Zinc in PDB 4hje: Crystal Structure of P53 Core Domain in Complex with Dna

The structure of Crystal Structure of P53 Core Domain in Complex with Dna, PDB code: 4hje was solved by Y.Chen, L.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.66 / 1.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.420, 93.880, 145.634, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.8

The binding sites of Zinc atom in the Crystal Structure of P53 Core Domain in Complex with Dna (pdb code 4hje). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of P53 Core Domain in Complex with Dna, PDB code: 4hje:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of P53 Core Domain in 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 Crystal Structure of P53 Core Domain in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:20.3 occ:1.00 ND1 A:HIS179 2.1 21.3 1.0 SG A:CYS242 2.3 17.9 1.0 SG A:CYS238 2.4 19.8 1.0 SG A:CYS176 2.4 17.8 1.0 CE1 A:HIS179 3.0 20.9 1.0 CB A:CYS242 3.1 18.9 1.0 CG A:HIS179 3.1 23.1 1.0 CB A:CYS238 3.4 19.8 1.0 CB A:CYS176 3.4 21.2 1.0 CB A:HIS179 3.5 15.8 1.0 CA A:CYS238 3.9 16.4 1.0 N A:CYS176 4.0 17.8 1.0 NE2 A:HIS179 4.2 20.4 1.0 CD2 A:HIS179 4.2 23.3 1.0 CA A:CYS176 4.3 19.5 1.0 CE B:MET243 4.3 23.7 1.0 N A:HIS179 4.5 18.8 1.0 CA A:CYS242 4.5 21.2 1.0 N A:ASN239 4.5 17.6 1.0 CA A:HIS179 4.6 24.3 1.0 O A:HOH403 4.7 16.7 1.0 O A:MET237 4.7 17.6 1.0 C A:CYS238 4.7 18.6 1.0 SD B:MET243 5.0 42.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of P53 Core Domain in 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 Crystal Structure of P53 Core Domain in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:20.2 occ:1.00 ND1 B:HIS179 2.1 19.8 1.0 SG B:CYS238 2.3 20.5 1.0 SG B:CYS242 2.3 18.7 1.0 SG B:CYS176 2.3 17.9 1.0 CE1 B:HIS179 3.1 21.3 1.0 CB B:CYS242 3.1 22.5 1.0 CG B:HIS179 3.1 19.5 1.0 CB B:CYS238 3.3 19.4 1.0 CB B:CYS176 3.4 20.3 1.0 CB B:HIS179 3.4 17.0 1.0 CA B:CYS238 3.9 21.1 1.0 N B:CYS176 4.0 18.2 1.0 NE2 B:HIS179 4.2 19.5 1.0 CD2 B:HIS179 4.2 22.6 1.0 CA B:CYS176 4.2 17.8 1.0 CE A:MET243 4.3 22.8 1.0 N B:HIS179 4.4 20.9 1.0 CA B:CYS242 4.5 18.7 1.0 CA B:HIS179 4.6 25.0 1.0 N B:ASN239 4.6 18.8 1.0 O B:HOH404 4.6 19.7 1.0 O B:MET237 4.7 16.6 1.0 C B:CYS238 4.8 18.1 1.0 C B:CYS176 4.9 19.4 1.0 O B:CYS176 5.0 18.7 1.0 N B:CYS238 5.0 16.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of P53 Core Domain in 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 Crystal Structure of P53 Core Domain in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:22.8 occ:1.00 ND1 C:HIS179 2.1 23.2 1.0 SG C:CYS238 2.3 21.3 1.0 SG C:CYS176 2.3 22.4 1.0 SG C:CYS242 2.3 20.6 1.0 CE1 C:HIS179 3.1 24.1 1.0 CB C:CYS242 3.1 22.6 1.0 CG C:HIS179 3.1 24.3 1.0 CB C:CYS238 3.3 22.6 1.0 CB C:CYS176 3.4 22.1 1.0 CB C:HIS179 3.5 24.0 1.0 CA C:CYS238 3.9 21.6 1.0 N C:CYS176 4.0 22.7 1.0 NE2 C:HIS179 4.2 25.7 1.0 CD2 C:HIS179 4.2 25.9 1.0 CA C:CYS176 4.3 21.0 1.0 CE D:MET243 4.3 21.8 1.0 N C:HIS179 4.5 25.6 1.0 CA C:CYS242 4.5 19.2 1.0 N C:ASN239 4.6 18.9 1.0 CA C:HIS179 4.6 28.8 1.0 O C:HOH405 4.6 22.9 1.0 O C:MET237 4.6 21.5 1.0 C C:CYS238 4.8 20.2 1.0 C C:CYS176 5.0 22.4 1.0 O C:CYS176 5.0 23.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of P53 Core Domain in 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 Crystal Structure of P53 Core Domain in 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 2.1 17.6 1.0 SG D:CYS176 2.3 18.8 1.0 SG D:CYS238 2.3 19.5 1.0 SG D:CYS242 2.3 17.7 1.0 CE1 D:HIS179 3.0 19.1 1.0 CG D:HIS179 3.1 19.7 1.0 CB D:CYS242 3.1 20.6 1.0 CB D:CYS238 3.3 18.9 1.0 CB D:CYS176 3.4 21.8 1.0 CB D:HIS179 3.4 16.1 1.0 CA D:CYS238 3.9 18.9 1.0 N D:CYS176 4.0 18.4 1.0 NE2 D:HIS179 4.2 22.4 1.0 CD2 D:HIS179 4.2 21.1 1.0 CE C:MET243 4.2 28.7 1.0 CA D:CYS176 4.3 17.1 1.0 N D:HIS179 4.4 17.5 1.0 CA D:HIS179 4.5 19.0 1.0 N D:ASN239 4.6 14.8 1.0 CA D:CYS242 4.6 19.6 1.0 O D:MET237 4.6 16.0 1.0 O D:HOH410 4.7 21.8 1.0 C D:CYS238 4.7 16.4 1.0 SD C:MET243 4.9 43.0 1.0 C D:CYS176 4.9 18.6 1.0 N D:CYS238 5.0 13.9 1.0 O D:CYS176 5.0 16.9 1.0

Y.Chen, X.Zhang, A.C.Dantas Machado, Y.Ding, Z.Chen, P.Z.Qin, R.Rohs, L.Chen. Structure of P53 Binding to the Bax Response Element Reveals Dna Unwinding and Compression to Accommodate Base-Pair Insertion. Nucleic Acids Res. V. 41 8368 2013.
ISSN: ISSN 0305-1048
PubMed: 23836939
DOI: 10.1093/NAR/GKT584