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Zinc in PDB 2ac0: Structural Basis of Dna Recognition By P53 Tetramers (Complex I)

Protein crystallography data

The structure of Structural Basis of Dna Recognition By P53 Tetramers (Complex I), PDB code: 2ac0 was solved by M.Kitayner, H.Rozenberg, N.Kessler, D.Rabinovich, Z.Shakked, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.52 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.439, 58.146, 77.539, 82.93, 87.99, 73.60
R / Rfree (%) 15.3 / 21.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis of Dna Recognition By P53 Tetramers (Complex I) (pdb code 2ac0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Basis of Dna Recognition By P53 Tetramers (Complex I), PDB code: 2ac0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2ac0

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Zinc binding site 1 out of 4 in the Structural Basis of Dna Recognition By P53 Tetramers (Complex I)


Mono view


Stereo pair view

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

b:17.9
occ:1.00
ND1 A:HIS179 1.9 13.3 1.0
SG A:CYS242 2.3 17.4 1.0
SG A:CYS176 2.3 16.6 1.0
SG A:CYS238 2.3 16.7 1.0
CE1 A:HIS179 2.9 16.0 1.0
CG A:HIS179 3.0 19.6 1.0
CB A:CYS242 3.1 14.8 1.0
CB A:CYS238 3.3 18.5 1.0
CB A:HIS179 3.4 16.6 1.0
CB A:CYS176 3.4 17.8 1.0
CA A:CYS238 3.8 15.3 1.0
N A:CYS176 3.9 18.0 1.0
NE2 A:HIS179 4.0 20.8 1.0
CD2 A:HIS179 4.1 17.8 1.0
CA A:CYS176 4.3 14.8 1.0
N A:HIS179 4.4 18.5 1.0
N A:ASN239 4.5 14.2 1.0
CA A:HIS179 4.5 17.6 1.0
O A:HOH512 4.6 39.0 1.0
CA A:CYS242 4.6 17.9 1.0
CE B:MET243 4.6 31.2 1.0
C A:CYS238 4.6 15.7 1.0
O A:MET237 4.7 15.6 1.0
O A:HOH320 4.7 15.0 1.0
N A:CYS238 4.9 15.0 1.0
C A:CYS176 4.9 18.9 1.0
O A:CYS176 5.0 17.7 1.0

Zinc binding site 2 out of 4 in 2ac0

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Zinc binding site 2 out of 4 in the Structural Basis of Dna Recognition By P53 Tetramers (Complex I)


Mono view


Stereo pair view

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

b:20.3
occ:1.00
ND1 B:HIS179 2.1 20.9 1.0
SG B:CYS238 2.3 16.1 1.0
SG B:CYS242 2.3 18.0 1.0
SG B:CYS176 2.3 20.1 1.0
CE1 B:HIS179 3.0 20.9 1.0
CB B:CYS242 3.0 16.4 1.0
CG B:HIS179 3.1 18.8 1.0
CB B:CYS238 3.3 18.8 1.0
CB B:CYS176 3.4 17.6 1.0
CB B:HIS179 3.5 17.0 1.0
CA B:CYS238 3.8 14.5 1.0
N B:CYS176 4.1 16.1 1.0
NE2 B:HIS179 4.1 19.5 1.0
CD2 B:HIS179 4.2 20.5 1.0
CA B:CYS176 4.3 17.8 1.0
CE A:MET243 4.4 18.5 1.0
N B:HIS179 4.4 17.1 1.0
CA B:CYS242 4.5 17.4 1.0
N B:ASN239 4.5 13.2 1.0
CA B:HIS179 4.6 13.8 1.0
O B:MET237 4.6 15.5 1.0
O B:HOH301 4.7 16.4 1.0
C B:CYS238 4.7 14.1 1.0
N B:CYS238 4.9 14.7 1.0
C B:CYS176 5.0 18.6 1.0

Zinc binding site 3 out of 4 in 2ac0

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Zinc binding site 3 out of 4 in the Structural Basis of Dna Recognition By P53 Tetramers (Complex I)


Mono view


Stereo pair view

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

b:17.1
occ:1.00
ND1 C:HIS179 2.1 14.2 1.0
SG C:CYS242 2.2 16.8 1.0
SG C:CYS238 2.3 15.1 1.0
SG C:CYS176 2.4 16.7 1.0
CG C:HIS179 3.1 17.4 1.0
CE1 C:HIS179 3.1 16.3 1.0
CB C:CYS242 3.1 16.2 1.0
CB C:CYS238 3.2 13.9 1.0
CB C:HIS179 3.4 13.4 1.0
CB C:CYS176 3.5 15.0 1.0
CA C:CYS238 3.8 12.2 1.0
N C:CYS176 4.0 13.6 1.0
NE2 C:HIS179 4.2 16.8 1.0
CD2 C:HIS179 4.2 19.2 1.0
CA C:CYS176 4.4 15.7 1.0
N C:HIS179 4.4 14.7 1.0
N C:ASN239 4.5 13.2 1.0
CA C:CYS242 4.5 19.2 1.0
CA C:HIS179 4.5 14.3 1.0
O C:HOH306 4.6 17.7 1.0
CE D:MET243 4.6 37.8 1.0
O C:MET237 4.7 13.7 1.0
C C:CYS238 4.7 15.6 1.0
N C:CYS238 4.9 11.7 1.0
O C:CYS176 5.0 16.4 1.0

Zinc binding site 4 out of 4 in 2ac0

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Zinc binding site 4 out of 4 in the Structural Basis of Dna Recognition By P53 Tetramers (Complex I)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis of Dna Recognition By P53 Tetramers (Complex I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:19.3
occ:1.00
ND1 D:HIS179 2.0 17.6 1.0
SG D:CYS242 2.3 19.9 1.0
SG D:CYS176 2.4 16.7 1.0
SG D:CYS238 2.4 17.5 1.0
CE1 D:HIS179 2.9 17.4 1.0
CG D:HIS179 3.0 17.1 1.0
CB D:CYS242 3.1 19.7 1.0
CB D:CYS238 3.3 20.0 1.0
CB D:HIS179 3.4 16.8 1.0
CB D:CYS176 3.4 17.7 1.0
CA D:CYS238 3.9 18.3 1.0
N D:CYS176 4.0 13.6 1.0
NE2 D:HIS179 4.1 20.4 1.0
CD2 D:HIS179 4.1 23.2 1.0
CA D:CYS176 4.3 15.9 1.0
CE C:MET243 4.4 31.0 1.0
N D:HIS179 4.5 20.0 1.0
CA D:CYS242 4.5 19.3 1.0
N D:ASN239 4.5 17.4 1.0
O D:MET237 4.6 13.9 1.0
CA D:HIS179 4.6 18.0 1.0
O D:HOH305 4.7 19.6 1.0
C D:CYS238 4.7 17.5 1.0
O D:CYS176 4.9 17.8 1.0
C D:CYS176 5.0 18.0 1.0
N D:CYS238 5.0 15.9 1.0

Reference:

M.Kitayner, H.Rozenberg, N.Kessler, D.Rabinovich, L.Shaulov, T.E.Haran, Z.Shakked. Structural Basis of Dna Recognition By P53 Tetramers Mol.Cell V. 22 741 2006.
ISSN: ISSN 1097-2765
PubMed: 16793544
DOI: 10.1016/J.MOLCEL.2006.05.015
Page generated: Wed Dec 16 03:17:11 2020

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