Zinc in PDB 4lo9: Human P53 Core Domain Mutant N235K

The structure of Human P53 Core Domain Mutant N235K, PDB code: 4lo9 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)	53.38 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.164, 69.213, 83.851, 90.00, 90.11, 90.00
R / Rfree (%)	17.6 / 24.7

The binding sites of Zinc atom in the Human P53 Core Domain Mutant N235K (pdb code 4lo9). 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 N235K, PDB code: 4lo9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human P53 Core Domain Mutant N235K


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 N235K within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:40.6 occ:1.00 ND1 A:HIS179 1.9 36.3 1.0 SG A:CYS238 2.4 54.3 1.0 SG A:CYS176 2.4 45.2 1.0 SG A:CYS242 2.5 45.2 1.0 CE1 A:HIS179 2.8 37.6 1.0 CG A:HIS179 3.0 44.7 1.0 CB A:CYS242 3.3 53.0 1.0 CB A:CYS176 3.3 46.5 1.0 CB A:HIS179 3.5 43.0 1.0 CB A:CYS238 3.7 36.0 1.0 NE2 A:HIS179 3.9 43.9 1.0 N A:CYS176 3.9 33.4 1.0 CA A:CYS238 4.0 46.0 1.0 CD2 A:HIS179 4.0 44.6 1.0 CA A:CYS176 4.2 41.5 1.0 N A:ASN239 4.2 44.4 1.0 N A:HIS179 4.4 44.3 1.0 O A:HOH519 4.6 45.9 1.0 CA A:HIS179 4.6 43.3 1.0 C A:CYS238 4.6 36.2 1.0 CA A:CYS242 4.7 57.0 1.0 O A:CYS176 4.7 36.3 1.0 C A:CYS176 4.8 35.6 1.0 O A:MET237 5.0 36.9 1.0

Zinc binding site 2 out of 4 in the Human P53 Core Domain Mutant N235K


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 N235K within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:43.0 occ:1.00 ND1 B:HIS179 1.9 37.8 1.0 SG B:CYS242 2.4 42.4 1.0 SG B:CYS238 2.4 48.0 1.0 SG B:CYS176 2.4 38.7 1.0 CE1 B:HIS179 2.7 50.1 1.0 CG B:HIS179 3.0 45.9 1.0 CB B:CYS242 3.2 54.6 1.0 CB B:CYS176 3.4 38.1 1.0 CB B:HIS179 3.6 36.6 1.0 CB B:CYS238 3.7 42.7 1.0 NE2 B:HIS179 3.9 50.1 1.0 CA B:CYS238 4.0 42.1 1.0 N B:CYS176 4.0 35.4 1.0 CD2 B:HIS179 4.1 45.9 1.0 N B:ASN239 4.2 48.4 1.0 CA B:CYS176 4.3 37.0 1.0 N B:HIS179 4.4 38.5 1.0 C B:CYS238 4.6 40.8 1.0 CA B:CYS242 4.6 57.2 1.0 CA B:HIS179 4.6 40.2 1.0 O B:CYS176 4.9 41.2 1.0 O B:MET237 4.9 29.8 1.0 C B:CYS176 5.0 38.0 1.0 CD2 B:HIS178 5.0 45.6 1.0

Zinc binding site 3 out of 4 in the Human P53 Core Domain Mutant N235K


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 N235K within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:52.1 occ:1.00 ND1 C:HIS179 1.9 32.6 1.0 SG C:CYS242 2.3 45.2 1.0 SG C:CYS238 2.4 56.6 1.0 CE1 C:HIS179 2.5 41.3 1.0 SG C:CYS176 2.5 37.4 1.0 CB C:CYS242 3.0 50.2 1.0 CG C:HIS179 3.1 42.9 1.0 CB C:CYS176 3.3 42.6 1.0 NE2 C:HIS179 3.7 40.7 1.0 CB C:CYS238 3.8 42.5 1.0 CB C:HIS179 3.8 43.3 1.0 CA C:CYS238 4.0 40.2 1.0 N C:CYS176 4.0 40.9 1.0 CD2 C:HIS179 4.0 44.2 1.0 N C:ASN239 4.1 37.4 1.0 CA C:CYS176 4.3 42.2 1.0 CA C:CYS242 4.5 52.4 1.0 C C:CYS238 4.5 39.0 1.0 N C:HIS179 4.7 47.9 1.0 O C:ASN239 4.8 51.9 1.0 CA C:HIS179 4.9 47.8 1.0 O C:CYS176 4.9 39.2 1.0 C C:CYS176 5.0 42.4 1.0

Zinc binding site 4 out of 4 in the Human P53 Core Domain Mutant N235K


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 N235K within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:56.8 occ:1.00 ND1 D:HIS179 1.9 45.5 1.0 SG D:CYS242 2.3 53.9 1.0 SG D:CYS176 2.5 48.5 1.0 SG D:CYS238 2.5 55.6 1.0 CE1 D:HIS179 2.5 48.9 1.0 CB D:CYS242 3.0 57.7 1.0 CG D:HIS179 3.1 51.6 1.0 CB D:CYS176 3.1 59.8 1.0 NE2 D:HIS179 3.7 51.9 1.0 CB D:CYS238 3.7 37.9 1.0 CB D:HIS179 3.8 49.2 1.0 CA D:CYS238 3.9 37.9 1.0 N D:CYS176 4.0 50.1 1.0 CD2 D:HIS179 4.0 53.5 1.0 CA D:CYS176 4.1 55.0 1.0 N D:ASN239 4.1 42.9 1.0 CA D:CYS242 4.5 59.9 1.0 C D:CYS238 4.5 42.1 1.0 N D:HIS179 4.6 50.4 1.0 CA D:HIS179 4.8 50.9 1.0 O D:ASN239 4.9 50.9 1.0 C D:CYS176 4.9 51.7 1.0 O D:MET237 4.9 39.4 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