Iodine in PDB 4agm: Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086

The structure of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086, PDB code: 4agm was solved by A.C.Joerger, R.Wilcken, F.M.Boeckler, A.R.Fersht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.62 / 1.52
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.980, 71.170, 104.960, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 19.7

The structure of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Iodine atom in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086 (pdb code 4agm). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086, PDB code: 4agm:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086 within 5.0Å range: probe atom residue distance (Å) B Occ A:I400 b:18.6 occ:1.00 I1 A:P86400 0.0 18.6 1.0 C01 A:P86400 2.1 14.2 1.0 C3 A:P86400 3.0 14.8 1.0 C02 A:P86400 3.1 10.8 1.0 N A:PRO222 3.8 11.6 1.0 C A:GLU221 3.8 11.7 1.0 O A:CYS220 3.8 16.3 1.0 CD A:PRO151 3.9 8.8 1.0 CD A:PRO222 4.1 16.9 1.0 O A:HOH2115 4.1 34.3 1.0 CG A:PRO222 4.1 19.3 1.0 CG2 A:THR150 4.1 15.1 1.0 SG A:CYS220 4.1 14.4 1.0 O A:GLU221 4.2 10.7 1.0 O A:HOH2118 4.2 29.1 1.0 C A:CYS220 4.2 12.8 1.0 CA A:PRO222 4.2 12.7 1.0 CA A:GLU221 4.2 15.4 1.0 O A:HOH2114 4.3 34.7 1.0 O A:HOH2120 4.3 23.5 1.0 C1 A:P86400 4.4 14.1 1.0 C4 A:P86400 4.4 10.4 1.0 N A:GLU221 4.4 12.8 1.0 O A:PRO151 4.4 10.7 1.0 CG A:PRO151 4.5 16.1 1.0 CB A:PRO222 4.6 17.1 1.0 CB A:CYS220 4.7 8.6 1.0 N A:PRO151 4.8 10.2 1.0 C7 A:P86400 4.9 16.0 1.0

Iodine binding site 2 out of 4 in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086 within 5.0Å range: probe atom residue distance (Å) B Occ A:I400 b:12.4 occ:1.00 I2 A:P86400 0.0 12.4 1.0 C4 A:P86400 2.1 10.4 1.0 O A:LEU145 3.0 7.4 1.0 C02 A:P86400 3.0 10.8 1.0 C7 A:P86400 3.1 16.0 1.0 O1 A:P86400 3.2 12.3 1.0 O A:HOH2103 3.7 13.5 1.0 C A:LEU145 3.7 5.9 1.0 N A:THR230 3.9 7.9 1.0 OG1 A:THR230 3.9 9.0 1.0 CG2 A:VAL147 4.1 9.7 1.0 CB A:THR230 4.1 9.7 1.0 CB A:LEU145 4.2 6.7 1.0 N A:VAL147 4.2 8.8 1.0 CA A:TRP146 4.2 6.8 1.0 N A:TRP146 4.3 6.7 1.0 C01 A:P86400 4.4 14.2 1.0 C1 A:P86400 4.4 14.1 1.0 O A:HOH2243 4.4 22.9 1.0 C A:TRP146 4.4 7.7 1.0 CG1 A:VAL147 4.4 8.8 1.0 CA A:CYS229 4.5 10.1 1.0 C A:CYS229 4.6 8.8 1.0 CG A:PRO223 4.6 11.6 1.0 CA A:LEU145 4.6 6.6 1.0 CA A:THR230 4.6 7.7 1.0 CD A:PRO223 4.7 13.0 1.0 O A:GLU221 4.7 10.7 1.0 CB A:VAL147 4.8 7.9 1.0 C3 A:P86400 4.9 14.8 1.0

Iodine binding site 3 out of 4 in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086 within 5.0Å range: probe atom residue distance (Å) B Occ B:I400 b:22.1 occ:1.00 I1 B:P86400 0.0 22.1 1.0 C01 B:P86400 2.1 14.9 1.0 C3 B:P86400 3.0 16.1 1.0 C02 B:P86400 3.1 14.2 1.0 N B:PRO222 3.7 14.9 1.0 C B:GLU221 3.8 15.1 1.0 O B:HOH2116 3.9 35.0 1.0 O B:CYS220 3.9 18.4 1.0 CD B:PRO151 4.0 13.1 1.0 O B:GLU221 4.1 13.2 1.0 CD B:PRO222 4.1 19.6 1.0 CG B:PRO222 4.1 21.7 1.0 CA B:PRO222 4.1 15.5 1.0 CG2 B:THR150 4.1 15.5 1.0 SG B:CYS220 4.2 14.6 1.0 CG B:PRO151 4.2 14.3 1.0 O B:PRO151 4.3 12.3 1.0 C B:CYS220 4.3 14.4 1.0 CA B:GLU221 4.4 18.0 1.0 C4 B:P86400 4.4 13.1 1.0 C1 B:P86400 4.4 16.3 1.0 O B:HOH2117 4.5 30.0 1.0 CB B:PRO222 4.5 18.9 1.0 N B:GLU221 4.6 14.2 1.0 N B:PRO151 4.8 11.8 1.0 CB B:CYS220 4.9 9.3 1.0 C7 B:P86400 4.9 16.3 1.0

Iodine binding site 4 out of 4 in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5086 within 5.0Å range: probe atom residue distance (Å) B Occ B:I400 b:14.1 occ:1.00 I2 B:P86400 0.0 14.1 1.0 C4 B:P86400 2.1 13.1 1.0 O B:LEU145 3.0 9.0 1.0 C02 B:P86400 3.0 14.2 1.0 C7 B:P86400 3.1 16.3 1.0 O1 B:P86400 3.3 15.0 1.0 O B:HOH2103 3.6 14.6 1.0 C B:LEU145 3.7 8.0 1.0 N B:THR230 3.8 10.4 1.0 OG1 B:THR230 4.0 11.5 1.0 CG2 B:VAL147 4.0 10.4 1.0 CB B:LEU145 4.1 6.9 1.0 CB B:THR230 4.1 10.7 1.0 CA B:TRP146 4.2 6.8 1.0 N B:VAL147 4.2 10.4 1.0 N B:TRP146 4.2 6.6 1.0 C01 B:P86400 4.4 14.9 1.0 C B:TRP146 4.4 8.7 1.0 C1 B:P86400 4.4 16.3 1.0 CA B:CYS229 4.4 12.6 1.0 CG1 B:VAL147 4.5 9.6 1.0 C B:CYS229 4.5 12.0 1.0 CG B:PRO223 4.6 14.4 1.0 CA B:LEU145 4.6 5.8 1.0 CA B:THR230 4.6 10.6 1.0 CD B:PRO223 4.7 17.1 1.0 CB B:VAL147 4.7 8.3 1.0 C3 B:P86400 4.9 16.1 1.0 CB B:CYS229 5.0 12.8 1.0 O B:GLU221 5.0 13.2 1.0

R.Wilcken, X.Liu, M.O.Zimmermann, T.J.Rutherford, A.R.Fersht, A.C.Joerger, F.M.Boeckler. Halogen-Enriched Fragment Libraries As Leads For Drug Rescue of Mutant P53. J.Am.Chem.Soc. V. 134 6810 2012.
ISSN: ISSN 0002-7863
PubMed: 22439615
DOI: 10.1021/JA301056A