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Zinc in PDB 2ybg: Structure of LYS120-Acetylated P53 Core Domain

Protein crystallography data

The structure of Structure of LYS120-Acetylated P53 Core Domain, PDB code: 2ybg was solved by E.Arbely, M.D.Allen, A.C.Joerger, A.R.Fersht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.212 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.926, 69.581, 83.494, 90.00, 90.12, 90.00
R / Rfree (%) 17.44 / 22.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of LYS120-Acetylated P53 Core Domain (pdb code 2ybg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of LYS120-Acetylated P53 Core Domain, PDB code: 2ybg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2ybg

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Zinc binding site 1 out of 4 in the Structure of LYS120-Acetylated P53 Core Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of LYS120-Acetylated P53 Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:18.8
occ:1.00
 ND1 A:HIS179 2.1 11.9 1.0
SG A:CYS242 2.3 20.2 1.0
SG A:CYS238 2.4 21.0 1.0
SG A:CYS176 2.4 18.1 1.0
CE1 A:HIS179 3.0 16.3 1.0
CB A:CYS242 3.0 20.4 1.0
CG A:HIS179 3.1 17.6 1.0
CB A:HIS179 3.5 18.2 1.0
CB A:CYS176 3.6 19.8 1.0
CB A:CYS238 3.7 20.8 1.0
CA A:CYS238 3.9 16.5 1.0
N A:CYS176 4.1 20.4 1.0
NE2 A:HIS179 4.2 15.8 1.0
N A:ASN239 4.2 19.3 1.0
CD2 A:HIS179 4.2 17.9 1.0
N A:HIS179 4.4 21.2 1.0
CA A:CYS242 4.4 23.4 1.0
OG B:SER106 4.4 29.8 1.0
CA A:CYS176 4.5 19.9 1.0
CA A:HIS179 4.5 19.6 1.0
C A:CYS238 4.6 18.0 1.0
O A:HOH2085 4.7 20.6 1.0
O A:MET237 4.9 14.0 1.0
CD2 A:HIS178 4.9 17.1 1.0

Zinc binding site 2 out of 4 in 2ybg

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Zinc binding site 2 out of 4 in the Structure of LYS120-Acetylated P53 Core Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of LYS120-Acetylated P53 Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:21.1
occ:1.00
 ND1 B:HIS179 2.1 18.0 1.0
SG B:CYS242 2.3 22.0 1.0
SG B:CYS176 2.4 18.0 1.0
SG B:CYS238 2.5 25.3 1.0
CB B:CYS242 3.0 19.4 1.0
CE1 B:HIS179 3.0 20.5 1.0
CG B:HIS179 3.1 20.4 1.0
CB B:CYS176 3.5 21.4 1.0
CB B:HIS179 3.5 22.2 1.0
CB B:CYS238 3.7 18.7 1.0
CA B:CYS238 4.0 17.2 1.0
N B:CYS176 4.0 20.0 1.0
NE2 B:HIS179 4.2 17.5 1.0
CD2 B:HIS179 4.3 18.6 1.0
CA B:CYS176 4.3 22.2 1.0
N B:ASN239 4.4 16.1 1.0
CA B:CYS242 4.4 24.6 1.0
N B:HIS179 4.4 20.3 1.0
CA B:HIS179 4.6 22.9 1.0
C B:CYS238 4.7 16.3 1.0
O B:HOH2144 4.7 30.0 1.0
O B:HOH2081 4.7 20.8 1.0
O B:MET237 4.7 17.5 1.0
O B:CYS176 4.9 19.5 1.0
C B:CYS176 4.9 19.9 1.0

Zinc binding site 3 out of 4 in 2ybg

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Zinc binding site 3 out of 4 in the Structure of LYS120-Acetylated P53 Core Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of LYS120-Acetylated P53 Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:18.9
occ:1.00
 ND1 C:HIS179 2.2 15.7 1.0
SG C:CYS176 2.4 19.2 1.0
SG C:CYS242 2.4 22.1 1.0
SG C:CYS238 2.7 23.5 1.0
CB C:CYS242 3.1 19.1 1.0
CG C:HIS179 3.2 18.1 1.0
CE1 C:HIS179 3.2 18.7 1.0
CB C:HIS179 3.4 18.1 1.0
CB C:CYS176 3.5 19.3 1.0
CB C:CYS238 3.6 22.5 1.0
CA C:CYS238 3.9 19.9 1.0
N C:CYS176 4.1 22.6 1.0
O C:HOH2076 4.1 21.6 1.0
N C:ASN239 4.3 20.0 1.0
NE2 C:HIS179 4.3 19.3 1.0
CD2 C:HIS179 4.3 17.6 1.0
N C:HIS179 4.3 20.8 1.0
O C:HOH2134 4.4 22.8 1.0
CA C:CYS176 4.4 22.1 1.0
CA C:CYS242 4.5 25.2 1.0
CA C:HIS179 4.5 17.7 1.0
C C:CYS238 4.7 20.0 1.0
O C:MET237 4.8 17.2 1.0
O C:CYS176 4.9 19.9 1.0
ND1 C:HIS178 4.9 19.2 1.0
C C:CYS176 5.0 21.1 1.0

Zinc binding site 4 out of 4 in 2ybg

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Zinc binding site 4 out of 4 in the Structure of LYS120-Acetylated P53 Core Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of LYS120-Acetylated P53 Core Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:23.2
occ:1.00
 ND1 D:HIS179 2.0 17.0 1.0
SG D:CYS176 2.4 20.5 1.0
SG D:CYS242 2.4 23.0 1.0
SG D:CYS238 2.7 27.4 1.0
CE1 D:HIS179 2.7 18.7 1.0
CB D:CYS242 3.1 20.2 1.0
CG D:HIS179 3.2 19.6 1.0
CB D:CYS176 3.7 21.4 1.0
CB D:CYS238 3.7 22.4 1.0
CB D:HIS179 3.8 21.1 1.0
NE2 D:HIS179 3.9 18.0 1.0
CA D:CYS238 3.9 18.9 1.0
N D:CYS176 4.1 23.0 1.0
CD2 D:HIS179 4.2 19.6 1.0
N D:ASN239 4.2 19.1 1.0
CA D:CYS176 4.5 23.0 1.0
CA D:CYS242 4.6 20.9 1.0
N D:HIS179 4.6 24.6 1.0
O D:HOH2119 4.6 22.0 1.0
C D:CYS238 4.6 21.2 1.0
CA D:HIS179 4.8 21.3 1.0
O D:HOH2121 4.8 24.1 1.0
O D:ASN239 4.9 19.8 1.0
O D:MET237 4.9 20.1 1.0
O D:HOH2067 4.9 26.4 1.0

Reference:

E.Arbely, E.Natan, T.Brandt, M.D.Allen, D.B.Veprintsev, C.V.Robinson, J.W.Chin, A.C.Joerger, A.R.Fersht. Acetylation of Lysine 120 of P53 Endows Dna- Binding Specificity at Effective Physiological Salt Concentration. Proc.Natl.Acad.Sci.Usa V. 108 8251 2011.
ISSN: ISSN 0027-8424
PubMed: 21525412
DOI: 10.1073/PNAS.1105028108
Page generated: Thu Oct 17 05:47:56 2024

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