Zinc in PDB 8e7b: Crystal Structure of the P53 (Y107H) Core Domain Monoclinic P Form

The structure of Crystal Structure of the P53 (Y107H) Core Domain Monoclinic P Form, PDB code: 8e7b was solved by S.Lovell, L.Liu, K.P.Battaile, S.Miller, J.Karanicolas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.13 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.394, 68.636, 66.951, 90, 96.32, 90
R / Rfree (%)	21.9 / 27.9

The binding sites of Zinc atom in the Crystal Structure of the P53 (Y107H) Core Domain Monoclinic P Form (pdb code 8e7b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the P53 (Y107H) Core Domain Monoclinic P Form, PDB code: 8e7b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the P53 (Y107H) Core Domain Monoclinic P Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the P53 (Y107H) Core Domain Monoclinic P Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:29.0 occ:1.00 ND1 A:HIS179 2.0 32.9 1.0 SG A:CYS238 2.3 41.4 1.0 SG A:CYS242 2.3 31.5 1.0 SG A:CYS176 2.3 31.5 1.0 CE1 A:HIS179 2.9 31.1 1.0 CG A:HIS179 3.0 26.4 1.0 CB A:CYS242 3.3 45.9 1.0 CB A:HIS179 3.4 35.5 1.0 CB A:CYS176 3.6 39.7 1.0 CB A:CYS238 3.7 39.0 1.0 NE2 A:HIS179 4.0 42.8 1.0 CA A:CYS238 4.0 38.9 1.0 CD2 A:HIS179 4.1 30.5 1.0 N A:CYS176 4.1 30.0 1.0 N A:ASN239 4.4 35.8 1.0 CA A:CYS176 4.5 32.0 1.0 N A:HIS179 4.5 39.9 1.0 CA A:HIS179 4.6 36.9 1.0 CA A:CYS242 4.7 46.9 1.0 C A:CYS238 4.7 41.7 1.0 O A:MET237 4.8 25.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the P53 (Y107H) Core Domain Monoclinic P Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the P53 (Y107H) Core Domain Monoclinic P Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:31.0 occ:1.00 ND1 B:HIS179 2.0 24.5 1.0 SG B:CYS238 2.3 25.3 1.0 SG B:CYS176 2.3 29.1 1.0 SG B:CYS242 2.3 30.3 1.0 CE1 B:HIS179 2.9 30.2 1.0 CG B:HIS179 3.0 35.9 1.0 CB B:CYS242 3.1 43.6 1.0 CB B:CYS176 3.3 41.7 1.0 CB B:CYS238 3.4 42.2 1.0 CB B:HIS179 3.4 36.8 1.0 N B:CYS176 3.8 36.4 1.0 CA B:CYS238 3.8 38.7 1.0 NE2 B:HIS179 4.1 34.2 1.0 CD2 B:HIS179 4.1 35.8 1.0 CA B:CYS176 4.1 41.9 1.0 O B:MET237 4.3 23.7 1.0 CA B:CYS242 4.5 47.3 1.0 N B:ASN239 4.5 26.9 1.0 N B:HIS179 4.6 33.5 1.0 CA B:HIS179 4.6 36.5 1.0 C B:CYS238 4.7 32.1 1.0 O B:CYS176 4.8 47.4 1.0 C B:CYS176 4.9 56.8 1.0 N B:CYS238 4.9 31.9 1.0 C B:ARG175 4.9 32.1 1.0

A.Indeglia, J.C.Leung, S.A.Miller, J.I.Leu, J.F.Dougherty, N.L.Clarke, N.A.Kirven, C.Shao, L.Ke, S.Lovell, T.Barnoud, D.Y.Lu, C.Lin, T.Kannan, K.P.Battaile, T.H.L.Yang, I.Batista Oliva, D.T.Claiborne, P.Vogel, L.Liu, Q.Liu, Y.Nefedova, J.Cassel, N.Auslander, A.V.Kossenkov, J.Karanicolas, M.E.Murphy. An African-Specific Variant of TP53 Reveals PADI4 As A Regulator of P53-Mediated Tumor Suppression. Cancer Discov 2023.
ISSN: ESSN 2159-8290
PubMed: 37140445
DOI: 10.1158/2159-8290.CD-22-1315