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

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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

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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

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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: Wed Apr 5 09:25:57 2023

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