Zinc in PDB 7dvd: The Crystal Structure of P53 Dna Binding Domain and Puma Complex

The structure of The Crystal Structure of P53 Dna Binding Domain and Puma Complex, PDB code: 7dvd was solved by C.W.Han, H.N.Lee, M.S.Jeong, S.B.Jang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.28 / 2.59
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	68.612, 73.411, 84.408, 89.94, 89.82, 90
R / Rfree (%)	27 / 31.8

The binding sites of Zinc atom in the The Crystal Structure of P53 Dna Binding Domain and Puma Complex (pdb code 7dvd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of P53 Dna Binding Domain and Puma Complex, PDB code: 7dvd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the The Crystal Structure of P53 Dna Binding Domain and Puma Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of P53 Dna Binding Domain and Puma Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:59.9 occ:1.00 SG A:CYS238 1.9 67.8 1.0 ND1 A:HIS179 2.3 36.9 1.0 SG A:CYS176 2.5 57.5 1.0 SG A:CYS242 2.7 53.7 1.0 CB A:CYS242 3.2 53.8 1.0 CE1 A:HIS179 3.2 33.7 1.0 CG A:HIS179 3.3 38.1 1.0 CB A:CYS176 3.4 53.3 1.0 CB A:CYS238 3.5 45.1 1.0 CB A:HIS179 3.6 40.0 1.0 CA A:CYS238 3.9 44.5 1.0 N A:CYS176 4.1 47.4 1.0 N A:ASN239 4.3 54.5 1.0 CA A:CYS176 4.3 50.9 1.0 NE2 A:HIS179 4.3 39.9 1.0 N A:HIS179 4.4 41.0 1.0 CD2 A:HIS179 4.4 41.2 1.0 C A:CYS238 4.5 53.7 1.0 OG B:SER106 4.5 56.6 1.0 CA A:HIS179 4.7 40.1 1.0 CA A:CYS242 4.7 53.3 1.0 O A:MET237 4.8 37.2 1.0 O A:CYS176 4.9 48.4 1.0 CD2 A:HIS178 4.9 38.2 1.0 C A:CYS176 5.0 44.7 1.0

Zinc binding site 2 out of 4 in the The Crystal Structure of P53 Dna Binding Domain and Puma Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of P53 Dna Binding Domain and Puma Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:76.2 occ:1.00 ND1 B:HIS179 2.2 40.6 1.0 SG B:CYS238 2.3 52.0 1.0 SG B:CYS242 2.4 63.4 1.0 SG B:CYS176 2.9 46.2 1.0 CE1 B:HIS179 3.0 39.1 1.0 CB B:CYS242 3.1 42.4 1.0 CG B:HIS179 3.3 37.6 1.0 CB B:HIS179 3.7 36.2 1.0 CB B:CYS238 3.7 40.7 1.0 CB B:CYS176 3.7 50.3 1.0 CA B:CYS238 3.9 36.8 1.0 N B:ASN239 4.1 42.3 1.0 NE2 B:HIS179 4.2 42.6 1.0 CD2 B:HIS179 4.4 45.2 1.0 C B:CYS238 4.5 43.1 1.0 CA B:CYS242 4.5 41.8 1.0 N B:CYS176 4.6 40.1 1.0 CA B:CYS176 4.7 45.2 1.0 N B:HIS179 4.8 46.1 1.0 O B:ASN239 4.9 38.3 1.0 CA B:HIS179 4.9 43.7 1.0 CD2 B:HIS178 4.9 45.9 1.0 O B:MET237 4.9 41.0 1.0

Zinc binding site 3 out of 4 in the The Crystal Structure of P53 Dna Binding Domain and Puma Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of P53 Dna Binding Domain and Puma Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:54.3 occ:1.00 SG C:CYS238 2.2 45.6 1.0 SG C:CYS242 2.2 57.0 1.0 SG C:CYS176 2.3 54.2 1.0 ND1 C:HIS179 2.5 42.4 1.0 CB C:CYS242 2.6 45.4 1.0 CB C:CYS176 2.9 43.3 1.0 CE1 C:HIS179 3.3 39.5 1.0 CB C:CYS238 3.6 41.2 1.0 CG C:HIS179 3.7 45.4 1.0 N C:CYS176 3.9 42.1 1.0 CA C:CYS238 4.0 38.2 1.0 CA C:CYS176 4.0 43.3 1.0 CB C:HIS179 4.0 45.5 1.0 CA C:CYS242 4.0 41.1 1.0 N C:ASN239 4.1 40.0 1.0 C C:CYS238 4.5 36.1 1.0 NE2 C:HIS179 4.5 47.0 1.0 O C:ASN239 4.7 38.6 1.0 CD2 C:HIS179 4.7 43.2 1.0 N C:HIS179 4.8 38.3 1.0 C C:CYS176 4.8 45.6 1.0 C C:CYS242 4.8 40.1 1.0 N C:CYS242 5.0 43.6 1.0 O C:CYS176 5.0 49.7 1.0

Zinc binding site 4 out of 4 in the The Crystal Structure of P53 Dna Binding Domain and Puma Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of P53 Dna Binding Domain and Puma Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:62.4 occ:1.00 SG D:CYS238 1.7 63.9 1.0 SG D:CYS176 2.3 57.4 1.0 SG D:CYS242 2.4 48.8 1.0 ND1 D:HIS179 2.5 52.6 1.0 CB D:CYS176 2.9 43.3 1.0 CB D:CYS242 3.2 40.7 1.0 CE1 D:HIS179 3.2 47.9 1.0 CB D:CYS238 3.4 45.8 1.0 CG D:HIS179 3.5 56.4 1.0 CB D:HIS179 3.9 55.7 1.0 N D:CYS176 4.0 42.2 1.0 CA D:CYS176 4.0 40.8 1.0 CA D:CYS238 4.3 35.6 1.0 NE2 D:HIS179 4.4 53.9 1.0 N D:ASN239 4.5 36.8 1.0 CD2 D:HIS179 4.5 56.8 1.0 N D:HIS179 4.5 55.1 1.0 CA D:CYS242 4.6 40.4 1.0 C D:CYS238 4.9 37.9 1.0 C D:CYS176 4.9 47.2 1.0 CA D:HIS179 4.9 56.4 1.0

C.W.Han, H.N.Lee, M.S.Jeong, S.Y.Park, S.B.Jang. Structural Basis of the P53 Dna Binding Domain and Puma Complex. Biochem.Biophys.Res.Commun. V. 548 39 2021.
ISSN: ESSN 1090-2104
PubMed: 33631672
DOI: 10.1016/J.BBRC.2021.02.049