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Zinc in PDB 1tsr: P53 Core Domain in Complex with Dna

Protein crystallography data

The structure of P53 Core Domain in Complex with Dna, PDB code: 1tsr was solved by Y.Cho, S.Gorina, P.Jeffrey, N.Pavletich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 117.500, 67.900, 108.800, 90.00, 105.50, 90.00
R / Rfree (%) n/a / n/a

Zinc Binding Sites:

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

Zinc binding site 1 out of 3 in 1tsr

Go back to Zinc Binding Sites List in 1tsr
Zinc binding site 1 out of 3 in the P53 Core Domain in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of P53 Core Domain in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:27.1
occ:1.00
ND1 A:HIS179 2.0 26.1 1.0
SG A:CYS242 2.2 28.1 1.0
SG A:CYS238 2.3 24.5 1.0
SG A:CYS176 2.3 30.6 1.0
CE1 A:HIS179 2.9 26.9 1.0
CG A:HIS179 3.1 24.0 1.0
CB A:CYS242 3.1 25.8 1.0
CB A:CYS176 3.4 19.3 1.0
CB A:HIS179 3.5 28.1 1.0
CB A:CYS238 3.6 20.0 1.0
CA A:CYS238 3.9 15.0 1.0
N A:CYS176 4.0 16.7 1.0
N A:ASN239 4.0 17.4 1.0
NE2 A:HIS179 4.1 25.5 1.0
CD2 A:HIS179 4.2 24.6 1.0
CA A:CYS176 4.3 13.4 1.0
N A:HIS179 4.4 31.4 1.0
C A:CYS238 4.4 13.7 1.0
O A:HOH408 4.5 48.4 1.0
CA A:HIS179 4.5 30.1 1.0
CA A:CYS242 4.6 29.0 1.0
O A:HOH400 4.8 36.1 1.0
O A:ASN239 4.9 20.9 1.0
C A:CYS176 4.9 17.8 1.0
O A:MET237 5.0 19.0 1.0

Zinc binding site 2 out of 3 in 1tsr

Go back to Zinc Binding Sites List in 1tsr
Zinc binding site 2 out of 3 in the P53 Core Domain in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of P53 Core Domain in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:28.1
occ:1.00
ND1 B:HIS179 2.1 23.8 1.0
SG B:CYS238 2.2 25.0 1.0
SG B:CYS242 2.2 27.8 1.0
SG B:CYS176 2.3 29.7 1.0
CE1 B:HIS179 3.0 20.3 1.0
CG B:HIS179 3.1 18.6 1.0
CB B:CYS238 3.2 21.7 1.0
CB B:CYS242 3.2 27.2 1.0
CB B:CYS176 3.4 22.7 1.0
CB B:HIS179 3.5 23.6 1.0
CA B:CYS238 3.8 19.2 1.0
N B:CYS176 4.0 25.9 1.0
NE2 B:HIS179 4.1 21.4 1.0
CD2 B:HIS179 4.2 19.3 1.0
CA B:CYS176 4.3 24.2 1.0
O B:HOH333 4.4 53.4 1.0
N B:ASN239 4.5 15.5 1.0
CA B:CYS242 4.6 30.9 1.0
N B:HIS179 4.6 24.0 1.0
CA B:HIS179 4.6 22.6 1.0
C B:CYS238 4.7 15.5 1.0
O B:MET237 4.7 21.7 1.0
O B:HOH320 4.7 18.5 1.0
O B:CYS176 4.9 31.0 1.0
C B:CYS176 4.9 29.3 1.0
N B:CYS238 5.0 19.2 1.0

Zinc binding site 3 out of 3 in 1tsr

Go back to Zinc Binding Sites List in 1tsr
Zinc binding site 3 out of 3 in the P53 Core Domain in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of P53 Core Domain in Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:41.3
occ:1.00
ND1 C:HIS179 2.1 43.3 1.0
SG C:CYS242 2.1 36.6 1.0
SG C:CYS238 2.3 40.9 1.0
SG C:CYS176 2.4 46.4 1.0
CG C:HIS179 3.0 42.2 1.0
CB C:CYS242 3.1 36.8 1.0
CB C:HIS179 3.2 43.0 1.0
CE1 C:HIS179 3.2 43.7 1.0
CB C:CYS238 3.4 34.5 1.0
CB C:CYS176 3.4 40.3 1.0
N C:CYS176 3.8 32.0 1.0
CA C:CYS238 3.9 34.9 1.0
CD2 C:HIS179 4.2 41.5 1.0
CA C:CYS176 4.3 36.8 1.0
NE2 C:HIS179 4.3 41.6 1.0
CA C:HIS179 4.4 42.0 1.0
N C:ASN239 4.4 29.2 1.0
N C:HIS179 4.4 46.6 1.0
CA C:CYS242 4.5 38.7 1.0
C C:CYS238 4.6 33.7 1.0
O C:HOH316 4.8 30.9 1.0
O C:HOH337 4.9 30.9 1.0
O C:MET237 4.9 43.2 1.0
O C:CYS176 4.9 32.0 1.0
C C:ARG175 4.9 35.3 1.0
C C:CYS176 5.0 38.0 1.0
CB C:ARG175 5.0 38.1 1.0

Reference:

Y.Cho, S.Gorina, P.D.Jeffrey, N.P.Pavletich. Crystal Structure of A P53 Tumor Suppressor-Dna Complex: Understanding Tumorigenic Mutations. Science V. 265 346 1994.
ISSN: ISSN 0036-8075
PubMed: 8023157
Page generated: Mon Jan 25 16:14:24 2021

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