Iodine in PDB 3vkx: Structure of Pcna

The structure of Structure of Pcna, PDB code: 3vkx was solved by H.Hashimoto, A.Hishiki, T.Shimizu, M.Sato, C.Punchihewa, M.Connelly, M.Actis, B.Waddell, V.Pagala, N.Fujii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.10
Space group	I 21 3
Cell size a, b, c (Å), α, β, γ (°)	143.107, 143.107, 143.107, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24.9

The structure of Structure of Pcna also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iodine atom in the Structure of Pcna (pdb code 3vkx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Structure of Pcna, PDB code: 3vkx:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in the Structure of Pcna


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:60.7 occ:1.00 I1 A:T3301 0.0 60.7 1.0 C5 A:T3301 2.1 48.4 1.0 C3 A:T3301 3.0 50.1 1.0 C7 A:T3301 3.2 47.5 1.0 O2 A:T3301 3.5 43.7 1.0 O A:TYR250 3.6 37.6 1.0 O A:VAL45 3.9 48.2 1.0 C2 A:T3301 3.9 44.2 1.0 C A:TYR250 4.0 40.3 1.0 CB A:TYR250 4.0 41.2 1.0 CL A:CL268 4.1 74.0 1.0 N A:LEU47 4.1 43.6 1.0 CG A:PRO234 4.2 44.7 1.0 CB A:LEU47 4.3 42.9 1.0 C4 A:T3301 4.3 43.8 1.0 C1 A:T3301 4.4 51.5 1.0 N A:LEU251 4.5 39.3 1.0 N A:ALA252 4.5 40.5 1.0 CA A:SER46 4.5 44.0 1.0 CB A:PRO234 4.5 42.5 1.0 C9 A:T3301 4.6 49.1 1.0 C A:SER46 4.6 43.8 1.0 C12 A:T3301 4.6 44.9 1.0 CA A:LEU251 4.7 39.1 1.0 CA A:TYR250 4.7 39.4 1.0 CA A:LEU47 4.9 42.8 1.0 C A:VAL45 4.9 45.8 1.0 C A:LEU251 4.9 38.9 1.0

Iodine binding site 2 out of 3 in the Structure of Pcna


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:51.7 occ:1.00 I2 A:T3301 0.0 51.7 1.0 C6 A:T3301 2.1 46.3 1.0 C4 A:T3301 3.1 43.8 1.0 C8 A:T3301 3.1 45.6 1.0 O1 A:T3301 3.2 48.6 1.0 CD A:PRO234 3.8 44.3 1.0 CG A:PRO129 4.0 52.8 1.0 NE2 A:GLN131 4.0 49.1 1.0 CG A:PRO234 4.3 44.7 1.0 CL A:CL268 4.4 74.0 1.0 C2 A:T3301 4.4 44.2 1.0 C10 A:T3301 4.4 46.6 1.0 CD A:PRO129 4.7 53.1 1.0 C12 A:T3301 4.9 44.9 1.0

Iodine binding site 3 out of 3 in the Structure of Pcna


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:51.9 occ:1.00 I3 A:T3301 0.0 51.9 1.0 C9 A:T3301 2.1 49.1 1.0 C11 A:T3301 3.0 48.7 1.0 O A:GLY127 3.1 54.8 1.0 C7 A:T3301 3.1 47.5 1.0 O2 A:T3301 3.2 43.7 1.0 C2 A:T3301 3.7 44.2 1.0 CD1 A:LEU47 3.8 49.2 1.0 C4 A:T3301 3.9 43.8 1.0 C A:GLY127 4.0 56.3 1.0 CB A:LEU126 4.3 56.0 1.0 C1 A:T3301 4.3 51.5 1.0 CA A:ILE128 4.3 53.4 1.0 CD1 A:LEU126 4.4 57.0 1.0 C5 A:T3301 4.5 48.4 1.0 CD A:PRO129 4.5 53.1 1.0 N A:ILE128 4.5 53.2 1.0 CG1 A:ILE128 4.6 54.0 1.0 C12 A:T3301 4.6 44.9 1.0 N A:GLY127 4.9 56.9 1.0 C6 A:T3301 4.9 46.3 1.0 C3 A:T3301 4.9 50.1 1.0

C.Punchihewa, A.Inoue, A.Hishiki, Y.Fujikawa, M.Connelly, B.Evison, Y.Shao, R.Heath, I.Kuraoka, P.Rodrigues, H.Hashimoto, M.Kawanishi, M.Sato, T.Yagi, N.Fujii. Identification of Small Molecule Proliferating Cell Nuclear Antigen (Pcna) Inhibitor That Disrupts Interactions with Pip-Box Proteins and Inhibits Dna Replication J.Biol.Chem. V. 287 14289 2012.
ISSN: ISSN 0021-9258
PubMed: 22383522
DOI: 10.1074/JBC.M112.353201