Atomistry » Iodine » PDB 8a24-8e5b » 8a31
Atomistry »
  Iodine »
    PDB 8a24-8e5b »
      8a31 »

Iodine in PDB 8a31: P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694

Protein crystallography data

The structure of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694, PDB code: 8a31 was solved by D.I.Balourdas, J.R.Stephenson Clarke, M.G.J.Baud, S.Knapp, A.C.Joerger, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.98 / 1.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.981, 71.063, 105.089, 90, 90, 90
R / Rfree (%) 15.7 / 19.1

Other elements in 8a31:

The structure of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694 also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694 (pdb code 8a31). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694, PDB code: 8a31:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 8a31

Go back to Iodine Binding Sites List in 8a31
Iodine binding site 1 out of 6 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:41.1
occ:0.74
 I A:KV0401 0.0 41.1 0.7
I A:KV0401 0.3 44.3 0.3
C4 A:KV0401 2.1 30.5 0.7
C4 A:KV0401 2.2 45.4 0.3
C3 A:KV0401 3.0 45.8 0.3
C3 A:KV0401 3.0 30.0 0.7
C5 A:KV0401 3.1 23.5 0.7
C5 A:KV0401 3.2 44.4 0.3
N A:KV0401 3.5 40.9 0.3
N A:KV0401 3.5 18.9 0.7
C6 A:KV0401 3.8 39.0 0.3
C9 A:KV0401 3.8 17.6 0.7
CB A:CYS220 3.9 19.6 1.0
N A:PRO222 3.9 24.8 1.0
C A:GLU221 4.0 23.5 1.0
CG A:PRO151 4.0 19.1 1.0
CD A:PRO151 4.0 17.4 1.0
C A:CYS220 4.2 20.6 1.0
CD A:PRO222 4.2 26.5 1.0
CG2 A:THR150 4.2 22.5 1.0
N A:GLU221 4.3 21.4 1.0
C9 A:KV0401 4.3 39.3 0.3
CA A:PRO222 4.3 25.1 1.0
O A:GLU221 4.3 22.0 1.0
C1 A:KV0401 4.3 45.6 0.3
C6 A:KV0401 4.3 18.8 0.7
C1 A:KV0401 4.3 27.6 0.7
O A:CYS220 4.4 22.8 1.0
CA A:GLU221 4.4 24.3 1.0
C10 A:KV0401 4.5 46.5 0.3
C10 A:KV0401 4.5 20.3 0.7
O A:PRO151 4.6 17.7 1.0
C7 A:KV0401 4.6 37.8 0.3
CA A:CYS220 4.7 18.6 1.0
CB A:PRO222 4.7 27.1 1.0
C8 A:KV0401 4.8 18.6 0.7
C A:KV0401 4.9 46.0 0.3
N A:PRO151 4.9 16.7 1.0
C8 A:KV0401 4.9 38.3 0.3
C A:KV0401 4.9 23.7 0.7
CG A:PRO222 5.0 27.9 1.0

