Zinc in PDB 7b47: Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-Mq (I)

The structure of Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-Mq (I), PDB code: 7b47 was solved by O.Degtjarik, H.Rozenberg, Z.Shakked, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.50 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.043, 71, 85.115, 90, 90.34, 90
R / Rfree (%)	17.8 / 20.2

The binding sites of Zinc atom in the Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-Mq (I) (pdb code 7b47). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-Mq (I), PDB code: 7b47:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-Mq (I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-Mq (I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:45.7 occ:1.00 ND1 A:HIS179 2.0 51.8 1.0 SG A:CYS238 2.3 36.8 0.6 SG A:CYS238 2.3 36.5 0.4 SG A:CYS242 2.3 43.0 1.0 SG A:CYS176 2.4 38.3 1.0 CG A:HIS179 3.0 51.1 1.0 CE1 A:HIS179 3.1 50.1 1.0 CB A:CYS242 3.1 47.6 1.0 CB A:HIS179 3.2 49.9 1.0 CB A:CYS238 3.4 43.1 0.4 CB A:CYS238 3.4 43.0 0.6 CB A:CYS176 3.5 46.1 1.0 CA A:CYS238 3.9 33.2 0.4 CA A:CYS238 3.9 33.1 0.6 N A:CYS176 4.0 33.7 1.0 CD2 A:HIS179 4.1 54.6 1.0 NE2 A:HIS179 4.2 57.5 1.0 N A:HIS179 4.3 55.8 1.0 CA A:CYS176 4.3 51.6 1.0 CA A:HIS179 4.4 48.8 1.0 N A:ASN239 4.4 39.0 1.0 CA A:CYS242 4.5 55.5 1.0 O A:MET237 4.5 36.7 1.0 C A:CYS238 4.7 37.8 1.0 O A:CYS176 4.9 35.1 1.0 C A:CYS176 4.9 45.2 1.0 N A:CYS238 5.0 32.7 1.0

Zinc binding site 2 out of 4 in the Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-Mq (I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-Mq (I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:21.5 occ:1.00 ND1 B:HIS179 2.0 18.6 1.0 SG B:CYS238 2.3 23.7 1.0 SG B:CYS242 2.3 25.0 1.0 SG B:CYS176 2.3 23.1 1.0 CE1 B:HIS179 2.9 29.2 1.0 CG B:HIS179 3.1 20.0 1.0 CB B:CYS242 3.2 25.1 1.0 CB B:CYS238 3.2 21.3 1.0 CB B:CYS176 3.5 26.6 1.0 CB B:HIS179 3.5 16.6 1.0 CA B:CYS238 3.9 17.9 1.0 N B:CYS176 3.9 23.6 1.0 O A:HOH509 3.9 27.2 0.7 NE2 B:HIS179 4.1 20.9 1.0 CD2 B:HIS179 4.2 24.8 1.0 CA B:CYS176 4.3 24.8 1.0 N B:HIS179 4.4 24.5 1.0 OG A:SER106 4.4 35.1 0.3 N B:ASN239 4.5 23.4 1.0 O B:HOH464 4.5 28.6 1.0 CA B:CYS242 4.6 35.4 1.0 CA B:HIS179 4.6 19.9 1.0 O B:MET237 4.7 26.4 1.0 C B:CYS238 4.8 18.5 1.0 O B:CYS176 4.9 22.2 1.0 N B:CYS238 5.0 19.5 1.0 C B:CYS176 5.0 24.3 1.0

Zinc binding site 3 out of 4 in the Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-Mq (I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-Mq (I) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:30.7 occ:1.00 ND1 C:HIS179 2.0 33.2 1.0 SG C:CYS238 2.3 35.8 1.0 SG C:CYS242 2.3 38.1 1.0 SG C:CYS176 2.3 35.6 1.0 CE1 C:HIS179 2.9 40.9 1.0 CG C:HIS179 3.0 31.4 1.0 CB C:CYS242 3.1 36.2 1.0 CB C:CYS238 3.3 48.3 1.0 CB C:CYS176 3.4 34.8 1.0 CB C:HIS179 3.4 30.6 1.0 CA C:CYS238 3.8 28.0 1.0 N C:CYS176 4.0 37.4 1.0 NE2 C:HIS179 4.0 35.4 1.0 CD2 C:HIS179 4.1 42.3 1.0 CA C:CYS176 4.2 31.4 1.0 O C:HOH481 4.3 39.8 1.0 N C:ASN239 4.4 34.9 1.0 N C:HIS179 4.4 33.5 1.0 CA C:HIS179 4.5 31.3 1.0 CA C:CYS242 4.6 47.8 1.0 O C:MET237 4.6 35.1 1.0 C C:CYS238 4.7 30.8 1.0 O C:CYS176 4.9 33.7 1.0 C C:CYS176 4.9 37.1 1.0 N C:CYS238 5.0 32.1 1.0

Zinc binding site 4 out of 4 in the Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-Mq (I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-Mq (I) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:50.0 occ:1.00 ND1 D:HIS179 2.1 67.8 1.0 SG D:CYS238 2.3 43.6 0.6 SG D:CYS238 2.3 43.6 0.4 SG D:CYS176 2.3 45.9 1.0 SG D:CYS242 2.4 58.1 1.0 CG D:HIS179 3.1 63.6 1.0 CE1 D:HIS179 3.1 67.1 1.0 CB D:CYS242 3.2 61.2 1.0 CB D:HIS179 3.4 55.3 1.0 CB D:CYS176 3.4 58.8 1.0 CB D:CYS238 3.5 50.8 0.4 CB D:CYS238 3.6 50.8 0.6 CA D:CYS238 3.9 40.6 0.4 CA D:CYS238 3.9 40.5 0.6 N D:CYS176 4.0 40.0 1.0 NE2 D:HIS179 4.2 65.8 1.0 CD2 D:HIS179 4.2 68.0 1.0 CA D:CYS176 4.3 50.6 1.0 N D:HIS179 4.3 64.5 1.0 N D:ASN239 4.4 39.3 1.0 CA D:HIS179 4.5 62.3 1.0 CA D:CYS242 4.6 69.0 1.0 O D:MET237 4.6 44.5 1.0 O D:HOH458 4.7 43.1 1.0 C D:CYS238 4.7 37.9 0.4 C D:CYS238 4.7 37.7 0.6 O D:CYS176 4.9 42.5 1.0 C D:CYS176 4.9 53.0 1.0

O.Degtjarik, D.Golovenko, Y.Diskin-Posner, L.Abrahmsen, H.Rozenberg, Z.Shakked. P53 Structure 1 To Be Published.