Zinc in PDB 4ibu: Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R in Sequence-Specific Complex with Dna

The structure of Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R in Sequence-Specific Complex with Dna, PDB code: 4ibu 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)	30.12 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	54.537, 58.158, 77.968, 82.96, 87.78, 73.57
R / Rfree (%)	16.3 / 19.7

The binding sites of Zinc atom in the Human P53 Core Domain with Hot Spot Mutation R273C and Second-Site Suppressor Mutation T284R in Sequence-Specific Complex with Dna (pdb code 4ibu). 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 in Sequence-Specific Complex with Dna, PDB code: 4ibu:
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 in Sequence-Specific Complex with Dna


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 in Sequence-Specific Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.6 occ:1.00 ND1 A:HIS179 2.0 18.5 1.0 SG A:CYS238 2.3 18.0 1.0 SG A:CYS176 2.3 17.4 1.0 SG A:CYS242 2.3 20.4 1.0 CE1 A:HIS179 3.0 23.2 1.0 CG A:HIS179 3.1 17.0 1.0 CB A:CYS242 3.1 22.7 1.0 CB A:CYS176 3.4 18.8 1.0 CB A:HIS179 3.5 16.5 1.0 CB A:CYS238 3.6 15.2 1.0 CA A:CYS238 3.9 11.7 1.0 N A:CYS176 4.1 14.8 1.0 N A:ASN239 4.1 12.0 1.0 NE2 A:HIS179 4.1 21.4 1.0 CD2 A:HIS179 4.2 20.1 1.0 O A:HOH586 4.3 38.6 1.0 CA A:CYS176 4.3 16.1 1.0 N A:HIS179 4.4 19.6 1.0 C A:CYS238 4.5 10.8 1.0 CA A:HIS179 4.6 18.0 1.0 CA A:CYS242 4.6 18.1 1.0 O A:HOH608 4.7 21.2 0.7 O A:ASN239 4.9 13.2 1.0 O A:HOH552 4.9 30.1 1.0 O A:MET237 5.0 13.1 1.0 C A:CYS176 5.0 17.2 1.0 O A:CYS176 5.0 17.0 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 in Sequence-Specific Complex with Dna


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 in Sequence-Specific Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.3 occ:1.00 ND1 B:HIS179 2.1 17.9 1.0 SG B:CYS238 2.3 24.2 1.0 SG B:CYS242 2.3 22.9 1.0 SG B:CYS176 2.4 18.4 1.0 CE1 B:HIS179 3.0 20.2 1.0 CB B:CYS242 3.1 19.3 1.0 CG B:HIS179 3.1 20.4 1.0 CB B:CYS176 3.4 17.4 1.0 CB B:HIS179 3.5 18.8 1.0 CB B:CYS238 3.6 20.7 1.0 CA B:CYS238 3.8 13.2 1.0 N B:ASN239 4.1 13.5 1.0 N B:CYS176 4.1 13.0 1.0 NE2 B:HIS179 4.1 19.9 1.0 CD2 B:HIS179 4.2 19.4 1.0 CA B:CYS176 4.3 16.2 1.0 CE A:MET243 4.3 26.8 0.6 O B:HOH445 4.4 26.6 1.0 N B:HIS179 4.4 20.7 1.0 C B:CYS238 4.4 13.2 1.0 CA B:CYS242 4.5 18.5 1.0 CA B:HIS179 4.6 17.8 1.0 O B:ASN239 4.9 15.6 1.0 O B:MET237 5.0 15.2 1.0 C B:CYS176 5.0 16.2 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 in Sequence-Specific Complex with Dna


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 in Sequence-Specific Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:17.1 occ:1.00 ND1 C:HIS179 2.1 19.6 1.0 SG C:CYS238 2.2 24.0 1.0 SG C:CYS242 2.3 20.7 1.0 SG C:CYS176 2.3 14.9 1.0 CE1 C:HIS179 3.0 24.1 1.0 CB C:CYS242 3.1 14.8 1.0 CG C:HIS179 3.1 17.7 1.0 CB C:CYS176 3.4 16.9 1.0 CB C:HIS179 3.4 15.7 1.0 CB C:CYS238 3.6 18.4 1.0 CA C:CYS238 3.9 13.0 1.0 N C:CYS176 4.0 12.5 1.0 N C:ASN239 4.1 13.2 1.0 NE2 C:HIS179 4.2 19.7 1.0 O C:HOH600 4.2 30.4 1.0 CD2 C:HIS179 4.2 20.3 1.0 CA C:CYS176 4.3 14.7 1.0 N C:HIS179 4.4 19.0 1.0 O C:HOH402 4.4 7.9 0.3 C C:CYS238 4.5 10.3 1.0 CA C:HIS179 4.5 17.6 1.0 CA C:CYS242 4.5 16.3 1.0 O C:HOH604 4.8 33.2 1.0 O C:ASN239 4.9 11.4 1.0 O C:HOH402 4.9 16.4 0.7 C C:CYS176 4.9 15.4 1.0 O C:MET237 4.9 11.4 1.0 O C:CYS176 4.9 16.1 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 in Sequence-Specific Complex with Dna


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 in Sequence-Specific Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:19.1 occ:1.00 ND1 D:HIS179 2.0 18.1 1.0 SG D:CYS242 2.2 23.5 1.0 SG D:CYS238 2.2 25.2 1.0 SG D:CYS176 2.3 19.5 1.0 CE1 D:HIS179 3.0 25.2 1.0 CG D:HIS179 3.1 17.8 1.0 CB D:CYS242 3.1 19.9 1.0 CB D:CYS176 3.4 19.6 1.0 CB D:HIS179 3.4 20.7 1.0 CB D:CYS238 3.6 22.4 1.0 O D:HOH431 3.6 46.9 1.0 CA D:CYS238 3.9 18.3 1.0 N D:CYS176 4.0 17.6 1.0 NE2 D:HIS179 4.1 24.7 1.0 N D:ASN239 4.1 18.4 1.0 CD2 D:HIS179 4.2 28.2 1.0 CA D:CYS176 4.3 19.0 1.0 N D:HIS179 4.4 19.5 1.0 O D:HOH503 4.5 32.5 1.0 C D:CYS238 4.5 16.1 1.0 CA D:CYS242 4.5 21.5 1.0 CA D:HIS179 4.6 22.3 1.0 O D:HOH407 4.9 38.2 1.0 O D:MET237 4.9 16.4 1.0 O D:CYS176 5.0 20.9 1.0 C D:CYS176 5.0 19.6 1.0 O D:ASN239 5.0 18.6 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