:T2B302 4.5 35.1 1.0 CA B:ILE128 4.5 37.1 1.0 C9 B:T2B302 4.5 52.2 1.0 C1 B:T2B302 4.5 60.2 1.0 CB B:LEU126 4.6 49.2 1.0 N B:ILE128 4.8 38.6 1.0 O A:ASP232 4.8 45.7 1.0 C B:LEU126 4.9 49.5 1.0 CG B:PRO129 4.9 38.4 1.0 O B:LEU126 5.0 56.9 1.0 C10 B:T2B302 5.0 38.7 1.0

A.Inoue, S.Kikuchi, A.Hishiki, Y.Shao, R.Heath, B.J.Evison, M.Actis, C.E.Canman, H.Hashimoto, N.Fujii. A Small Molecule Inhibitor of Monoubiquitinated Proliferating Cell Nuclear Antigen (Pcna) Inhibits Repair of Interstrand Dna Crosslink, Enhances Dna Double-Strand Break, and Sensitizes Cancer Cells to Cisplatin J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
DOI: 10.1074/JBC.M113.520429