Zinc in PDB 4mzr: Crystal Structure of A Polypeptide P53 Mutant Bound to Dna

The structure of Crystal Structure of A Polypeptide P53 Mutant Bound to Dna, PDB code: 4mzr was solved by S.T.Emamzadah, L.Tropia, I.Vincenti, B.Falquet, T.D.Halazonetis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	80.00 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	163.298, 169.764, 55.664, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 28.1

The binding sites of Zinc atom in the Crystal Structure of A Polypeptide P53 Mutant Bound to Dna (pdb code 4mzr). 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 A Polypeptide P53 Mutant Bound to Dna, PDB code: 4mzr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of A Polypeptide P53 Mutant Bound to 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 A Polypeptide P53 Mutant Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:49.2 occ:1.00 ND1 A:HIS179 2.3 51.8 1.0 SG A:CYS242 2.4 47.0 1.0 SG A:CYS176 2.5 54.6 1.0 SG A:CYS238 2.5 50.2 1.0 CG A:HIS179 3.1 50.0 1.0 CE1 A:HIS179 3.1 51.8 1.0 CB A:CYS242 3.2 42.4 1.0 CB A:HIS179 3.4 51.0 1.0 CB A:CYS176 3.6 48.4 1.0 CB A:CYS238 3.7 40.8 1.0 CD2 A:HIS179 4.1 49.6 1.0 NE2 A:HIS179 4.1 52.6 1.0 CA A:CYS238 4.1 42.7 1.0 N A:CYS176 4.2 42.4 1.0 CA A:CYS176 4.5 47.3 1.0 N A:ASN239 4.5 43.8 1.0 N A:HIS179 4.5 53.8 1.0 O A:MET237 4.6 44.2 1.0 CA A:CYS242 4.6 46.3 1.0 CA A:HIS179 4.6 55.2 1.0 C A:CYS238 4.8 43.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of A Polypeptide P53 Mutant Bound to 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 A Polypeptide P53 Mutant Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:82.6 occ:1.00 SG B:CYS242 2.7 82.5 1.0 SG B:CYS238 2.7 62.8 1.0 SG B:CYS176 2.8 88.4 1.0 CG B:HIS179 3.2 87.2 1.0 CB B:CYS242 3.2 82.5 1.0 CD2 B:HIS179 3.3 86.4 1.0 ND1 B:HIS179 3.3 86.5 1.0 CB B:CYS176 3.3 82.7 1.0 NE2 B:HIS179 3.5 82.8 1.0 CE1 B:HIS179 3.5 85.1 1.0 N B:CYS176 3.6 80.2 1.0 CB B:HIS179 3.8 87.1 1.0 CB B:CYS238 4.1 75.0 1.0 CA B:CYS176 4.1 81.4 1.0 CA B:CYS238 4.3 74.0 1.0 N B:ASN239 4.5 75.1 1.0 CA B:CYS242 4.7 81.8 1.0 C B:ARG175 4.7 80.1 1.0 C B:CYS238 4.8 74.7 1.0 CB B:ARG175 4.9 82.7 1.0 CA B:ARG175 4.9 81.4 1.0 O B:ASN239 4.9 77.3 1.0 N B:HIS179 5.0 86.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of A Polypeptide P53 Mutant Bound to 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 A Polypeptide P53 Mutant Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:35.0 occ:1.00 ND1 C:HIS179 2.2 29.5 1.0 SG C:CYS242 2.4 31.1 1.0 SG C:CYS238 2.5 40.2 1.0 SG C:CYS176 2.5 33.9 1.0 CG C:HIS179 3.1 31.3 1.0 CE1 C:HIS179 3.2 29.4 1.0 CB C:CYS242 3.2 36.0 1.0 CB C:HIS179 3.4 38.5 1.0 CB C:CYS238 3.6 39.1 1.0 CB C:CYS176 3.7 32.2 1.0 CA C:CYS238 3.9 36.7 1.0 N C:CYS176 4.2 32.9 1.0 NE2 C:HIS179 4.2 30.5 1.0 CD2 C:HIS179 4.3 31.5 1.0 O C:MET237 4.4 37.0 1.0 N C:ASN239 4.4 39.1 1.0 N C:HIS179 4.5 40.3 1.0 CA C:CYS176 4.5 33.8 1.0 CA C:HIS179 4.6 40.8 1.0 CA C:CYS242 4.7 37.5 1.0 C C:CYS238 4.8 37.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of A Polypeptide P53 Mutant Bound to 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 A Polypeptide P53 Mutant Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:37.6 occ:1.00 ND1 D:HIS179 2.2 43.9 1.0 SG D:CYS242 2.3 40.0 1.0 SG D:CYS176 2.5 43.8 1.0 SG D:CYS238 2.5 37.4 1.0 CE1 D:HIS179 3.1 44.4 1.0 CG D:HIS179 3.1 44.7 1.0 CB D:CYS242 3.1 42.5 1.0 CB D:HIS179 3.5 46.8 1.0 CB D:CYS176 3.6 43.4 1.0 CB D:CYS238 3.7 38.0 1.0 NE2 D:HIS179 4.0 44.3 1.0 CA D:CYS238 4.0 38.6 1.0 CD2 D:HIS179 4.1 45.3 1.0 N D:CYS176 4.3 41.0 1.0 N D:ASN239 4.4 40.9 1.0 CA D:CYS242 4.5 44.5 1.0 N D:HIS179 4.6 50.0 1.0 CA D:CYS176 4.6 43.6 1.0 O D:MET237 4.6 44.5 1.0 CA D:HIS179 4.7 50.9 1.0 C D:CYS238 4.8 40.1 1.0

S.Emamzadah, L.Tropia, I.Vincenti, B.Falquet, T.D.Halazonetis. Reversal of the Dna-Binding-Induced Loop L1 Conformational Switch in An Engineered Human P53 Protein. J.Mol.Biol. V. 426 936 2014.
ISSN: ISSN 0022-2836
PubMed: 24374182
DOI: 10.1016/J.JMB.2013.12.020