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Iodine in PDB 3vkx: Structure of Pcna

Protein crystallography data

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

Other elements in 3vkx:

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

Chlorine (Cl) 1 atom

Iodine Binding Sites:

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 3vkx

Go back to Iodine Binding Sites List in 3vkx
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 3vkx

Go back to Iodine Binding Sites List in 3vkx
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 3vkx

Go back to Iodine Binding Sites List in 3vkx
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

Reference:

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
Page generated: Sun Dec 13 19:31:11 2020

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