Zinc in PDB 4ibz: Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R

The structure of Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R, PDB code: 4ibz was solved by A.Eldar, H.Rozenberg, Y.Diskin-Posner, Z.Shakked, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.69 / 1.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.742, 70.413, 84.585, 90.00, 89.92, 90.00
R / Rfree (%)	17.9 / 23.3

The binding sites of Zinc atom in the Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R (pdb code 4ibz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R, PDB code: 4ibz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:31.1 occ:1.00 ND1 A:HIS179 2.0 35.7 1.0 SG A:CYS242 2.3 36.4 1.0 SG A:CYS238 2.3 38.2 1.0 SG A:CYS176 2.4 32.5 1.0 CE1 A:HIS179 2.9 37.5 1.0 CG A:HIS179 3.1 34.3 1.0 CB A:CYS242 3.1 35.2 1.0 CB A:CYS176 3.5 34.9 1.0 CB A:HIS179 3.5 34.0 1.0 CB A:CYS238 3.7 31.6 1.0 CA A:CYS238 3.8 27.4 1.0 NE2 A:HIS179 4.0 38.3 1.0 N A:CYS176 4.0 32.5 1.0 CD2 A:HIS179 4.1 36.1 1.0 N A:ASN239 4.1 18.7 1.0 CA A:CYS176 4.3 35.9 1.0 C A:CYS238 4.5 22.6 1.0 CA A:CYS242 4.5 39.1 1.0 N A:HIS179 4.6 43.8 1.0 O A:HOH441 4.6 34.8 1.0 CA A:HIS179 4.7 39.1 1.0 O A:MET237 4.8 24.1 0.1 O A:MET237 4.8 24.4 0.9 O A:ASN239 4.9 35.5 1.0 O A:CYS176 4.9 36.9 1.0 C A:CYS176 5.0 37.6 1.0

Zinc binding site 2 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:33.8 occ:1.00 ND1 B:HIS179 1.9 28.2 1.0 SG B:CYS242 2.2 38.8 1.0 SG B:CYS176 2.4 36.2 1.0 SG B:CYS238 2.5 53.6 1.0 CE1 B:HIS179 2.8 31.9 1.0 CG B:HIS179 3.0 31.9 1.0 CB B:CYS242 3.1 32.4 1.0 CB B:CYS176 3.4 31.8 1.0 CB B:HIS179 3.4 28.3 1.0 CB B:CYS238 3.7 41.5 1.0 CA B:CYS238 3.8 33.5 1.0 NE2 B:HIS179 3.9 33.7 1.0 N B:CYS176 4.0 32.6 1.0 CD2 B:HIS179 4.0 32.9 1.0 O A:HOH429 4.2 28.8 1.0 CA B:CYS176 4.3 34.1 1.0 N B:ASN239 4.3 36.3 1.0 N B:HIS179 4.3 32.9 1.0 CA B:CYS242 4.5 41.8 1.0 CA B:HIS179 4.5 32.7 1.0 C B:CYS238 4.5 36.0 1.0 O B:MET237 4.8 27.0 1.0 O B:ASN239 4.9 35.0 1.0 O B:CYS176 4.9 29.8 1.0 C B:CYS176 4.9 32.6 1.0

Zinc binding site 3 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:47.9 occ:1.00 ND1 C:HIS179 2.0 35.9 1.0 CE1 C:HIS179 2.3 42.6 1.0 SG C:CYS176 2.4 51.9 1.0 SG C:CYS242 2.4 47.2 1.0 SG C:CYS238 2.5 48.0 1.0 CB C:CYS242 3.1 39.2 1.0 CG C:HIS179 3.3 48.0 1.0 CB C:CYS176 3.5 43.2 1.0 NE2 C:HIS179 3.5 44.9 1.0 CB C:CYS238 3.9 34.7 1.0 CD2 C:HIS179 4.0 47.0 1.0 CB C:HIS179 4.1 46.7 1.0 CA C:CYS238 4.1 30.3 1.0 N C:CYS176 4.2 39.0 1.0 N C:ASN239 4.3 27.9 1.0 CA C:CYS176 4.4 41.5 1.0 CA C:CYS242 4.5 43.9 1.0 C C:CYS238 4.7 30.1 1.0 O C:ASN239 4.8 32.8 1.0 N C:HIS179 4.8 47.0 1.0

Zinc binding site 4 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:31.4 occ:1.00 ND1 D:HIS179 1.9 20.4 1.0 SG D:CYS176 2.3 27.5 1.0 SG D:CYS242 2.4 35.5 1.0 SG D:CYS238 2.4 34.6 1.0 CE1 D:HIS179 2.7 24.9 1.0 CG D:HIS179 3.0 26.1 1.0 CB D:CYS242 3.2 33.8 1.0 CB D:HIS179 3.5 27.7 1.0 CB D:CYS176 3.5 27.3 1.0 CB D:CYS238 3.7 32.1 1.0 NE2 D:HIS179 3.9 28.8 1.0 CA D:CYS238 3.9 25.7 1.0 N D:CYS176 4.0 25.1 1.0 CD2 D:HIS179 4.0 26.6 1.0 N D:ASN239 4.2 31.9 1.0 CA D:CYS176 4.3 26.6 1.0 N D:HIS179 4.4 27.1 1.0 C D:CYS238 4.5 29.4 1.0 CA D:HIS179 4.6 29.5 1.0 CA D:CYS242 4.6 41.2 1.0 O D:CYS176 4.9 26.1 1.0 O D:ASN239 4.9 36.5 1.0 O D:MET237 5.0 24.9 1.0 C D:CYS176 5.0 24.7 1.0

A.Eldar, H.Rozenberg, Y.Diskin-Posner, R.Rohs, Z.Shakked. Structural Studies of P53 Inactivation By Dna-Contact Mutations and Its Rescue By Suppressor Mutations Via Alternative Protein-Dna Interactions. Nucleic Acids Res. V. 41 8748 2013.
ISSN: ISSN 0305-1048
PubMed: 23863845
DOI: 10.1093/NAR/GKT630