Zinc in PDB 7b46: Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human Wild-Type P53DBD Bound to Dna and Mq: Wt-Dna-Mq (P1)

The structure of Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human Wild-Type P53DBD Bound to Dna and Mq: Wt-Dna-Mq (P1), PDB code: 7b46 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)	47.73 / 2.02
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	54.867, 58.312, 78.122, 82.88, 87.47, 72.81
R / Rfree (%)	17.9 / 20.3

The binding sites of Zinc atom in the Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human Wild-Type P53DBD Bound to Dna and Mq: Wt-Dna-Mq (P1) (pdb code 7b46). 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 Wild-Type P53DBD Bound to Dna and Mq: Wt-Dna-Mq (P1), PDB code: 7b46:
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 Wild-Type P53DBD Bound to Dna and Mq: Wt-Dna-Mq (P1)


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 Wild-Type P53DBD Bound to Dna and Mq: Wt-Dna-Mq (P1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:33.0 occ:1.00 ND1 A:HIS179 2.0 30.4 1.0 SG A:CYS242 2.3 34.7 1.0 SG A:CYS176 2.3 29.9 1.0 SG A:CYS238 2.3 29.9 1.0 CE1 A:HIS179 2.9 35.8 1.0 CG A:HIS179 3.0 37.4 1.0 CB A:CYS242 3.2 39.5 1.0 CB A:CYS176 3.4 31.2 1.0 CB A:CYS238 3.4 33.4 1.0 CB A:HIS179 3.4 28.7 1.0 CA A:CYS238 3.9 31.0 1.0 N A:CYS176 4.0 31.0 1.0 NE2 A:HIS179 4.0 38.5 1.0 CD2 A:HIS179 4.1 34.2 1.0 CA A:CYS176 4.2 31.7 1.0 N A:HIS179 4.4 34.6 1.0 N A:ASN239 4.4 30.6 1.0 CA A:HIS179 4.6 40.7 1.0 CA A:CYS242 4.6 38.2 1.0 O A:MET237 4.6 31.2 1.0 O A:HOH461 4.7 35.3 1.0 C A:CYS238 4.7 29.8 1.0 CE B:MET243 4.9 50.2 0.6 O A:CYS176 4.9 32.7 1.0 C A:CYS176 4.9 34.7 1.0 N A:CYS238 5.0 27.0 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 Wild-Type P53DBD Bound to Dna and Mq: Wt-Dna-Mq (P1)


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 Wild-Type P53DBD Bound to Dna and Mq: Wt-Dna-Mq (P1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:33.7 occ:1.00 ND1 B:HIS179 2.1 37.1 1.0 SG B:CYS242 2.3 35.2 1.0 SG B:CYS176 2.3 39.5 1.0 SG B:CYS238 2.3 32.1 1.0 CE1 B:HIS179 3.0 44.4 1.0 CG B:HIS179 3.1 47.2 1.0 CB B:CYS242 3.2 32.5 1.0 CB B:CYS238 3.3 35.7 1.0 CB B:CYS176 3.4 39.5 1.0 CB B:HIS179 3.5 37.9 1.0 CA B:CYS238 3.8 34.5 1.0 N B:CYS176 3.9 31.1 1.0 NE2 B:HIS179 4.1 37.6 1.0 CD2 B:HIS179 4.2 36.0 1.0 CA B:CYS176 4.2 34.4 1.0 N B:HIS179 4.4 40.3 1.0 O B:MET237 4.5 35.0 1.0 CA B:CYS242 4.6 42.5 1.0 N B:ASN239 4.6 30.1 1.0 CA B:HIS179 4.6 44.1 1.0 O B:HOH437 4.7 35.7 1.0 C B:CYS238 4.7 32.5 1.0 C B:CYS176 4.9 39.3 1.0 O B:CYS176 5.0 39.0 1.0 N B:CYS238 5.0 33.4 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 Wild-Type P53DBD Bound to Dna and Mq: Wt-Dna-Mq (P1)


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 Wild-Type P53DBD Bound to Dna and Mq: Wt-Dna-Mq (P1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:38.2 occ:1.00 ND1 C:HIS179 1.9 38.9 1.0 SG C:CYS242 2.3 44.5 1.0 SG C:CYS176 2.3 39.2 1.0 SG C:CYS238 2.3 38.1 1.0 CE1 C:HIS179 2.8 48.4 1.0 CG C:HIS179 3.0 45.4 1.0 CB C:CYS242 3.1 43.7 1.0 CB C:CYS176 3.3 42.2 1.0 CB C:CYS238 3.3 36.8 1.0 CB C:HIS179 3.5 41.1 1.0 CA C:CYS238 3.9 37.8 1.0 N C:CYS176 4.0 40.5 1.0 NE2 C:HIS179 4.0 50.1 1.0 CD2 C:HIS179 4.1 43.3 1.0 CA C:CYS176 4.2 46.2 1.0 N C:HIS179 4.4 40.6 1.0 N C:ASN239 4.4 31.7 1.0 CA C:CYS242 4.5 46.5 1.0 CA C:HIS179 4.6 44.4 1.0 C C:CYS238 4.7 34.7 1.0 O C:MET237 4.7 33.0 1.0 CE D:MET243 4.7 57.0 0.4 O C:HOH454 4.8 45.5 1.0 C C:CYS176 4.9 42.6 1.0 O C:CYS176 4.9 43.8 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 Wild-Type P53DBD Bound to Dna and Mq: Wt-Dna-Mq (P1)


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 Wild-Type P53DBD Bound to Dna and Mq: Wt-Dna-Mq (P1) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:36.5 occ:1.00 ND1 D:HIS179 1.9 26.4 1.0 SG D:CYS242 2.3 44.1 1.0 SG D:CYS238 2.3 40.1 1.0 SG D:CYS176 2.3 37.2 1.0 CE1 D:HIS179 2.8 43.5 1.0 CG D:HIS179 3.0 39.2 1.0 CB D:CYS242 3.1 45.0 1.0 CB D:CYS176 3.4 39.8 1.0 CB D:CYS238 3.4 38.3 1.0 CB D:HIS179 3.5 37.0 1.0 CA D:CYS238 3.9 37.0 1.0 N D:CYS176 4.0 35.5 1.0 NE2 D:HIS179 4.0 43.8 1.0 CD2 D:HIS179 4.1 41.2 1.0 CA D:CYS176 4.2 39.6 1.0 N D:HIS179 4.5 38.9 1.0 CA D:CYS242 4.5 45.8 1.0 N D:ASN239 4.5 35.0 1.0 O D:MET237 4.6 32.5 1.0 O D:HOH426 4.6 41.3 1.0 CA D:HIS179 4.6 41.8 1.0 C D:CYS238 4.8 36.8 1.0 CE C:MET243 4.8 75.8 1.0 C D:CYS176 4.9 42.2 1.0 O D:CYS176 4.9 39.6 1.0

O.Degtjarik, D.Golovenko, Y.Diskin-Posner, L.Abrahmsen, H.Rozenberg, Z.Shakked. P53 Structure 14 To Be Published.