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Zinc in PDB 6si4: P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9323

Protein crystallography data

The structure of P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9323, PDB code: 6si4 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) 42.30 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.220, 71.193, 105.159, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the P53 Cancer Mutant Y220S in Complex with Small-Molecule Stabilizer PK9323 (pdb code 6si4). 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 Y220S in Complex with Small-Molecule Stabilizer PK9323, PDB code: 6si4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6si4

Go back to Zinc Binding Sites List in 6si4
Zinc binding site 1 out of 2 in the P53 Cancer Mutant Y220S 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 Y220S in Complex with Small-Molecule Stabilizer PK9323 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:19.2
occ:1.00
ND1 A:HIS179 2.0 16.9 1.0
SG A:CYS238 2.3 22.3 1.0
SG A:CYS176 2.3 18.7 1.0
SG A:CYS242 2.4 22.6 1.0
CE1 A:HIS179 2.9 19.9 1.0
CG A:HIS179 3.1 17.5 1.0
CB A:CYS242 3.1 23.4 1.0
CB A:CYS176 3.4 17.1 1.0
CB A:CYS238 3.4 26.8 1.0
CB A:HIS179 3.5 17.6 1.0
CA A:CYS238 3.9 17.6 1.0
N A:CYS176 4.0 20.2 1.0
NE2 A:HIS179 4.1 18.9 1.0
CD2 A:HIS179 4.2 17.6 1.0
CA A:CYS176 4.3 19.2 1.0
N A:TYR239 4.3 15.8 1.0
N A:HIS179 4.3 20.5 1.0
CA A:HIS179 4.5 20.2 1.0
CA A:CYS242 4.6 22.1 1.0
C A:CYS238 4.6 19.7 1.0
O A:HOH581 4.7 22.1 1.0
O A:MET237 4.7 17.8 1.0
C A:CYS176 5.0 19.4 1.0

Zinc binding site 2 out of 2 in 6si4

Go back to Zinc Binding Sites List in 6si4
Zinc binding site 2 out of 2 in the P53 Cancer Mutant Y220S 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 Y220S in Complex with Small-Molecule Stabilizer PK9323 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:18.4
occ:1.00
ND1 B:HIS179 2.0 17.5 1.0
SG B:CYS176 2.3 18.9 1.0
SG B:CYS238 2.3 18.2 1.0
SG B:CYS242 2.4 22.4 1.0
CE1 B:HIS179 2.9 20.9 1.0
CG B:HIS179 3.0 19.5 1.0
CB B:CYS242 3.1 16.6 1.0
CB B:CYS176 3.3 14.8 1.0
CB B:CYS238 3.4 21.3 1.0
CB B:HIS179 3.5 15.4 1.0
CA B:CYS238 3.9 18.4 1.0
N B:CYS176 4.0 19.4 1.0
NE2 B:HIS179 4.0 21.5 1.0
CD2 B:HIS179 4.1 17.6 1.0
CA B:CYS176 4.3 15.8 1.0
N B:HIS179 4.4 21.0 1.0
N B:TYR239 4.4 19.8 1.0
CA B:HIS179 4.6 20.0 1.0
CA B:CYS242 4.6 18.2 1.0
O B:HOH634 4.6 21.5 1.0
O B:MET237 4.6 17.7 1.0
C B:CYS238 4.7 20.8 1.0
C B:CYS176 5.0 17.8 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 12:48:23 2020

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