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Zinc in PDB 3d0a: Human P53 Core Domain with Hot Spot Mutation R249S and Second Site Suppressor Mutation H168R in Sequence-Specific Complex with Dna

Protein crystallography data

The structure of Human P53 Core Domain with Hot Spot Mutation R249S and Second Site Suppressor Mutation H168R in Sequence-Specific Complex with Dna, PDB code: 3d0a was solved by O.Suad, H.Rozenberg, Z.Shakked, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.76 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 54.299, 57.986, 78.926, 83.05, 88.11, 74.08
R / Rfree (%) 18.3 / 24.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Human P53 Core Domain with Hot Spot Mutation R249S and Second Site Suppressor Mutation H168R in Sequence-Specific Complex with Dna (pdb code 3d0a). 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 with Hot Spot Mutation R249S and Second Site Suppressor Mutation H168R in Sequence-Specific Complex with Dna, PDB code: 3d0a:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3d0a

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Zinc binding site 1 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R249S and Second Site Suppressor Mutation H168R in Sequence-Specific 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 Human P53 Core Domain with Hot Spot Mutation R249S and Second Site Suppressor Mutation H168R in Sequence-Specific Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:23.7
occ:1.00
ND1 A:HIS179 2.0 21.2 1.0
SG A:CYS176 2.3 20.2 1.0
SG A:CYS242 2.3 25.8 1.0
SG A:CYS238 2.3 17.9 0.5
SG A:CYS238 2.4 16.7 0.5
CE1 A:HIS179 2.8 21.4 1.0
CG A:HIS179 3.1 21.8 1.0
CB A:CYS242 3.2 21.7 1.0
CB A:CYS238 3.5 22.3 0.5
CB A:CYS176 3.5 20.9 1.0
CB A:CYS238 3.5 22.7 0.5
CB A:HIS179 3.6 21.1 1.0
CA A:CYS238 3.8 19.1 0.5
CA A:CYS238 3.8 19.2 0.5
NE2 A:HIS179 4.0 23.1 1.0
N A:CYS176 4.0 22.7 1.0
CD2 A:HIS179 4.1 26.4 1.0
N A:ASN239 4.2 15.5 1.0
CA A:CYS176 4.3 23.6 1.0
N A:HIS179 4.5 25.8 1.0
C A:CYS238 4.5 16.7 1.0
O A:HOH458 4.6 44.1 1.0
CA A:CYS242 4.6 22.4 1.0
CA A:HIS179 4.7 25.8 1.0
O A:HOH332 4.7 28.6 1.0
O A:HOH347 4.7 30.8 1.0
O A:ASN239 4.9 18.0 1.0
O A:MET237 4.9 18.1 1.0
C A:CYS176 5.0 23.1 1.0

Zinc binding site 2 out of 4 in 3d0a

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Zinc binding site 2 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R249S and Second Site Suppressor Mutation H168R in Sequence-Specific 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 Human P53 Core Domain with Hot Spot Mutation R249S and Second Site Suppressor Mutation H168R in Sequence-Specific Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:26.2
occ:1.00
ND1 B:HIS179 2.0 24.0 1.0
SG B:CYS242 2.3 27.4 1.0
SG B:CYS238 2.3 25.1 0.5
SG B:CYS176 2.4 26.5 1.0
SG B:CYS238 2.4 16.4 0.5
CE1 B:HIS179 2.9 31.3 1.0
CB B:CYS242 3.0 22.8 1.0
CG B:HIS179 3.1 26.2 1.0
CB B:CYS238 3.3 22.7 0.5
CB B:CYS176 3.5 23.9 1.0
CB B:HIS179 3.5 27.2 1.0
CB B:CYS238 3.6 27.7 0.5
CA B:CYS238 3.7 22.2 0.5
CA B:CYS238 3.8 24.1 0.5
N B:CYS176 4.1 24.1 1.0
NE2 B:HIS179 4.1 27.1 1.0
CD2 B:HIS179 4.2 31.8 1.0
N B:ASN239 4.3 21.1 1.0
CA B:CYS176 4.4 25.5 1.0
N B:HIS179 4.5 28.9 1.0
CA B:CYS242 4.5 21.9 1.0
CE A:MET243 4.5 38.0 1.0
C B:CYS238 4.5 22.6 1.0
CA B:HIS179 4.6 27.1 1.0
O B:MET237 4.7 26.6 1.0
O B:HOH310 4.8 30.6 1.0
N B:CYS238 5.0 22.9 1.0

Zinc binding site 3 out of 4 in 3d0a

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Zinc binding site 3 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R249S and Second Site Suppressor Mutation H168R in Sequence-Specific 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 Human P53 Core Domain with Hot Spot Mutation R249S and Second Site Suppressor Mutation H168R in Sequence-Specific Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:23.7
occ:1.00
ND1 C:HIS179 1.8 21.1 1.0
SG C:CYS238 2.2 22.4 0.5
SG C:CYS242 2.3 29.1 1.0
SG C:CYS176 2.3 21.6 1.0
SG C:CYS238 2.5 17.8 0.5
CE1 C:HIS179 2.7 30.5 1.0
CG C:HIS179 3.0 23.5 1.0
CB C:CYS242 3.1 22.3 1.0
CB C:CYS176 3.4 22.1 1.0
CB C:CYS238 3.5 24.5 0.5
CB C:CYS238 3.5 24.6 0.5
CB C:HIS179 3.5 22.6 1.0
CA C:CYS238 3.8 18.9 0.5
CA C:CYS238 3.8 18.3 0.5
NE2 C:HIS179 3.9 29.1 1.0
N C:CYS176 4.0 19.1 1.0
CD2 C:HIS179 4.0 26.6 1.0
CE D:MET243 4.1 23.0 0.5
N C:ASN239 4.3 21.9 1.0
CA C:CYS176 4.3 22.3 1.0
N C:HIS179 4.5 27.1 1.0
CA C:CYS242 4.5 23.9 1.0
C C:CYS238 4.5 21.3 1.0
CA C:HIS179 4.6 23.6 1.0
O C:HOH492 4.6 28.0 1.0
O C:HOH526 4.7 32.4 1.0
O C:MET237 4.8 16.6 1.0
O C:ASN239 4.9 19.1 1.0
C C:CYS176 5.0 23.1 1.0

Zinc binding site 4 out of 4 in 3d0a

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Zinc binding site 4 out of 4 in the Human P53 Core Domain with Hot Spot Mutation R249S and Second Site Suppressor Mutation H168R in Sequence-Specific Complex with 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 with Hot Spot Mutation R249S and Second Site Suppressor Mutation H168R in Sequence-Specific Complex with Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:25.3
occ:1.00
ND1 D:HIS179 2.1 21.2 1.0
SG D:CYS242 2.1 28.7 1.0
SG D:CYS238 2.3 13.6 0.5
SG D:CYS176 2.3 23.7 1.0
SG D:CYS238 2.4 26.7 0.5
CE1 D:HIS179 3.0 29.1 1.0
CB D:CYS242 3.1 29.1 1.0
CG D:HIS179 3.1 25.1 1.0
CB D:CYS238 3.4 23.8 0.5
CB D:CYS176 3.4 22.9 1.0
CB D:HIS179 3.5 25.5 1.0
CB D:CYS238 3.6 26.2 0.5
CA D:CYS238 3.9 21.3 0.5
CA D:CYS238 3.9 23.4 0.5
N D:CYS176 4.0 22.4 1.0
NE2 D:HIS179 4.1 26.7 1.0
CD2 D:HIS179 4.2 32.0 1.0
CA D:CYS176 4.3 22.9 1.0
N D:ASN239 4.4 22.7 1.0
N D:HIS179 4.4 25.4 1.0
CA D:CYS242 4.5 25.4 1.0
CA D:HIS179 4.6 26.3 1.0
CE C:MET243 4.6 36.9 1.0
C D:CYS238 4.6 21.9 1.0
O D:MET237 4.7 21.3 1.0
O D:HOH321 4.8 31.9 1.0
C D:CYS176 4.9 23.4 1.0
O D:CYS176 5.0 21.1 1.0

Reference:

O.Suad, H.Rozenberg, R.Brosh, Y.Diskin-Posner, N.Kessler, L.J.W.Shimon, F.Frolow, A.Liran, V.Rotter, Z.Shakked. Structural Basis of Restoring Sequence-Specific Dna Binding and Transactivation to Mutant P53 By Suppressor Mutations J.Mol.Biol. V. 385 249 2009.
ISSN: ISSN 0022-2836
PubMed: 18996393
DOI: 10.1016/J.JMB.2008.10.063
Page generated: Wed Dec 16 04:11:47 2020

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