Zinc in PDB 8dc6: Crystal Structure of P53 Y220C Covalently Bound to Indole KG6

Protein crystallography data

The structure of Crystal Structure of P53 Y220C Covalently Bound to Indole KG6, PDB code: 8dc6 was solved by K.Z.Guiley, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.29 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 91.04, 105.75, 105.75, 90, 90, 90
R / Rfree (%) 18.1 / 20.2

Other elements in 8dc6:

The structure of Crystal Structure of P53 Y220C Covalently Bound to Indole KG6 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of P53 Y220C Covalently Bound to Indole KG6 (pdb code 8dc6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of P53 Y220C Covalently Bound to Indole KG6, PDB code: 8dc6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8dc6

Go back to Zinc Binding Sites List in 8dc6
Zinc binding site 1 out of 4 in the Crystal Structure of P53 Y220C Covalently Bound to Indole KG6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of P53 Y220C Covalently Bound to Indole KG6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:11.7
occ:1.00
 ND1 A:HIS179 2.1 11.3 1.0
SG A:CYS176 2.3 59.4 1.0
SG A:CYS242 2.3 11.9 1.0
SG A:CYS238 2.3 11.4 1.0
CE1 A:HIS179 3.0 10.3 1.0
CG A:HIS179 3.1 8.5 1.0
CB A:CYS242 3.2 10.9 1.0
CB A:CYS238 3.3 9.0 1.0
CB A:CYS176 3.5 13.1 1.0
CB A:HIS179 3.5 8.8 1.0
CA A:CYS238 3.9 9.8 1.0
N A:CYS176 4.0 11.9 1.0
NE2 A:HIS179 4.2 12.3 1.0
CD2 A:HIS179 4.2 13.4 1.0
CA A:CYS176 4.3 11.9 1.0
CD2 C:LEU188 4.4 14.6 1.0
O A:HOH621 4.5 16.3 1.0
CA A:CYS242 4.6 12.1 1.0
N A:TYR239 4.6 9.7 1.0
N A:HIS179 4.6 12.4 1.0
O A:HOH594 4.7 13.2 1.0
CA A:HIS179 4.7 10.9 1.0
O A:MET237 4.7 12.1 1.0
C A:CYS238 4.8 10.2 1.0
O A:CYS176 4.9 12.2 1.0
C A:CYS176 5.0 12.4 1.0

Zinc binding site 2 out of 4 in 8dc6

Go back to Zinc Binding Sites List in 8dc6
Zinc binding site 2 out of 4 in the Crystal Structure of P53 Y220C Covalently Bound to Indole KG6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of P53 Y220C Covalently Bound to Indole KG6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:12.5
occ:1.00
 ND1 B:HIS179 2.1 9.8 1.0
SG B:CYS238 2.3 11.4 1.0
SG B:CYS176 2.3 12.0 1.0
SG B:CYS242 2.3 12.9 1.0
CE1 B:HIS179 3.0 11.3 1.0
CG B:HIS179 3.1 10.0 1.0
CB B:CYS242 3.2 12.0 1.0
CB B:CYS238 3.3 8.7 1.0
CB B:CYS176 3.5 11.4 1.0
CB B:HIS179 3.5 11.1 1.0
CA B:CYS238 3.9 8.7 1.0
N B:CYS176 3.9 11.5 1.0
NE2 B:HIS179 4.1 12.3 1.0
CD2 B:HIS179 4.2 13.6 1.0
CA B:CYS176 4.3 13.0 1.0
O B:HOH604 4.5 15.6 1.0
CA B:CYS242 4.6 14.3 1.0
N B:TYR239 4.6 9.3 1.0
N B:HIS179 4.6 12.2 1.0
O B:MET237 4.7 11.3 1.0
CA B:HIS179 4.7 12.0 1.0
O B:HOH587 4.7 14.4 1.0
C B:CYS238 4.8 8.6 1.0
O B:CYS176 4.9 12.8 1.0
C B:CYS176 4.9 14.1 1.0

Zinc binding site 3 out of 4 in 8dc6

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Zinc binding site 3 out of 4 in the Crystal Structure of P53 Y220C Covalently Bound to Indole KG6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of P53 Y220C Covalently Bound to Indole KG6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:11.5
occ:1.00
 ND1 C:HIS179 2.1 10.3 1.0
SG C:CYS176 2.3 11.7 1.0
SG C:CYS242 2.3 12.1 1.0
SG C:CYS238 2.3 11.0 1.0
CE1 C:HIS179 3.0 11.6 1.0
CG C:HIS179 3.1 8.8 1.0
CB C:CYS242 3.2 12.6 1.0
CB C:CYS238 3.3 10.6 1.0
CB C:CYS176 3.4 12.5 1.0
CB C:HIS179 3.5 9.7 1.0
CA C:CYS238 3.9 9.4 1.0
N C:CYS176 3.9 9.6 1.0
NE2 C:HIS179 4.2 13.0 1.0
CD2 C:HIS179 4.2 12.0 1.0
CA C:CYS176 4.3 11.8 1.0
O C:HOH502 4.6 15.4 1.0
N C:TYR239 4.6 8.7 1.0
CA C:CYS242 4.6 10.5 1.0
N C:HIS179 4.6 10.0 1.0
CA C:HIS179 4.7 10.5 1.0
O C:MET237 4.7 10.5 1.0
O C:HOH583 4.7 12.5 1.0
C C:CYS238 4.8 9.5 1.0
O C:CYS176 4.9 12.1 1.0
C C:CYS176 5.0 13.1 1.0

Zinc binding site 4 out of 4 in 8dc6

Go back to Zinc Binding Sites List in 8dc6
Zinc binding site 4 out of 4 in the Crystal Structure of P53 Y220C Covalently Bound to Indole KG6


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of P53 Y220C Covalently Bound to Indole KG6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:12.7
occ:1.00
 ND1 D:HIS179 2.1 10.0 1.0
SG D:CYS238 2.3 11.5 1.0
SG D:CYS242 2.3 13.8 1.0
SG D:CYS176 2.3 12.7 1.0
CE1 D:HIS179 3.0 11.3 1.0
CG D:HIS179 3.1 9.8 1.0
CB D:CYS242 3.2 11.8 1.0
CB D:CYS238 3.3 11.0 1.0
CB D:CYS176 3.5 13.1 1.0
CB D:HIS179 3.5 9.2 1.0
CA D:CYS238 3.9 9.5 1.0
N D:CYS176 4.0 12.1 1.0
NE2 D:HIS179 4.2 12.7 1.0
CD2 D:HIS179 4.2 14.3 1.0
CA D:CYS176 4.3 13.5 1.0
O D:HOH602 4.5 18.2 1.0
CD2 A:LEU188 4.6 14.9 1.0
N D:TYR239 4.6 10.1 1.0
CA D:CYS242 4.6 13.7 1.0
N D:HIS179 4.6 12.6 1.0
O D:MET237 4.7 11.7 1.0
CA D:HIS179 4.7 12.2 1.0
O D:HOH572 4.8 14.2 1.0
C D:CYS238 4.8 10.9 1.0
O D:CYS176 4.9 14.0 1.0
C D:CYS176 5.0 12.9 1.0

Reference:

K.Z.Guiley, K.M.Shokat. A Small Molecule Reacts with the P53 Somatic Mutant Y220C to Rescue Wild-Type Thermal Stability. Cancer Discov 2022.
ISSN: ESSN 2159-8290
PubMed: 36197521
DOI: 10.1158/2159-8290.CD-22-0381
Page generated: Wed Oct 30 19:09:54 2024

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