Zinc in PDB 3q06: An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity

The structure of An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity, PDB code: 3q06 was solved by T.J.Petty, T.D.Halazonetis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	164.591, 169.363, 55.336, 90.00, 90.00, 90.00
R / Rfree (%)	25.8 / 31.4

The binding sites of Zinc atom in the An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity (pdb code 3q06). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity, PDB code: 3q06:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:17.6 occ:1.00 SG A:CYS242 2.4 41.7 1.0 SG A:CYS238 2.4 12.3 1.0 SG A:CYS176 2.4 27.7 1.0 ND1 A:HIS179 2.5 20.3 1.0 CE1 A:HIS179 2.8 17.8 1.0 CB A:CYS242 2.8 30.0 1.0 CB A:CYS176 3.1 27.9 1.0 CG A:HIS179 3.3 16.0 1.0 CB A:CYS238 3.5 18.1 1.0 NE2 A:HIS179 3.6 13.6 1.0 CD2 A:HIS179 3.9 14.1 1.0 CA A:CYS238 3.9 18.3 1.0 CB A:HIS179 4.0 20.9 1.0 N A:ASN239 4.2 20.8 1.0 CA A:CYS242 4.3 26.4 1.0 CA A:CYS176 4.3 29.6 1.0 N A:CYS176 4.4 27.3 1.0 C A:CYS238 4.5 18.9 1.0 SD B:MET243 4.7 0.9 1.0 N A:HIS179 4.9 32.1 1.0 CE B:MET243 4.9 0.5 1.0 O A:MET237 5.0 13.3 1.0

Zinc binding site 2 out of 4 in the An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1 b:18.0 occ:1.00 ND1 C:HIS179 2.2 4.6 1.0 SG C:CYS238 2.3 25.1 1.0 SG C:CYS242 2.3 4.7 1.0 SG C:CYS176 2.4 34.6 1.0 CB C:CYS242 3.0 14.7 1.0 CG C:HIS179 3.1 4.4 1.0 CE1 C:HIS179 3.1 4.4 1.0 CB C:CYS176 3.1 21.9 1.0 CB C:HIS179 3.4 6.8 1.0 CB C:CYS238 3.6 9.7 1.0 N C:CYS176 3.7 23.2 1.0 CA C:CYS176 4.0 21.0 1.0 N C:HIS179 4.2 21.2 1.0 CA C:CYS238 4.2 8.5 1.0 NE2 C:HIS179 4.2 4.4 1.0 CD2 C:HIS179 4.2 4.4 1.0 O C:CYS176 4.4 14.5 1.0 CA C:HIS179 4.5 17.1 1.0 CA C:CYS242 4.5 16.4 1.0 C C:CYS176 4.5 17.8 1.0 O C:MET237 4.7 7.2 1.0 N C:ASN239 4.8 4.4 1.0 C C:ARG175 4.8 22.5 1.0 C C:CYS238 4.9 6.0 1.0

Zinc binding site 3 out of 4 in the An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1 b:12.1 occ:1.00 ND1 D:HIS179 2.3 12.8 1.0 SG D:CYS176 2.3 21.5 1.0 SG D:CYS238 2.4 9.6 1.0 SG D:CYS242 2.5 35.2 1.0 CE1 D:HIS179 2.7 5.7 1.0 CB D:CYS242 2.9 28.4 1.0 CB D:CYS176 3.1 23.8 1.0 CG D:HIS179 3.2 10.0 1.0 NE2 D:HIS179 3.5 4.4 1.0 CB D:CYS238 3.6 18.6 1.0 CD2 D:HIS179 3.8 12.6 1.0 CB D:HIS179 3.9 16.5 1.0 CA D:CYS238 3.9 17.4 1.0 N D:ASN239 4.2 18.5 1.0 CA D:CYS176 4.4 27.1 1.0 CA D:CYS242 4.4 25.6 1.0 N D:CYS176 4.5 27.2 1.0 C D:CYS238 4.6 17.4 1.0 N D:HIS179 4.8 30.1 1.0 O D:MET237 4.9 12.3 1.0 C D:CYS176 5.0 29.9 1.0

Zinc binding site 4 out of 4 in the An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1 b:64.1 occ:1.00 SG B:CYS238 2.7 72.3 1.0 SG B:CYS176 2.8 83.4 1.0 ND1 B:HIS179 2.9 81.9 1.0 SG B:CYS242 3.0 77.6 1.0 CB B:CYS242 3.5 81.6 1.0 CG B:HIS179 3.6 80.5 1.0 CE1 B:HIS179 3.7 80.6 1.0 CB B:HIS179 3.8 79.4 1.0 CB B:CYS238 3.8 78.5 1.0 CB B:CYS176 4.0 78.5 1.0 CA B:CYS238 4.3 76.3 1.0 N B:CYS176 4.3 75.9 1.0 N B:ASN239 4.6 75.7 1.0 CD2 B:HIS179 4.6 82.2 1.0 NE2 B:HIS179 4.7 80.6 1.0 CA B:CYS176 4.7 76.3 1.0 N B:HIS179 4.8 78.7 1.0 O B:MET237 4.9 75.2 1.0 CA B:HIS179 4.9 81.0 1.0 C B:CYS238 4.9 77.0 1.0

T.J.Petty, S.Emamzadah, L.Costantino, I.Petkova, E.S.Stavridi, J.G.Saven, E.Vauthey, T.D.Halazonetis. An Induced Fit Mechanism Regulates P53 Dna Binding Kinetics to Confer Sequence Specificity. Embo J. V. 30 2167 2011.
ISSN: ISSN 0261-4189
PubMed: 21522129
DOI: 10.1038/EMBOJ.2011.127