Iodine binding site 2 out of 6 in 8a31

Go back to Iodine Binding Sites List in 8a31
Iodine binding site 2 out of 6 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:44.3
occ:0.26
 I A:KV0401 0.0 44.3 0.3
I A:KV0401 0.3 41.1 0.7
C4 A:KV0401 2.1 30.5 0.7
C4 A:KV0401 2.1 45.4 0.3
C3 A:KV0401 3.0 45.8 0.3
C5 A:KV0401 3.0 23.5 0.7
C3 A:KV0401 3.0 30.0 0.7
C5 A:KV0401 3.1 44.4 0.3
N A:KV0401 3.3 40.9 0.3
N A:KV0401 3.3 18.9 0.7
C6 A:KV0401 3.6 39.0 0.3
C9 A:KV0401 3.7 17.6 0.7
CB A:CYS220 3.7 19.6 1.0
CG A:PRO151 3.8 19.1 1.0
CD A:PRO151 3.9 17.4 1.0
C9 A:KV0401 4.0 39.3 0.3
C A:GLU221 4.1 23.5 1.0
C6 A:KV0401 4.1 18.8 0.7
N A:PRO222 4.1 24.8 1.0
C A:CYS220 4.2 20.6 1.0
N A:GLU221 4.3 21.4 1.0
CG2 A:THR150 4.3 22.5 1.0
C1 A:KV0401 4.3 45.6 0.3
O A:GLU221 4.3 22.0 1.0
C1 A:KV0401 4.3 27.6 0.7
C10 A:KV0401 4.4 46.5 0.3
C10 A:KV0401 4.4 20.3 0.7
O A:CYS220 4.4 22.8 1.0
CA A:PRO222 4.4 25.1 1.0
CD A:PRO222 4.4 26.5 1.0
C7 A:KV0401 4.4 37.8 0.3
CA A:GLU221 4.5 24.3 1.0
O A:PRO151 4.6 17.7 1.0
CA A:CYS220 4.6 18.6 1.0
C8 A:KV0401 4.6 18.6 0.7
C8 A:KV0401 4.7 38.3 0.3
N A:PRO151 4.8 16.7 1.0
C7 A:KV0401 4.8 19.1 0.7
C A:KV0401 4.9 46.0 0.3
C A:KV0401 4.9 23.7 0.7
CB A:PRO222 4.9 27.1 1.0
SG A:CYS220 4.9 22.6 1.0

Iodine binding site 3 out of 6 in 8a31

Go back to Iodine Binding Sites List in 8a31
Iodine binding site 3 out of 6 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:14.9
occ:0.74
 I1 A:KV0401 0.0 14.9 0.7
I1 A:KV0401 0.2 48.6 0.3
C10 A:KV0401 2.1 20.3 0.7
C10 A:KV0401 2.2 46.5 0.3
O A:LEU145 2.9 14.7 1.0
C A:KV0401 3.0 23.7 0.7
C5 A:KV0401 3.1 44.4 0.3
O A:KV0401 3.1 23.3 0.7
C5 A:KV0401 3.1 23.5 0.7
C A:KV0401 3.2 46.0 0.3
N A:KV0401 3.2 40.9 0.3
N A:KV0401 3.2 18.9 0.7
O A:KV0401 3.3 45.9 0.3
C6 A:KV0401 3.4 18.8 0.7
C9 A:KV0401 3.5 39.3 0.3
O A:HOH604 3.6 18.2 1.0
C A:LEU145 3.6 13.4 1.0
N A:THR230 3.8 14.7 1.0
C6 A:KV0401 3.8 39.0 0.3
C9 A:KV0401 3.9 17.6 0.7
CG2 A:VAL147 4.0 15.4 1.0
OG1 A:THR230 4.0 19.0 1.0
CA A:TRP146 4.1 13.0 1.0
C7 A:KV0401 4.1 19.1 0.7
N A:TRP146 4.1 12.5 1.0
CB A:THR230 4.1 17.4 1.0
CA A:CYS229 4.2 14.6 1.0
N A:VAL147 4.2 14.4 1.0
C8 A:KV0401 4.3 38.3 0.3
CB A:LEU145 4.3 14.0 1.0
C A:TRP146 4.3 14.0 1.0
C8 A:KV0401 4.4 18.6 0.7
C1 A:KV0401 4.4 27.6 0.7
C A:CYS229 4.4 14.8 1.0
C7 A:KV0401 4.4 37.8 0.3
C4 A:KV0401 4.4 45.4 0.3
C4 A:KV0401 4.5 30.5 0.7
CG A:PRO223 4.5 25.5 1.0
C1 A:KV0401 4.5 45.6 0.3
CA A:THR230 4.6 16.0 1.0
CA A:LEU145 4.6 12.5 1.0
CG1 A:VAL147 4.7 15.0 1.0
CD A:PRO223 4.7 24.1 1.0
CB A:CYS229 4.8 15.9 1.0
CB A:VAL147 4.8 14.2 1.0
O A:ASP228 4.9 20.0 1.0
F A:KV0401 4.9 20.1 0.7
C3 A:KV0401 5.0 30.0 0.7
C3 A:KV0401 5.0 45.8 0.3

Iodine binding site 4 out of 6 in 8a31

Go back to Iodine Binding Sites List in 8a31
Iodine binding site 4 out of 6 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:48.6
occ:0.26
 I1 A:KV0401 0.0 48.6 0.3
I1 A:KV0401 0.2 14.9 0.7
C10 A:KV0401 2.0 20.3 0.7
C10 A:KV0401 2.1 46.5 0.3
C A:KV0401 2.9 23.7 0.7
O A:KV0401 3.0 23.3 0.7
C5 A:KV0401 3.0 44.4 0.3
C A:KV0401 3.0 46.0 0.3
C5 A:KV0401 3.1 23.5 0.7
O A:LEU145 3.1 14.7 1.0
O A:KV0401 3.1 45.9 0.3
N A:KV0401 3.2 40.9 0.3
N A:KV0401 3.2 18.9 0.7
C6 A:KV0401 3.4 18.8 0.7
O A:HOH604 3.5 18.2 1.0
C9 A:KV0401 3.5 39.3 0.3
C A:LEU145 3.7 13.4 1.0
CG2 A:VAL147 3.8 15.4 1.0
C6 A:KV0401 3.9 39.0 0.3
C9 A:KV0401 3.9 17.6 0.7
N A:THR230 3.9 14.7 1.0
N A:VAL147 4.1 14.4 1.0
CA A:TRP146 4.1 13.0 1.0
C7 A:KV0401 4.1 19.1 0.7
N A:TRP146 4.2 12.5 1.0
OG1 A:THR230 4.2 19.0 1.0
C A:TRP146 4.3 14.0 1.0
C1 A:KV0401 4.3 27.6 0.7
CA A:CYS229 4.3 14.6 1.0
C8 A:KV0401 4.3 38.3 0.3
CB A:THR230 4.3 17.4 1.0
C4 A:KV0401 4.4 45.4 0.3
C1 A:KV0401 4.4 45.6 0.3
C4 A:KV0401 4.4 30.5 0.7
C8 A:KV0401 4.4 18.6 0.7
CB A:LEU145 4.4 14.0 1.0
C7 A:KV0401 4.5 37.8 0.3
CG A:PRO223 4.5 25.5 1.0
CG1 A:VAL147 4.5 15.0 1.0
C A:CYS229 4.5 14.8 1.0
CB A:VAL147 4.6 14.2 1.0
CD A:PRO223 4.7 24.1 1.0
CA A:LEU145 4.7 12.5 1.0
CA A:THR230 4.8 16.0 1.0
C3 A:KV0401 4.8 30.0 0.7
CB A:CYS229 4.9 15.9 1.0
C3 A:KV0401 4.9 45.8 0.3
O A:ASP228 4.9 20.0 1.0
CA A:VAL147 5.0 13.5 1.0
F A:KV0401 5.0 20.1 0.7

Iodine binding site 5 out of 6 in 8a31

Go back to Iodine Binding Sites List in 8a31
Iodine binding site 5 out of 6 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I401

