Zinc in PDB 4ibt: Human P53 Core Domain with Hot Spot Mutation R273H and Second-Site Suppressor Mutation T284R

The structure of Human P53 Core Domain with Hot Spot Mutation R273H and Second-Site Suppressor Mutation T284R, PDB code: 4ibt was solved by Y.Diskin-Posner, A.Eldar, H.Rozenberg, Z.Shakked, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.88 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.928, 70.211, 84.010, 90.00, 90.05, 90.00
R / Rfree (%)	17 / 18.2

The binding sites of Zinc atom in the Human P53 Core Domain with Hot Spot Mutation R273H and Second-Site Suppressor Mutation T284R (pdb code 4ibt). 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 R273H and Second-Site Suppressor Mutation T284R, PDB code: 4ibt:
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 R273H 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 R273H and Second-Site Suppressor Mutation T284R within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:21.8 occ:1.00 ND1 A:HIS179 2.0 28.4 1.0 SG A:CYS176 2.4 22.0 1.0 SG A:CYS238 2.4 20.6 1.0 SG A:CYS242 2.5 26.4 1.0 CE1 A:HIS179 2.9 28.9 1.0 CB A:CYS242 3.1 26.1 1.0 CG A:HIS179 3.1 28.5 1.0 CB A:CYS238 3.5 17.8 1.0 CB A:CYS176 3.5 22.3 1.0 CB A:HIS179 3.5 27.5 1.0 CA A:CYS238 3.9 15.8 1.0 N A:CYS176 4.0 20.1 1.0 NE2 A:HIS179 4.1 28.9 1.0 CD2 A:HIS179 4.2 27.9 1.0 CA A:CYS176 4.3 23.1 1.0 N A:ASN239 4.4 18.4 1.0 CA A:CYS242 4.5 29.5 1.0 O A:HOH465 4.5 18.5 1.0 N A:HIS179 4.5 27.3 1.0 O A:MET237 4.6 15.1 1.0 CA A:HIS179 4.7 28.6 1.0 C A:CYS238 4.7 16.7 1.0 O A:CYS176 4.9 27.3 1.0 C A:CYS176 5.0 27.1 1.0

Zinc binding site 2 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273H 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 R273H and Second-Site Suppressor Mutation T284R within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:22.2 occ:1.00 ND1 B:HIS179 2.1 15.6 1.0 SG B:CYS176 2.4 20.3 1.0 SG B:CYS242 2.4 20.2 1.0 SG B:CYS238 2.5 17.4 1.0 CB B:CYS242 2.9 15.6 1.0 CE1 B:HIS179 3.0 19.5 1.0 CG B:HIS179 3.2 18.1 1.0 CB B:CYS176 3.3 17.8 1.0 CB B:CYS238 3.5 18.2 1.0 CB B:HIS179 3.6 18.8 1.0 N B:CYS176 3.9 19.0 1.0 CA B:CYS238 4.0 17.2 1.0 O A:HOH459 4.1 20.4 1.0 NE2 B:HIS179 4.1 20.2 1.0 CA B:CYS176 4.2 20.1 1.0 CD2 B:HIS179 4.2 18.7 1.0 O B:HOH446 4.3 19.4 1.0 CA B:CYS242 4.3 23.3 1.0 N B:ASN239 4.5 18.3 1.0 N B:HIS179 4.6 22.2 1.0 CA B:HIS179 4.7 20.6 1.0 C B:CYS238 4.8 18.1 1.0 O B:MET237 4.8 17.2 1.0 O B:ASN239 4.9 16.6 1.0 O B:CYS176 4.9 19.6 1.0 C B:CYS176 5.0 20.0 1.0

Zinc binding site 3 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273H 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 R273H and Second-Site Suppressor Mutation T284R within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:23.8 occ:1.00 ND1 C:HIS179 2.0 25.5 1.0 SG C:CYS242 2.4 27.3 1.0 SG C:CYS176 2.4 21.1 1.0 SG C:CYS238 2.4 21.6 1.0 CE1 C:HIS179 2.9 26.6 1.0 CB C:CYS242 3.0 24.0 1.0 CG C:HIS179 3.1 23.9 1.0 CB C:CYS238 3.5 24.9 1.0 CB C:CYS176 3.5 21.4 1.0 CB C:HIS179 3.6 22.8 1.0 N C:CYS176 3.9 18.6 1.0 CA C:CYS238 4.0 21.4 1.0 NE2 C:HIS179 4.0 25.4 1.0 CD2 C:HIS179 4.2 24.2 1.0 CA C:CYS176 4.3 19.6 1.0 N C:ASN239 4.4 22.7 1.0 CA C:CYS242 4.4 23.7 1.0 O C:HOH456 4.5 21.0 1.0 O C:HOH628 4.6 30.5 1.0 N C:HIS179 4.7 21.3 1.0 C C:CYS238 4.7 22.5 1.0 CA C:HIS179 4.7 22.7 1.0 O C:MET237 4.8 17.6 1.0 O C:CYS176 4.8 20.3 1.0 O C:ASN239 4.9 20.2 1.0 C C:CYS176 5.0 21.0 1.0

Zinc binding site 4 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273H 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 R273H and Second-Site Suppressor Mutation T284R within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:19.5 occ:1.00 ND1 D:HIS179 2.0 16.3 1.0 SG D:CYS176 2.4 21.1 1.0 SG D:CYS238 2.4 19.9 1.0 SG D:CYS242 2.4 20.8 1.0 CE1 D:HIS179 3.0 19.9 1.0 CB D:CYS242 3.0 17.5 1.0 CG D:HIS179 3.1 21.0 1.0 CB D:CYS238 3.4 21.6 1.0 CB D:CYS176 3.4 18.9 1.0 CB D:HIS179 3.5 17.4 1.0 N D:CYS176 3.9 17.9 1.0 CA D:CYS238 4.0 19.7 1.0 NE2 D:HIS179 4.1 20.6 1.0 CD2 D:HIS179 4.2 21.0 1.0 CA D:CYS176 4.2 18.4 1.0 O D:HOH425 4.3 16.9 1.0 CA D:CYS242 4.4 18.4 1.0 N D:HIS179 4.6 17.9 1.0 N D:ASN239 4.6 16.4 1.0 CA D:HIS179 4.6 16.9 1.0 O D:MET237 4.7 14.5 1.0 C D:CYS238 4.8 16.4 1.0 O D:CYS176 4.9 17.6 1.0 C D:CYS176 4.9 18.7 1.0 O D:ASN239 5.0 18.9 1.0 C D:ARG175 5.0 18.3 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