Zinc in PDB 4iby: Human P53 Core Domain with Hot Spot Mutation R273H and Second-Site Suppressor Mutation S240R

The structure of Human P53 Core Domain with Hot Spot Mutation R273H and Second-Site Suppressor Mutation S240R, PDB code: 4iby 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)	21.78 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.524, 69.212, 67.195, 90.00, 96.61, 90.00
R / Rfree (%)	16.9 / 20

The binding sites of Zinc atom in the Human P53 Core Domain with Hot Spot Mutation R273H and Second-Site Suppressor Mutation S240R (pdb code 4iby). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human P53 Core Domain with Hot Spot Mutation R273H and Second-Site Suppressor Mutation S240R, PDB code: 4iby:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human P53 Core Domain with Hot Spot Mutation R273H and Second-Site Suppressor Mutation S240R


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 S240R within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:8.0 occ:1.00 ND1 A:HIS179 2.1 10.6 1.0 SG A:CYS242 2.3 8.2 1.0 SG A:CYS176 2.3 7.7 1.0 SG A:CYS238 2.3 7.0 1.0 CE1 A:HIS179 3.0 11.3 1.0 CG A:HIS179 3.1 10.8 1.0 CB A:CYS242 3.2 9.9 1.0 CB A:CYS238 3.3 6.8 1.0 CB A:CYS176 3.4 7.3 1.0 CB A:HIS179 3.5 10.2 1.0 CA A:CYS238 3.8 5.6 1.0 N A:CYS176 4.0 7.8 1.0 NE2 A:HIS179 4.2 14.3 1.0 CD2 A:HIS179 4.2 13.8 1.0 CA A:CYS176 4.3 7.2 1.0 O A:MET237 4.4 8.2 1.0 N A:HIS179 4.4 10.8 1.0 CA A:CYS242 4.4 13.2 1.0 CA A:HIS179 4.6 10.9 1.0 O A:HOH658 4.6 34.0 1.0 N A:ASN239 4.6 7.8 1.0 C A:CYS238 4.7 6.1 1.0 O A:HOH437 4.8 9.1 1.0 N A:CYS238 4.8 6.8 1.0 O A:CYS176 4.9 7.8 1.0 C A:CYS176 4.9 7.9 1.0

Zinc binding site 2 out of 2 in the Human P53 Core Domain with Hot Spot Mutation R273H and Second-Site Suppressor Mutation S240R


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 S240R within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:11.0 occ:1.00 ND1 B:HIS179 2.1 17.7 1.0 SG B:CYS242 2.2 12.5 1.0 SG B:CYS176 2.3 11.0 1.0 SG B:CYS238 2.3 10.5 1.0 CE1 B:HIS179 3.0 17.4 1.0 CG B:HIS179 3.1 20.2 1.0 CB B:CYS242 3.2 12.5 1.0 CB B:CYS238 3.3 11.2 1.0 CB B:CYS176 3.4 13.3 1.0 CB B:HIS179 3.5 15.2 1.0 CA B:CYS238 3.8 7.6 1.0 N B:CYS176 3.9 8.8 1.0 O B:HOH555 4.1 19.7 1.0 NE2 B:HIS179 4.2 18.7 1.0 CA B:CYS176 4.2 10.3 1.0 CD2 B:HIS179 4.2 21.1 1.0 O B:MET237 4.3 8.5 1.0 CA B:CYS242 4.4 12.2 1.0 N B:HIS179 4.6 17.8 1.0 CA B:HIS179 4.7 16.9 1.0 N B:ASN239 4.8 8.8 1.0 N B:CYS238 4.8 7.5 1.0 O B:CYS176 4.8 10.9 1.0 O B:HOH436 4.8 12.9 1.0 C B:CYS238 4.8 7.7 1.0 O B:HOH546 4.9 23.6 1.0 C B:CYS176 4.9 9.5 1.0 O B:HOH524 4.9 19.1 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