Zinc in PDB 3d07: Human P53 Core Domain with Hot Spot Mutation R249S (III)

The structure of Human P53 Core Domain with Hot Spot Mutation R249S (III), PDB code: 3d07 was solved by O.Suad, H.Rozenberg, Z.Shakked, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.24 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.224, 68.477, 57.832, 90.00, 101.34, 90.00
R / Rfree (%)	16.3 / 25.6

The binding sites of Zinc atom in the Human P53 Core Domain with Hot Spot Mutation R249S (III) (pdb code 3d07). 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 R249S (III), PDB code: 3d07:
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 R249S (III)


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 R249S (III) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:25.6 occ:1.00 SG A:CYS242 2.1 17.0 1.0 ND1 A:HIS179 2.2 18.0 1.0 SG A:CYS176 2.3 22.8 1.0 SG A:CYS238 2.4 22.8 1.0 CB A:CYS242 2.8 31.0 1.0 CG A:HIS179 3.2 22.4 1.0 CE1 A:HIS179 3.2 27.1 1.0 CB A:CYS238 3.2 7.9 1.0 CB A:HIS179 3.4 24.4 1.0 CB A:CYS176 3.5 19.8 1.0 CA A:CYS238 3.7 11.9 1.0 N A:CYS176 4.0 19.3 1.0 CA A:CYS242 4.2 29.7 1.0 CA A:CYS176 4.3 22.8 1.0 N A:HIS179 4.3 35.0 1.0 CD2 A:HIS179 4.3 24.0 1.0 NE2 A:HIS179 4.3 25.8 1.0 N A:ASN239 4.3 12.4 1.0 CA A:HIS179 4.5 29.4 1.0 C A:CYS238 4.6 13.2 1.0 O A:MET237 4.8 11.5 1.0 O A:CYS176 4.8 24.3 1.0 C A:CYS176 4.9 26.5 1.0 N A:CYS238 4.9 11.8 1.0 C A:CYS242 5.0 33.9 1.0

Zinc binding site 2 out of 2 in the Human P53 Core Domain with Hot Spot Mutation R249S (III)


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 R249S (III) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:10.8 occ:1.00 ND1 B:HIS179 2.1 3.5 1.0 SG B:CYS238 2.3 5.7 1.0 SG B:CYS242 2.3 14.1 1.0 SG B:CYS176 2.3 5.3 1.0 CE1 B:HIS179 3.1 2.0 1.0 CG B:HIS179 3.1 2.0 1.0 CB B:CYS242 3.2 20.5 1.0 CB B:CYS238 3.4 7.6 1.0 CB B:CYS176 3.4 2.0 1.0 CB B:HIS179 3.4 4.2 1.0 CA B:CYS238 3.8 8.7 1.0 N B:ASN239 3.9 15.8 1.0 N B:CYS176 3.9 3.8 1.0 NE2 B:HIS179 4.2 3.6 1.0 CD2 B:HIS179 4.2 5.7 1.0 CA B:CYS176 4.3 4.0 1.0 C B:CYS238 4.4 12.3 1.0 N B:HIS179 4.5 8.2 1.0 CA B:CYS242 4.6 19.8 1.0 CA B:HIS179 4.6 6.0 1.0 O B:ASN239 4.8 17.6 1.0 O B:CYS176 4.9 7.9 1.0 C B:CYS176 4.9 4.7 1.0 CA B:ASN239 5.0 19.1 1.0

O.Suad, H.Rozenberg, R.Brosh, Y.Diskin-Posner, N.Kessler, L.J.W.Shimon, F.Frolow, A.Liran, V.Rotter, Z.Shakked. Structural Basis of Restoring Sequence-Specific Dna Binding and Transactivation to Mutant P53 By Suppressor Mutations J.Mol.Biol. V. 385 249 2009.
ISSN: ISSN 0022-2836
PubMed: 18996393
DOI: 10.1016/J.JMB.2008.10.063