Zinc in PDB 2j1y: Human P53 Core Domain Mutant M133L-V203A-N239Y-G245S-N268D

The structure of Human P53 Core Domain Mutant M133L-V203A-N239Y-G245S-N268D, PDB code: 2j1y was solved by A.C.Joerger, A.R.Fersht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.4 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.514, 73.076, 84.760, 90.00, 90.05, 90.00
R / Rfree (%)	18.9 / 21.8

The structure of Human P53 Core Domain Mutant M133L-V203A-N239Y-G245S-N268D also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Zinc atom in the Human P53 Core Domain Mutant M133L-V203A-N239Y-G245S-N268D (pdb code 2j1y). 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 M133L-V203A-N239Y-G245S-N268D, PDB code: 2j1y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Human P53 Core Domain Mutant M133L-V203A-N239Y-G245S-N268D


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 M133L-V203A-N239Y-G245S-N268D within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1290 b:27.1 occ:1.00 ND1 A:HIS179 2.1 21.5 1.0 SG A:CYS176 2.3 17.8 1.0 SG A:CYS238 2.3 16.3 1.0 SG A:CYS242 2.4 17.5 1.0 CE1 A:HIS179 3.0 19.1 1.0 CB A:CYS242 3.2 19.8 1.0 CG A:HIS179 3.2 23.1 1.0 CB A:CYS238 3.4 16.0 1.0 CB A:CYS176 3.4 19.2 1.0 CB A:HIS179 3.6 24.2 1.0 CA A:CYS238 3.7 15.1 1.0 N A:CYS176 4.0 17.8 1.0 OG A:SER245 4.0 22.5 1.0 NE2 A:HIS179 4.2 19.3 1.0 CA A:CYS176 4.3 19.5 1.0 CD2 A:HIS179 4.3 20.5 1.0 O A:MET237 4.3 16.2 1.0 N A:TYR239 4.4 14.0 1.0 N A:HIS179 4.5 26.9 1.0 O A:HOH2167 4.5 24.1 1.0 C A:CYS238 4.6 15.4 1.0 CA A:CYS242 4.6 21.1 1.0 CA A:HIS179 4.7 27.9 1.0 O A:HOH2100 4.7 31.6 1.0 N A:CYS238 4.8 14.2 1.0 O A:CYS176 4.9 20.4 1.0 C A:CYS176 4.9 19.4 1.0 C A:MET237 5.0 16.2 1.0 CG A:ARG175 5.0 23.2 1.0

Zinc binding site 2 out of 4 in the Human P53 Core Domain Mutant M133L-V203A-N239Y-G245S-N268D


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 M133L-V203A-N239Y-G245S-N268D within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1290 b:22.6 occ:1.00 ND1 B:HIS179 2.0 12.4 1.0 SG B:CYS242 2.3 15.6 1.0 SG B:CYS176 2.3 14.6 1.0 SG B:CYS238 2.4 21.3 1.0 CE1 B:HIS179 2.9 14.8 1.0 CG B:HIS179 3.1 14.8 1.0 CB B:CYS242 3.1 11.3 1.0 CB B:CYS176 3.4 15.4 1.0 CB B:CYS238 3.5 19.5 1.0 CB B:HIS179 3.6 14.6 1.0 CA B:CYS238 3.7 16.1 1.0 N B:CYS176 4.0 18.7 1.0 NE2 B:HIS179 4.1 11.7 1.0 CD2 B:HIS179 4.2 14.3 1.0 OG B:SER245 4.3 24.1 1.0 N B:TYR239 4.3 14.0 1.0 CA B:CYS176 4.3 17.6 1.0 O B:HOH2162 4.3 21.5 1.0 N B:HIS179 4.5 14.7 1.0 C B:CYS238 4.5 16.5 1.0 O B:MET237 4.5 15.6 1.0 CA B:CYS242 4.6 13.8 1.0 CA B:HIS179 4.7 15.8 1.0 N B:CYS238 4.9 13.5 1.0 C B:CYS176 5.0 17.4 1.0 O B:CYS176 5.0 16.3 1.0

Zinc binding site 3 out of 4 in the Human P53 Core Domain Mutant M133L-V203A-N239Y-G245S-N268D


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 M133L-V203A-N239Y-G245S-N268D within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1290 b:29.6 occ:1.00 ND1 C:HIS179 2.2 26.8 1.0 SG C:CYS238 2.3 21.4 1.0 SG C:CYS176 2.4 22.7 1.0 SG C:CYS242 2.4 24.3 1.0 CE1 C:HIS179 3.1 25.3 1.0 CB C:CYS242 3.2 27.2 1.0 CG C:HIS179 3.2 29.6 1.0 CB C:CYS238 3.4 21.2 1.0 CB C:CYS176 3.4 26.0 1.0 CB C:HIS179 3.5 28.9 1.0 CA C:CYS238 3.7 16.7 1.0 OG C:SER245 4.0 30.5 1.0 N C:CYS176 4.0 23.9 1.0 NE2 C:HIS179 4.2 25.2 1.0 CA C:CYS176 4.3 25.0 1.0 CD2 C:HIS179 4.3 25.4 1.0 N C:TYR239 4.4 17.8 1.0 N C:HIS179 4.4 31.9 1.0 O C:MET237 4.4 19.6 1.0 O C:HOH2152 4.5 38.8 1.0 C C:CYS238 4.6 16.0 1.0 CA C:CYS242 4.6 27.6 1.0 CA C:HIS179 4.6 31.5 1.0 N C:CYS238 4.8 15.2 1.0 O C:CYS176 4.9 24.4 1.0 C C:CYS176 4.9 26.4 1.0

Zinc binding site 4 out of 4 in the Human P53 Core Domain Mutant M133L-V203A-N239Y-G245S-N268D


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 M133L-V203A-N239Y-G245S-N268D within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1290 b:22.1 occ:1.00 ND1 D:HIS179 2.0 11.8 1.0 SG D:CYS176 2.3 14.7 1.0 SG D:CYS242 2.3 14.4 1.0 SG D:CYS238 2.4 19.6 1.0 CE1 D:HIS179 2.8 13.2 1.0 CG D:HIS179 3.1 15.7 1.0 CB D:CYS242 3.2 12.2 1.0 CB D:CYS176 3.4 13.7 1.0 CB D:HIS179 3.5 14.7 1.0 CB D:CYS238 3.5 19.1 1.0 CA D:CYS238 3.7 12.2 1.0 NE2 D:HIS179 4.0 13.2 1.0 N D:CYS176 4.1 15.1 1.0 OG D:SER245 4.1 22.0 1.0 CD2 D:HIS179 4.1 14.7 1.0 N D:TYR239 4.3 15.4 1.0 O D:HOH2148 4.3 23.9 1.0 CA D:CYS176 4.3 17.5 1.0 N D:HIS179 4.5 13.6 1.0 C D:CYS238 4.5 15.9 1.0 O D:MET237 4.6 17.2 1.0 CA D:CYS242 4.6 15.4 1.0 CA D:HIS179 4.6 14.8 1.0 N D:CYS238 4.9 12.6 1.0 C D:CYS176 5.0 16.5 1.0

A.C.Joerger, H.C.Ang, A.R.Fersht. Structural Basis For Understanding Oncogenic P53 Mutations and Designing Rescue Drugs. Proc.Natl.Acad.Sci.Usa V. 103 15056 2006.
ISSN: ISSN 0027-8424
PubMed: 17015838
DOI: 10.1073/PNAS.0607286103