Zinc in PDB 4ibq: Human P53 Core Domain with Hot Spot Mutation R273C

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

Resolution Low / High (Å)	29.14 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.731, 69.719, 83.510, 90.00, 90.10, 90.00
R / Rfree (%)	13.4 / 16.3

The binding sites of Zinc atom in the Human P53 Core Domain with Hot Spot Mutation R273C (pdb code 4ibq). 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, PDB code: 4ibq:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:19.9 occ:1.00 CD2 A:HIS179 2.1 15.3 1.0 SG A:CYS176 2.4 18.7 1.0 SG A:CYS238 2.4 14.6 0.5 SG A:CYS238 2.5 8.7 0.5 SG A:CYS242 2.6 24.9 1.0 CG A:HIS179 2.9 14.5 1.0 CB A:CYS242 3.1 11.6 1.0 NE2 A:HIS179 3.2 22.2 1.0 CB A:HIS179 3.3 18.1 1.0 CB A:CYS176 3.3 16.4 1.0 CB A:CYS238 3.6 16.7 0.5 CB A:CYS238 3.7 17.2 0.5 CA A:CYS238 3.9 16.2 0.5 CA A:CYS238 3.9 16.2 0.5 N A:CYS176 4.0 11.8 1.0 ND1 A:HIS179 4.2 15.7 1.0 CA A:CYS176 4.2 13.6 1.0 CE1 A:HIS179 4.3 18.0 1.0 N A:ASN239 4.3 17.2 1.0 N A:HIS179 4.4 20.5 1.0 CA A:HIS179 4.5 20.7 1.0 CA A:CYS242 4.6 15.1 1.0 C A:CYS238 4.6 15.8 0.5 C A:CYS238 4.6 15.8 0.5 O A:HOH516 4.7 17.4 1.0 O A:MET237 4.8 15.2 1.0 C A:CYS176 4.9 16.6 1.0 O A:CYS176 4.9 16.9 1.0 O A:HOH483 5.0 29.2 0.3

Zinc binding site 2 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273C


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:17.5 occ:1.00 ND1 B:HIS179 1.8 5.9 1.0 SG B:CYS242 2.3 20.2 1.0 SG B:CYS176 2.4 19.4 1.0 SG B:CYS238 2.4 20.3 1.0 CE1 B:HIS179 2.6 18.3 1.0 CG B:HIS179 3.0 15.1 1.0 CB B:CYS242 3.0 19.1 1.0 CB B:CYS176 3.4 13.6 1.0 CB B:HIS179 3.5 16.9 1.0 CB B:CYS238 3.6 22.6 1.0 NE2 B:HIS179 3.8 16.7 1.0 CA B:CYS238 3.8 16.4 1.0 CD2 B:HIS179 4.0 17.2 1.0 N B:CYS176 4.0 15.9 1.0 N B:ASN239 4.1 21.7 1.0 O A:HOH507 4.2 23.4 1.0 CA B:CYS176 4.3 16.9 1.0 C B:CYS238 4.4 18.3 1.0 CA B:CYS242 4.5 21.7 1.0 N B:HIS179 4.5 18.8 1.0 OG A:SER106 4.5 31.4 1.0 O B:HOH520 4.6 29.2 1.0 CA B:HIS179 4.6 17.8 1.0 O B:ASN239 4.7 23.4 1.0 CD2 B:HIS178 4.9 20.2 1.0

Zinc binding site 3 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273C


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:21.3 occ:1.00 ND1 C:HIS179 1.9 13.0 1.0 SG C:CYS176 2.4 22.4 1.0 SG C:CYS242 2.4 24.2 1.0 SG C:CYS238 2.4 24.3 0.5 SG C:CYS238 2.5 22.3 0.6 CE1 C:HIS179 2.9 17.1 1.0 CG C:HIS179 2.9 12.2 1.0 CB C:CYS242 3.2 14.8 1.0 CB C:HIS179 3.3 15.9 1.0 CB C:CYS176 3.5 14.1 1.0 CB C:CYS238 3.6 16.1 0.6 CB C:CYS238 3.7 16.5 0.5 CA C:CYS238 3.9 13.8 0.6 CA C:CYS238 4.0 14.3 0.5 NE2 C:HIS179 4.0 16.4 1.0 N C:CYS176 4.0 18.6 1.0 CD2 C:HIS179 4.1 12.9 1.0 CA C:CYS176 4.3 17.0 1.0 N C:ASN239 4.3 20.0 1.0 N C:HIS179 4.4 15.1 1.0 CA C:HIS179 4.4 15.7 1.0 CA C:CYS242 4.6 20.7 1.0 C C:CYS238 4.7 15.9 0.5 C C:CYS238 4.7 15.9 0.6 O C:MET237 4.7 10.8 1.0 O C:CYS176 4.8 16.3 1.0 CD2 C:HIS178 4.9 18.7 1.0 C C:CYS176 4.9 15.7 1.0

Zinc binding site 4 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R273C


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 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:20.7 occ:1.00 ND1 D:HIS179 2.0 14.7 1.0 SG D:CYS242 2.3 26.8 1.0 SG D:CYS238 2.3 23.4 1.0 SG D:CYS176 2.4 18.7 1.0 CE1 D:HIS179 2.9 16.9 1.0 CG D:HIS179 3.1 15.9 1.0 CB D:CYS242 3.2 21.8 1.0 CB D:HIS179 3.5 19.7 1.0 CB D:CYS176 3.5 13.5 1.0 CB D:CYS238 3.8 23.0 1.0 N D:CYS176 4.0 16.9 1.0 NE2 D:HIS179 4.1 15.9 1.0 CA D:CYS238 4.1 18.8 1.0 CD2 D:HIS179 4.2 13.5 1.0 N D:ASN239 4.3 22.5 1.0 CA D:CYS176 4.4 16.9 1.0 N D:HIS179 4.4 20.4 1.0 CA D:CYS242 4.6 23.0 1.0 CA D:HIS179 4.6 17.2 1.0 C D:CYS238 4.7 20.1 1.0 O D:HOH546 4.8 21.1 1.0 O D:ASN239 4.8 22.0 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