Zinc in PDB 6si0: P53 Cancer Mutant Y220C in Complex with Small-Molecule Stabilizer PK9323

Protein crystallography data

The structure of P53 Cancer Mutant Y220C in Complex with Small-Molecule Stabilizer PK9323, PDB code: 6si0 was solved by A.C.Joerger, A.Kraemer, S.Knapp, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.94 / 1.53
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.878, 71.140, 104.740, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 17.1

Zinc Binding Sites:

The binding sites of Zinc atom in the P53 Cancer Mutant Y220C in Complex with Small-Molecule Stabilizer PK9323 (pdb code 6si0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the P53 Cancer Mutant Y220C in Complex with Small-Molecule Stabilizer PK9323, PDB code: 6si0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6si0

Go back to Zinc Binding Sites List in 6si0
Zinc binding site 1 out of 2 in the P53 Cancer Mutant Y220C in Complex with Small-Molecule Stabilizer PK9323


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of P53 Cancer Mutant Y220C in Complex with Small-Molecule Stabilizer PK9323 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:16.5
occ:1.00
ND1 A:HIS179 2.0 15.8 1.0
SG A:CYS238 2.2 15.9 0.4
SG A:CYS176 2.3 14.8 1.0
SG A:CYS242 2.3 18.7 1.0
SG A:CYS238 2.4 15.6 0.6
CE1 A:HIS179 3.0 16.9 1.0
CG A:HIS179 3.1 15.8 1.0
CB A:CYS242 3.2 18.3 1.0
CB A:CYS238 3.3 15.1 0.6
CB A:CYS176 3.3 15.2 1.0
CB A:HIS179 3.5 14.7 1.0
CB A:CYS238 3.5 16.1 0.4
CA A:CYS238 3.8 15.6 0.4
CA A:CYS238 3.8 14.8 0.6
N A:CYS176 4.0 15.0 1.0
NE2 A:HIS179 4.1 17.1 1.0
CD2 A:HIS179 4.2 17.9 1.0
CA A:CYS176 4.3 15.6 1.0
N A:TYR239 4.3 15.8 1.0
N A:HIS179 4.3 15.5 1.0
CA A:HIS179 4.5 15.1 1.0
CA A:CYS242 4.6 16.7 1.0
C A:CYS238 4.6 15.9 0.4
C A:CYS238 4.6 15.8 0.6
O A:HOH612 4.7 18.3 1.0
O A:MET237 4.7 14.8 1.0
C A:CYS176 5.0 16.0 1.0

Zinc binding site 2 out of 2 in 6si0

Go back to Zinc Binding Sites List in 6si0
Zinc binding site 2 out of 2 in the P53 Cancer Mutant Y220C in Complex with Small-Molecule Stabilizer PK9323


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of P53 Cancer Mutant Y220C in Complex with Small-Molecule Stabilizer PK9323 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:16.9
occ:1.00
ND1 B:HIS179 2.0 18.1 1.0
SG B:CYS238 2.3 19.1 1.0
SG B:CYS176 2.3 15.8 1.0
SG B:CYS242 2.4 20.6 1.0
CE1 B:HIS179 3.0 19.6 1.0
CG B:HIS179 3.1 17.7 1.0
CB B:CYS242 3.2 17.9 1.0
CB B:CYS176 3.4 14.6 1.0
CB B:CYS238 3.4 16.4 1.0
CB B:HIS179 3.4 15.5 1.0
CA B:CYS238 3.8 14.9 1.0
N B:CYS176 4.0 13.1 1.0
NE2 B:HIS179 4.1 20.1 1.0
CD2 B:HIS179 4.2 19.1 1.0
CA B:CYS176 4.3 13.9 1.0
N B:HIS179 4.3 16.5 1.0
N B:TYR239 4.4 16.1 1.0
CA B:HIS179 4.5 15.7 1.0
CA B:CYS242 4.6 17.9 1.0
C B:CYS238 4.7 15.9 1.0
O B:HOH615 4.7 16.7 1.0
O B:MET237 4.7 14.2 1.0
C B:CYS176 5.0 15.7 1.0

Reference:

M.R.Bauer, A.Kramer, G.Settanni, R.N.Jones, X.Ni, R.Khan Tareque, A.R.Fersht, J.Spencer, A.C.Joerger. Targeting Cavity-Creating P53 Cancer Mutations with Small-Molecule Stabilizers: the Y220X Paradigm. Acs Chem.Biol. 2020.
ISSN: ESSN 1554-8937
PubMed: 31990523
DOI: 10.1021/ACSCHEMBIO.9B00748
Page generated: Wed Dec 16 12:48:19 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy