Zinc in PDB 4kvp: Human P53 Core Domain Mutant V157F

The structure of Human P53 Core Domain Mutant V157F, PDB code: 4kvp was solved by B.D.Wallentine, Y.Wang, H.Luecke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.35 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.656, 70.279, 83.559, 90.00, 90.06, 90.00
R / Rfree (%)	17.4 / 21

The binding sites of Zinc atom in the Human P53 Core Domain Mutant V157F (pdb code 4kvp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human P53 Core Domain Mutant V157F, PDB code: 4kvp:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human P53 Core Domain Mutant V157F


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 Mutant V157F within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:15.7 occ:1.00 ND1 A:HIS179 2.0 14.8 1.0 SG A:CYS176 2.3 21.8 1.0 SG A:CYS242 2.4 20.6 1.0 SG A:CYS238 2.4 20.3 1.0 CE1 A:HIS179 2.9 17.7 1.0 CG A:HIS179 3.0 16.5 1.0 CB A:CYS242 3.2 20.8 1.0 CB A:HIS179 3.4 17.6 1.0 CB A:CYS238 3.5 19.0 1.0 CB A:CYS176 3.5 20.4 1.0 CA A:CYS238 3.9 16.9 1.0 N A:CYS176 4.0 20.0 1.0 NE2 A:HIS179 4.1 18.8 1.0 CD2 A:HIS179 4.1 17.7 1.0 CA A:CYS176 4.3 20.4 1.0 N A:HIS179 4.4 19.1 1.0 N A:ASN239 4.5 16.0 1.0 CA A:HIS179 4.5 19.0 1.0 CA A:CYS242 4.6 22.4 1.0 O A:HOH548 4.6 20.6 1.0 O A:MET237 4.7 13.9 1.0 C A:CYS238 4.7 15.3 1.0 O A:CYS176 4.8 20.0 1.0 C A:CYS176 4.9 20.8 1.0

Zinc binding site 2 out of 4 in the Human P53 Core Domain Mutant V157F


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 Mutant V157F within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:17.2 occ:1.00 ND1 B:HIS179 1.9 16.1 1.0 SG B:CYS242 2.3 19.4 1.0 SG B:CYS238 2.4 22.9 1.0 SG B:CYS176 2.4 19.6 1.0 CE1 B:HIS179 2.8 19.1 1.0 CG B:HIS179 3.0 18.5 1.0 CB B:CYS242 3.1 18.6 1.0 CB B:HIS179 3.4 20.1 1.0 CB B:CYS238 3.5 21.1 1.0 CB B:CYS176 3.6 19.8 1.0 CA B:CYS238 3.9 18.4 1.0 NE2 B:HIS179 4.0 20.1 1.0 N B:CYS176 4.0 19.9 1.0 O D:HOH592 4.1 26.8 1.0 CD2 B:HIS179 4.1 19.2 1.0 CA B:CYS176 4.4 20.6 1.0 O B:HOH551 4.4 21.4 1.0 N B:ASN239 4.4 18.0 1.0 N B:HIS179 4.4 22.8 1.0 CA B:CYS242 4.5 19.8 1.0 CA B:HIS179 4.6 22.9 1.0 C B:CYS238 4.7 17.9 1.0 O B:MET237 4.7 15.1 1.0 O B:CYS176 4.9 20.2 1.0

Zinc binding site 3 out of 4 in the Human P53 Core Domain Mutant V157F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human P53 Core Domain Mutant V157F within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:20.7 occ:1.00 ND1 C:HIS179 2.0 16.2 1.0 SG C:CYS238 2.3 24.3 1.0 SG C:CYS242 2.3 23.8 1.0 SG C:CYS176 2.4 18.9 1.0 CE1 C:HIS179 2.8 19.0 1.0 CG C:HIS179 3.0 17.8 1.0 CB C:CYS242 3.2 23.4 1.0 CB C:CYS176 3.4 18.0 1.0 CB C:HIS179 3.5 19.9 1.0 CB C:CYS238 3.7 22.0 1.0 CA C:CYS238 3.9 18.9 1.0 N C:CYS176 4.0 17.8 1.0 NE2 C:HIS179 4.0 18.9 1.0 CD2 C:HIS179 4.1 18.2 1.0 O A:HOH761 4.2 43.7 1.0 N C:ASN239 4.2 18.0 1.0 CA C:CYS176 4.3 17.9 1.0 N C:HIS179 4.5 20.8 1.0 CA C:CYS242 4.6 23.3 1.0 CA C:HIS179 4.6 21.1 1.0 C C:CYS238 4.6 18.8 1.0 O C:HOH739 4.7 49.6 1.0 O C:MET237 4.9 16.6 1.0 O C:CYS176 4.9 18.9 1.0 C C:CYS176 4.9 18.8 1.0 O C:ASN239 5.0 15.9 1.0

Zinc binding site 4 out of 4 in the Human P53 Core Domain Mutant V157F


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human P53 Core Domain Mutant V157F within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:15.7 occ:1.00 ND1 D:HIS179 2.0 10.9 1.0 SG D:CYS238 2.3 19.3 1.0 SG D:CYS176 2.3 19.2 1.0 SG D:CYS242 2.4 20.1 1.0 CE1 D:HIS179 2.9 11.6 1.0 CG D:HIS179 3.0 11.3 1.0 CB D:CYS242 3.1 19.7 1.0 CB D:HIS179 3.4 12.3 1.0 CB D:CYS176 3.5 13.0 1.0 CB D:CYS238 3.7 18.2 1.0 CA D:CYS238 3.9 14.4 1.0 N D:CYS176 4.0 11.8 1.0 O D:HOH589 4.1 25.7 1.0 NE2 D:HIS179 4.1 12.3 1.0 CD2 D:HIS179 4.1 10.6 1.0 N D:ASN239 4.3 14.2 1.0 CA D:CYS176 4.3 12.2 1.0 N D:HIS179 4.4 15.8 1.0 CA D:HIS179 4.5 14.4 1.0 CA D:CYS242 4.6 20.0 1.0 C D:CYS238 4.6 14.2 1.0 O D:HOH568 4.7 22.9 1.0 O D:CYS176 4.8 13.0 1.0 O D:MET237 4.8 13.1 1.0 C D:CYS176 4.9 13.3 1.0 O D:HOH714 5.0 38.4 1.0 O D:HOH627 5.0 30.0 1.0

B.D.Wallentine, Y.Wang, V.Tretyachenko-Ladokhina, M.Tan, D.F.Senear, H.Luecke. Structures of Oncogenic, Suppressor and Rescued P53 Core-Domain Variants: Mechanisms of Mutant P53 Rescue. Acta Crystallogr.,Sect.D V. 69 2146 2013.
ISSN: ISSN 0907-4449
PubMed: 24100332
DOI: 10.1107/S0907444913020830