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Zinc in PDB 2ocj: Human P53 Core Domain in the Absence of Dna

Protein crystallography data

The structure of Human P53 Core Domain in the Absence of Dna, PDB code: 2ocj was solved by Y.Wang, A.Rosengarth, H.Luecke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.913, 69.364, 84.179, 90.00, 90.11, 90.00
R / Rfree (%) 20.9 / 24.6

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 2ocj

Go back to Zinc Binding Sites List in 2ocj
Zinc binding site 1 out of 4 in the Human P53 Core Domain in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human P53 Core Domain in the Absence of Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:26.8
occ:1.00
ND1 A:HIS179 2.1 31.9 1.0
SG A:CYS242 2.4 35.0 1.0
SG A:CYS238 2.5 32.1 1.0
SG A:CYS176 2.5 29.3 1.0
CE1 A:HIS179 3.0 33.5 1.0
CG A:HIS179 3.1 33.8 1.0
CB A:CYS242 3.1 37.8 1.0
CB A:HIS179 3.5 33.2 1.0
CB A:CYS176 3.6 23.3 1.0
CB A:CYS238 3.7 31.4 1.0
CA A:CYS238 4.0 29.0 1.0
N A:CYS176 4.1 23.6 1.0
NE2 A:HIS179 4.1 34.6 1.0
CD2 A:HIS179 4.2 33.9 1.0
N A:ASN239 4.3 32.2 1.0
N A:HIS179 4.4 31.6 1.0
CA A:CYS176 4.4 25.6 1.0
CA A:CYS242 4.5 41.7 1.0
CA A:HIS179 4.6 34.0 1.0
O A:MET237 4.7 25.5 1.0
C A:CYS238 4.7 31.1 1.0

Zinc binding site 2 out of 4 in 2ocj

Go back to Zinc Binding Sites List in 2ocj
Zinc binding site 2 out of 4 in the Human P53 Core Domain in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human P53 Core Domain in the Absence of Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:24.5
occ:1.00
ND1 B:HIS179 2.1 17.0 1.0
SG B:CYS242 2.4 29.8 1.0
SG B:CYS238 2.5 31.1 1.0
SG B:CYS176 2.5 24.9 1.0
CE1 B:HIS179 3.0 21.4 1.0
CB B:CYS242 3.1 29.4 1.0
CG B:HIS179 3.1 22.2 1.0
CB B:CYS176 3.5 20.6 1.0
CB B:HIS179 3.5 24.3 1.0
CB B:CYS238 3.7 27.6 1.0
CA B:CYS238 3.9 23.5 1.0
N B:CYS176 4.0 21.7 1.0
NE2 B:HIS179 4.1 20.6 1.0
N B:ASN239 4.2 25.8 1.0
CD2 B:HIS179 4.2 20.8 1.0
CA B:CYS176 4.3 22.8 1.0
N B:HIS179 4.4 25.1 1.0
CA B:CYS242 4.5 32.0 1.0
C B:CYS238 4.6 24.9 1.0
CA B:HIS179 4.6 27.0 1.0
O B:CYS176 4.9 21.1 1.0
O B:HOH612 4.9 27.3 1.0
O B:ASN239 4.9 23.7 1.0
O B:MET237 4.9 15.7 1.0
C B:CYS176 5.0 22.9 1.0

Zinc binding site 3 out of 4 in 2ocj

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Zinc binding site 3 out of 4 in the Human P53 Core Domain in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human P53 Core Domain in the Absence of Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:44.8
occ:1.00
ND1 C:HIS179 2.4 54.5 1.0
SG C:CYS238 2.5 43.8 1.0
SG C:CYS176 2.6 43.8 1.0
SG C:CYS242 2.7 61.0 1.0
CE1 C:HIS179 3.1 54.3 1.0
CG C:HIS179 3.2 55.3 1.0
CB C:CYS242 3.2 57.9 1.0
CB C:HIS179 3.6 56.4 1.0
CB C:CYS238 3.8 40.4 1.0
CA C:CYS238 4.0 37.5 1.0
CB C:CYS176 4.0 44.0 1.0
NE2 C:HIS179 4.0 54.5 1.0
CD2 C:HIS179 4.1 55.5 1.0
N C:ASN239 4.2 38.4 1.0
N C:CYS176 4.3 41.5 1.0
N C:HIS179 4.5 57.2 1.0
C C:CYS238 4.5 38.5 1.0
CA C:CYS242 4.6 58.1 1.0
CA C:CYS176 4.7 44.4 1.0
CA C:HIS179 4.7 58.1 1.0
O C:MET237 4.8 33.5 1.0
O C:ASN239 4.8 40.4 1.0

Zinc binding site 4 out of 4 in 2ocj

Go back to Zinc Binding Sites List in 2ocj
Zinc binding site 4 out of 4 in the Human P53 Core Domain in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human P53 Core Domain in the Absence of Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn504

b:40.1
occ:1.00
ND1 D:HIS179 2.3 56.8 1.0
SG D:CYS238 2.4 40.2 1.0
SG D:CYS176 2.6 39.3 1.0
SG D:CYS242 2.6 48.2 1.0
CE1 D:HIS179 3.0 56.4 1.0
CG D:HIS179 3.1 56.2 1.0
CB D:CYS242 3.3 48.5 1.0
CB D:HIS179 3.5 56.2 1.0
CB D:CYS176 3.6 40.2 1.0
CB D:CYS238 3.8 37.4 1.0
NE2 D:HIS179 3.9 55.9 1.0
CA D:CYS238 4.0 34.9 1.0
CD2 D:HIS179 4.0 56.7 1.0
N D:CYS176 4.1 39.3 1.0
N D:ASN239 4.2 34.1 1.0
N D:HIS179 4.4 55.3 1.0
CA D:CYS176 4.4 40.8 1.0
C D:CYS238 4.6 35.8 1.0
CA D:HIS179 4.6 56.8 1.0
CA D:CYS242 4.7 48.9 1.0
O D:MET237 4.7 31.8 1.0
O D:CYS176 4.8 42.1 1.0
O D:ASN239 4.9 32.9 1.0
C D:CYS176 4.9 43.0 1.0

Reference:

Y.Wang, A.Rosengarth, H.Luecke. Structure of the Human P53 Core Domain in the Absence of Dna. Acta Crystallogr.,Sect.D V. 63 276 2007.
ISSN: ISSN 0907-4449
PubMed: 17327663
DOI: 10.1107/S0907444906048499
Page generated: Wed Dec 16 03:45:52 2020

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