Zinc in PDB 5lgy: Lysine 120-Acetylated P53 Dna Binding Domain in A Complex with the Bax Response Element.

The structure of Lysine 120-Acetylated P53 Dna Binding Domain in A Complex with the Bax Response Element., PDB code: 5lgy was solved by E.Arbely, R.Vainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.46 / 2.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.703, 70.344, 104.995, 90.00, 95.83, 90.00
R / Rfree (%)	23.8 / 27.7

The binding sites of Zinc atom in the Lysine 120-Acetylated P53 Dna Binding Domain in A Complex with the Bax Response Element. (pdb code 5lgy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Lysine 120-Acetylated P53 Dna Binding Domain in A Complex with the Bax Response Element., PDB code: 5lgy:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Lysine 120-Acetylated P53 Dna Binding Domain in A Complex with the Bax Response Element.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Lysine 120-Acetylated P53 Dna Binding Domain in A Complex with the Bax Response Element. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:37.5 occ:1.00 ND1 A:HIS179 2.1 35.1 1.0 SG A:CYS238 2.4 45.3 1.0 SG A:CYS242 2.4 38.8 1.0 SG A:CYS176 2.5 45.3 1.0 CE1 A:HIS179 2.9 33.7 1.0 CG A:HIS179 3.1 38.7 1.0 CB A:CYS242 3.1 35.7 1.0 CB A:CYS176 3.3 40.6 1.0 CB A:CYS238 3.4 36.0 1.0 CB A:HIS179 3.6 45.4 1.0 CA A:CYS238 3.8 36.1 1.0 NE2 A:HIS179 3.9 37.3 1.0 N A:CYS176 4.0 46.4 1.0 CD2 A:HIS179 4.1 39.0 1.0 CA A:CYS176 4.3 41.6 1.0 N A:ASN239 4.4 33.5 1.0 CA A:CYS242 4.5 39.5 1.0 O A:MET237 4.5 35.3 1.0 C A:CYS238 4.6 37.5 1.0 N A:HIS179 4.7 41.4 1.0 CA A:HIS179 4.7 41.1 1.0 CE B:MET243 4.8 37.0 1.0 O A:CYS176 5.0 48.1 1.0 SD B:MET243 5.0 50.6 1.0 O A:ASN239 5.0 35.0 1.0 N A:CYS238 5.0 37.9 1.0

Zinc binding site 2 out of 4 in the Lysine 120-Acetylated P53 Dna Binding Domain in A Complex with the Bax Response Element.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Lysine 120-Acetylated P53 Dna Binding Domain in A Complex with the Bax Response Element. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:30.9 occ:1.00 ND1 B:HIS179 2.3 31.1 1.0 SG B:CYS242 2.3 34.1 1.0 SG B:CYS176 2.4 37.3 1.0 SG B:CYS238 2.5 37.2 1.0 CB B:CYS242 2.8 35.5 1.0 CE1 B:HIS179 3.0 28.8 1.0 CB B:CYS176 3.1 36.6 1.0 CG B:HIS179 3.3 32.1 1.0 CB B:CYS238 3.7 32.4 1.0 CB B:HIS179 3.8 31.7 1.0 N B:CYS176 4.0 36.9 1.0 NE2 B:HIS179 4.0 33.1 1.0 CA B:CYS242 4.1 37.1 1.0 CA B:CYS176 4.2 34.9 1.0 CA B:CYS238 4.2 29.3 1.0 CD2 B:HIS179 4.2 35.9 1.0 CE A:MET243 4.5 42.6 1.0 N B:ASN239 4.6 29.9 1.0 N B:HIS179 4.7 38.0 1.0 C B:CYS238 4.9 29.0 1.0 C B:CYS242 4.9 43.3 1.0 CA B:HIS179 4.9 34.2 1.0 SD A:MET243 4.9 46.7 1.0 O B:ASN239 4.9 34.7 1.0 C B:CYS176 5.0 38.1 1.0 O B:MET237 5.0 33.4 1.0

Zinc binding site 3 out of 4 in the Lysine 120-Acetylated P53 Dna Binding Domain in A Complex with the Bax Response Element.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Lysine 120-Acetylated P53 Dna Binding Domain in A Complex with the Bax Response Element. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:34.7 occ:1.00 ND1 C:HIS179 2.1 42.2 1.0 SG C:CYS238 2.3 33.0 1.0 SG C:CYS242 2.4 47.9 1.0 SG C:CYS176 2.4 44.6 1.0 CE1 C:HIS179 2.8 39.9 1.0 CG C:HIS179 3.1 36.9 1.0 CB C:CYS242 3.2 37.7 1.0 CB C:CYS238 3.3 32.3 1.0 CB C:CYS176 3.5 33.7 1.0 CB C:HIS179 3.6 37.8 1.0 CA C:CYS238 3.7 30.7 1.0 NE2 C:HIS179 3.9 41.8 1.0 CD2 C:HIS179 4.1 41.9 1.0 N C:CYS176 4.1 40.1 1.0 N C:ASN239 4.3 31.0 1.0 CA C:CYS176 4.4 37.5 1.0 O C:MET237 4.4 29.7 1.0 C C:CYS238 4.5 34.7 1.0 CA C:CYS242 4.6 38.2 1.0 N C:HIS179 4.7 44.6 1.0 CA C:HIS179 4.8 39.1 1.0 CE D:MET243 4.8 35.2 1.0 N C:CYS238 4.9 32.8 1.0 O C:ASN239 4.9 34.3 1.0 CG C:ARG175 4.9 38.5 1.0 O C:CYS176 5.0 40.5 1.0

Zinc binding site 4 out of 4 in the Lysine 120-Acetylated P53 Dna Binding Domain in A Complex with the Bax Response Element.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Lysine 120-Acetylated P53 Dna Binding Domain in A Complex with the Bax Response Element. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:37.0 occ:1.00 ND1 D:HIS179 2.2 40.9 1.0 SG D:CYS176 2.3 47.7 1.0 SG D:CYS238 2.4 37.2 1.0 SG D:CYS242 2.4 37.0 1.0 CB D:CYS242 3.0 32.9 1.0 CE1 D:HIS179 3.0 40.2 1.0 CG D:HIS179 3.2 37.3 1.0 CB D:CYS176 3.2 36.3 1.0 CB D:CYS238 3.4 29.5 1.0 CB D:HIS179 3.6 34.8 1.0 N D:CYS176 3.9 38.7 1.0 CA D:CYS238 3.9 31.6 1.0 CA D:CYS176 4.1 32.5 1.0 NE2 D:HIS179 4.2 39.0 1.0 CD2 D:HIS179 4.2 33.4 1.0 CA D:CYS242 4.4 37.6 1.0 N D:ASN239 4.5 28.7 1.0 N D:HIS179 4.6 34.1 1.0 O D:MET237 4.7 35.2 1.0 C D:CYS238 4.7 32.2 1.0 CA D:HIS179 4.7 36.7 1.0 CE C:MET243 4.8 41.1 1.0 O D:CYS176 4.9 38.2 1.0 SD C:MET243 4.9 49.1 1.0 C D:CYS176 4.9 36.9 1.0 O D:ASN239 4.9 34.8 1.0

R.Vainer, S.Cohen, A.Shahar, R.Zarivach, E.Arbely. Structural Basis For P53 LYS120-Acetylation-Dependent Dna-Binding Mode. J.Mol.Biol. V. 428 3013 2016.
ISSN: ESSN 1089-8638
PubMed: 27338200
DOI: 10.1016/J.JMB.2016.06.009