b:47.0
occ:1.00
 I B:KV0401 0.0 47.0 1.0
C4 B:KV0401 2.1 38.2 1.0
C3 B:KV0401 3.0 37.3 1.0
C5 B:KV0401 3.1 31.4 1.0
N B:KV0401 3.4 27.2 1.0
C9 B:KV0401 3.8 25.2 1.0
C B:GLU221 4.0 21.9 1.0
CB B:CYS220 4.0 17.5 1.0
CG2 B:THR150 4.0 26.8 1.0
N B:PRO222 4.0 23.6 1.0
CD B:PRO151 4.1 17.7 1.0
O B:GLU221 4.2 21.0 1.0
CG B:PRO151 4.2 19.2 1.0
C6 B:KV0401 4.3 26.6 1.0
N B:GLU221 4.3 19.3 1.0
C B:CYS220 4.3 18.6 1.0
C1 B:KV0401 4.3 35.1 1.0
CA B:PRO222 4.3 24.8 1.0
CD B:PRO222 4.4 25.7 1.0
CA B:GLU221 4.4 20.8 1.0
C10 B:KV0401 4.5 27.5 1.0
O B:PRO151 4.5 18.4 1.0
O B:CYS220 4.5 21.3 1.0
C8 B:KV0401 4.7 26.4 1.0
CA B:CYS220 4.8 16.8 1.0
CB B:PRO222 4.9 26.4 1.0
N B:PRO151 4.9 17.1 1.0
C B:KV0401 4.9 31.5 1.0
C7 B:KV0401 5.0 27.0 1.0

Iodine binding site 6 out of 6 in 8a31

Go back to Iodine Binding Sites List in 8a31
Iodine binding site 6 out of 6 in the P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of P53 Cancer Mutant Y220C in Complex with Iodophenol-Based Small- Molecule Stabilizer JC694 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I401

b:20.9
occ:1.00
 I1 B:KV0401 0.0 20.9 1.0
C10 B:KV0401 2.1 27.5 1.0
O B:LEU145 2.9 17.4 1.0
C B:KV0401 3.0 31.5 1.0
C5 B:KV0401 3.1 31.4 1.0
O B:KV0401 3.1 31.5 1.0
N B:KV0401 3.2 27.2 1.0
C6 B:KV0401 3.4 26.6 1.0
O B:HOH671 3.5 21.0 1.0
C B:LEU145 3.6 15.2 1.0
N B:THR230 3.7 16.5 1.0
C9 B:KV0401 3.9 25.2 1.0
CA B:TRP146 4.1 14.1 1.0
OG1 B:THR230 4.1 19.7 1.0
CG2 B:VAL147 4.1 18.7 1.0
C7 B:KV0401 4.1 27.0 1.0
N B:TRP146 4.1 14.5 1.0
CB B:THR230 4.1 17.6 1.0
N B:VAL147 4.2 15.7 1.0
CA B:CYS229 4.2 18.3 1.0
CB B:LEU145 4.2 15.8 1.0
C B:TRP146 4.4 15.8 1.0
C8 B:KV0401 4.4 26.4 1.0
C1 B:KV0401 4.4 35.1 1.0
C B:CYS229 4.4 18.3 1.0
C4 B:KV0401 4.5 38.2 1.0
CA B:THR230 4.6 16.6 1.0
CA B:LEU145 4.6 13.6 1.0
CG B:PRO223 4.6 26.9 1.0
CB B:CYS229 4.7 18.8 1.0
CG1 B:VAL147 4.7 16.8 1.0
CB B:VAL147 4.9 17.2 1.0
CD B:PRO223 4.9 26.0 1.0
O B:ASP228 4.9 23.5 1.0
F B:KV0401 4.9 28.4 1.0
C3 B:KV0401 5.0 37.3 1.0

Reference:

J.R.Stephenson Clarke, L.R.Douglas, P.J.Duriez, D.I.Balourdas, A.C.Joerger, R.Khadiullina, E.Bulatov, M.G.J.Baud. Discovery of Nanomolar-Affinity Pharmacological Chaperones Stabilizing the Oncogenic P53 Mutant Y220C. Acs Pharmacol Transl Sci V. 5 1169 2022.
ISSN: ESSN 2575-910
PubMed: 36407959
DOI: 10.1021/ACSPTSCI.2C00164
Page generated: Mon Aug 12 02:27:50 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy