Atomistry » Iodine » PDB 3zh8-4cb6 » 4agp
Atomistry »
  Iodine »
    PDB 3zh8-4cb6 »
      4agp »

Iodine in PDB 4agp: Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5176

Protein crystallography data

The structure of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5176, PDB code: 4agp was solved by A.C.Joerger, R.Wilcken, A.R.Fersht, F.M.Boeckler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.62 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.080, 71.170, 104.980, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 18.7

Other elements in 4agp:

The structure of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5176 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5176 (pdb code 4agp). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5176, PDB code: 4agp:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 4agp

Go back to Iodine Binding Sites List in 4agp
Iodine binding site 1 out of 2 in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5176


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 PHIKAN5176 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1292

b:12.8
occ:1.00
I2 A:P511292 0.0 12.8 1.0
C4 A:P511292 2.1 7.7 1.0
C02 A:P511292 3.0 12.8 1.0
C7 A:P511292 3.0 14.2 1.0
O A:LEU145 3.1 6.7 1.0
O1 A:P511292 3.2 10.8 1.0
O A:HOH2096 3.7 11.4 1.0
C A:LEU145 3.7 5.0 1.0
OG1 A:THR230 3.9 11.8 1.0
N A:THR230 3.9 7.0 1.0
CG2 A:VAL147 4.0 9.9 1.0
CB A:THR230 4.1 8.7 1.0
CB A:LEU145 4.2 9.1 1.0
N A:VAL147 4.3 6.5 1.0
O A:HOH2237 4.3 13.8 1.0
CA A:TRP146 4.3 4.9 1.0
N A:TRP146 4.3 5.6 1.0
C01 A:P511292 4.4 11.7 1.0
C1 A:P511292 4.4 13.5 1.0
C A:TRP146 4.5 6.1 1.0
CG1 A:VAL147 4.5 7.2 1.0
CA A:CYS229 4.5 9.4 1.0
CD A:PRO223 4.6 13.7 1.0
CG A:PRO223 4.6 15.0 1.0
C A:CYS229 4.6 8.1 1.0
CA A:LEU145 4.6 6.9 1.0
CA A:THR230 4.7 6.4 1.0
O A:GLU221 4.7 11.1 1.0
CB A:VAL147 4.8 6.7 1.0
C3 A:P511292 4.9 13.6 1.0

Iodine binding site 2 out of 2 in 4agp

Go back to Iodine Binding Sites List in 4agp
Iodine binding site 2 out of 2 in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small Molecule PHIKAN5176


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 PHIKAN5176 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1291

b:12.0
occ:1.00
I2 B:P511291 0.0 12.0 1.0
C4 B:P511291 2.1 7.2 1.0
O B:LEU145 3.0 7.1 1.0
C7 B:P511291 3.0 10.2 1.0
C02 B:P511291 3.1 10.4 1.0
O1 B:P511291 3.2 11.0 1.0
C B:LEU145 3.7 6.1 1.0
O B:HOH2091 3.7 10.4 1.0
N B:THR230 3.9 8.0 1.0
OG1 B:THR230 4.0 12.3 1.0
CG2 B:VAL147 4.0 9.2 1.0
CB B:THR230 4.1 8.7 1.0
CB B:LEU145 4.2 10.0 1.0
N B:VAL147 4.2 7.3 1.0
CA B:TRP146 4.2 5.2 1.0
N B:TRP146 4.2 5.6 1.0
O B:HOH2223 4.4 15.9 1.0
C1 B:P511291 4.4 12.0 1.0
C01 B:P511291 4.4 11.6 1.0
C B:TRP146 4.4 5.8 1.0
CA B:CYS229 4.5 8.2 1.0
CG1 B:VAL147 4.5 7.5 1.0
CG B:PRO223 4.5 13.0 1.0
C B:CYS229 4.6 8.6 1.0
CD B:PRO223 4.6 12.7 1.0
CA B:LEU145 4.6 6.9 1.0
CA B:THR230 4.7 7.8 1.0
CB B:VAL147 4.8 7.7 1.0
O B:GLU221 4.9 12.3 1.0
C3 B:P511291 4.9 12.2 1.0

Reference:

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
Page generated: Sun Dec 13 19:31:48 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy