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

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

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

Zinc

(Zn)

4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of P53 Y220C Covalently Bound to Indole KG6, PDB code: 8dc6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of P53 Y220C Covalently Bound to Indole KG6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 B:Mg406 b:25.8 occ:1.00 O B:HOH634 2.0 27.3 1.0 O B:HOH545 2.2 29.8 1.0 O B:HOH585 2.2 29.5 1.0 O B:HOH513 2.2 25.6 1.0 O B:HOH576 2.4 20.6 1.0 OD2 B:ASP268 4.0 15.3 1.0 OD1 B:ASP268 4.0 17.8 1.0 OH B:TYR126 4.0 18.6 1.0 OD1 B:ASN131 4.1 15.7 1.0 CG B:ASP268 4.4 16.4 1.0 CG B:ASN131 4.5 13.9 1.0 O B:LEU111 4.7 15.5 1.0 ND2 B:ASN131 4.8 15.8 1.0 O B:SER269 5.0 13.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of P53 Y220C Covalently Bound to Indole KG6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 C:Mg405 b:36.3 occ:1.00 O C:HOH631 1.9 33.2 1.0 O C:HOH522 2.1 32.0 1.0 O C:HOH568 2.5 24.6 1.0 OH C:TYR126 3.9 19.1 1.0 OD1 C:ASN131 4.1 17.5 1.0 O C:HOH581 4.2 33.9 1.0 OD1 C:ASP268 4.3 16.5 1.0 OD2 C:ASP268 4.4 18.4 1.0 O C:LEU111 4.6 22.4 1.0 CG C:ASN131 4.7 15.0 1.0 CG C:ASP268 4.8 18.8 1.0

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