Zinc in PDB 6ff9: Mutant R280K of Human P53

The structure of Mutant R280K of Human P53, PDB code: 6ff9 was solved by F.G.Trovao, A.S.Gomes, B.Pinheiro, A.L.Carvalho, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.67 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.569, 69.445, 83.335, 90.00, 90.04, 90.00
R / Rfree (%)	18.2 / 22.6

The binding sites of Zinc atom in the Mutant R280K of Human P53 (pdb code 6ff9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Mutant R280K of Human P53, PDB code: 6ff9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Mutant R280K of Human P53


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mutant R280K of Human P53 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.0 occ:1.00 CD2 A:HIS179 2.0 20.4 1.0 SG A:CYS242 2.3 31.7 1.0 SG A:CYS238 2.3 37.7 1.0 SG A:CYS176 2.4 27.8 1.0 CG A:HIS179 3.0 24.2 1.0 NE2 A:HIS179 3.1 26.4 1.0 CB A:CYS242 3.1 30.3 1.0 CB A:CYS176 3.4 24.2 1.0 CB A:CYS238 3.5 33.8 1.0 CB A:HIS179 3.5 23.6 1.0 CA A:CYS238 3.9 30.3 1.0 N A:CYS176 4.0 26.7 1.0 ND1 A:HIS179 4.1 32.6 1.0 CE1 A:HIS179 4.2 27.5 1.0 CA A:CYS176 4.3 27.3 1.0 N A:HIS179 4.3 28.0 1.0 N A:ASN239 4.5 27.6 1.0 CA A:CYS242 4.5 38.7 1.0 CA A:HIS179 4.5 25.7 1.0 C A:CYS238 4.7 29.9 1.0 O A:MET237 4.8 26.7 1.0 C A:CYS176 4.9 29.4 1.0 O A:CYS176 5.0 29.8 1.0

Zinc binding site 2 out of 4 in the Mutant R280K of Human P53


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mutant R280K of Human P53 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:32.1 occ:1.00 SG B:CYS242 2.1 32.0 1.0 CD2 B:HIS179 2.2 28.5 1.0 SG B:CYS238 2.4 36.7 1.0 SG B:CYS176 2.4 33.0 1.0 CB B:CYS242 2.9 37.4 1.0 NE2 B:HIS179 3.1 36.0 1.0 CG B:HIS179 3.2 32.0 1.0 CB B:CYS176 3.4 34.7 1.0 CB B:CYS238 3.5 29.9 1.0 CB B:HIS179 3.7 30.0 1.0 CA B:CYS238 3.9 27.7 1.0 N B:CYS176 4.0 36.2 1.0 CE1 B:HIS179 4.3 30.3 1.0 CA B:CYS176 4.3 35.1 1.0 ND1 B:HIS179 4.3 35.5 1.0 N B:ASN239 4.4 24.0 1.0 CA B:CYS242 4.4 36.5 1.0 N B:HIS179 4.5 32.1 1.0 O B:HOH456 4.5 37.9 1.0 C B:CYS238 4.7 26.1 1.0 CA B:HIS179 4.7 34.3 1.0 O B:ASN239 4.9 24.5 1.0 O B:MET237 4.9 23.7 1.0 O B:HOH472 5.0 34.0 1.0

Zinc binding site 3 out of 4 in the Mutant R280K of Human P53


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mutant R280K of Human P53 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:24.5 occ:1.00 CD2 C:HIS179 2.1 15.3 1.0 SG C:CYS242 2.1 23.2 1.0 SG C:CYS176 2.4 26.1 1.0 SG C:CYS238 2.4 33.0 1.0 CB C:CYS242 2.9 22.8 1.0 NE2 C:HIS179 3.1 23.7 1.0 CG C:HIS179 3.1 23.4 1.0 CB C:CYS176 3.4 24.3 1.0 CB C:CYS238 3.5 30.1 1.0 CB C:HIS179 3.7 21.4 1.0 CA C:CYS238 3.9 28.3 1.0 N C:CYS176 4.0 24.3 1.0 O C:HOH465 4.3 25.1 1.0 CA C:CYS176 4.3 23.7 1.0 CE1 C:HIS179 4.3 20.1 1.0 ND1 C:HIS179 4.3 23.2 1.0 CA C:CYS242 4.3 28.9 1.0 N C:ASN239 4.4 28.5 1.0 N C:HIS179 4.5 26.7 1.0 C C:CYS238 4.7 25.9 1.0 CA C:HIS179 4.7 25.5 1.0 O C:ASN239 4.9 28.6 1.0 O C:MET237 4.9 26.8 1.0

Zinc binding site 4 out of 4 in the Mutant R280K of Human P53


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mutant R280K of Human P53 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:30.5 occ:1.00 CD2 D:HIS179 2.0 28.1 1.0 SG D:CYS242 2.2 32.2 1.0 SG D:CYS238 2.4 30.5 1.0 SG D:CYS176 2.4 31.4 1.0 NE2 D:HIS179 3.0 31.9 1.0 CG D:HIS179 3.0 31.4 1.0 CB D:CYS242 3.0 36.1 1.0 CB D:CYS238 3.5 27.0 1.0 CB D:CYS176 3.5 34.1 1.0 CB D:HIS179 3.5 29.1 1.0 CA D:CYS238 3.8 24.8 1.0 N D:CYS176 4.0 29.5 1.0 CE1 D:HIS179 4.1 25.8 1.0 ND1 D:HIS179 4.1 31.8 1.0 CA D:CYS176 4.3 31.8 1.0 N D:HIS179 4.4 30.0 1.0 N D:ASN239 4.4 20.4 1.0 CA D:CYS242 4.5 35.0 1.0 CA D:HIS179 4.6 30.8 1.0 C D:CYS238 4.6 23.1 1.0 O D:MET237 4.7 22.5 1.0 C D:CYS176 5.0 36.0 1.0

A.S.Gomes, F.Trovao, B.Andrade Pinheiro, F.Freire, S.Gomes, C.Oliveira, L.Domingues, M.J.Romao, L.Saraiva, A.L.Carvalho. The Crystal Structure of the R280K Mutant of Human P53 Explains the Loss of Dna Binding. Int J Mol Sci V. 19 2018.
ISSN: ESSN 1422-0067
PubMed: 29652801
DOI: 10.3390/IJMS19041184