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Zinc in PDB 7b4c: Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (II)

Protein crystallography data

The structure of Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (II), PDB code: 7b4c was solved by O.Degtjarik, H.Rozenberg, Z.Shakked, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.75 / 1.71
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.881, 71.083, 84.923, 90, 90.03, 90
R / Rfree (%) 14.9 / 18.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (II) (pdb code 7b4c). 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 Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (II), PDB code: 7b4c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7b4c

Go back to Zinc Binding Sites List in 7b4c
Zinc binding site 1 out of 4 in the Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (II)


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 Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:28.7
occ:1.00
 ND1 A:HIS179 1.9 35.0 1.0
SG A:CYS242 2.1 43.9 1.0
SG A:CYS176 2.3 29.3 1.0
SG A:CYS238 2.3 21.9 0.5
SG A:CYS238 2.4 23.4 0.5
CE1 A:HIS179 2.8 38.7 1.0
CG A:HIS179 2.9 35.4 1.0
CB A:CYS242 3.1 41.8 1.0
CB A:CYS176 3.2 29.9 1.0
CB A:HIS179 3.4 34.8 1.0
CB A:CYS238 3.5 21.6 0.5
CB A:CYS238 3.6 22.5 0.5
N A:CYS176 3.8 27.3 1.0
CA A:CYS238 3.9 22.0 0.5
CA A:CYS238 3.9 22.5 0.5
NE2 A:HIS179 4.0 39.5 1.0
CD2 A:HIS179 4.0 39.0 1.0
CA A:CYS176 4.1 29.2 1.0
N A:ASN239 4.2 25.4 1.0
N A:HIS179 4.4 38.5 1.0
CA A:HIS179 4.5 37.1 1.0
C A:CYS238 4.5 23.0 0.5
CA A:CYS242 4.5 42.7 1.0
C A:CYS238 4.6 23.3 0.5
C A:CYS176 4.8 32.1 1.0
O A:CYS176 4.8 31.0 1.0
O A:MET237 4.8 23.1 1.0

Zinc binding site 2 out of 4 in 7b4c

Go back to Zinc Binding Sites List in 7b4c
Zinc binding site 2 out of 4 in the Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (II)


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 Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:24.4
occ:1.00
 ND1 B:HIS179 1.8 23.7 1.0
SG B:CYS176 2.3 22.9 1.0
SG B:CYS238 2.3 21.2 0.7
SG B:CYS242 2.3 27.9 1.0
SG B:CYS238 2.7 21.3 0.3
CE1 B:HIS179 2.8 27.6 1.0
CG B:HIS179 2.8 25.3 1.0
CB B:CYS242 3.2 27.1 1.0
CB B:HIS179 3.2 24.8 1.0
CB B:CYS176 3.3 22.9 1.0
CB B:CYS238 3.5 20.4 0.7
CB B:CYS238 3.7 20.2 0.3
O B:HOH522 3.8 14.7 0.7
CA B:CYS238 3.9 20.1 0.3
NE2 B:HIS179 3.9 28.3 1.0
CA B:CYS238 3.9 20.0 0.7
CD2 B:HIS179 3.9 27.6 1.0
N B:CYS176 4.0 22.2 1.0
O B:HOH531 4.1 24.2 1.0
CA B:CYS176 4.2 23.2 1.0
N B:ASN239 4.3 22.2 1.0
N B:HIS179 4.4 26.9 1.0
CA B:HIS179 4.4 26.8 1.0
C B:CYS238 4.5 20.8 0.3
CA B:CYS242 4.6 29.6 1.0
C B:CYS238 4.6 20.9 0.7
O B:MET237 4.8 19.7 1.0
O B:CYS176 4.9 24.2 1.0
C B:CYS176 4.9 24.4 1.0
CD2 B:HIS178 5.0 28.6 1.0

Zinc binding site 3 out of 4 in 7b4c

Go back to Zinc Binding Sites List in 7b4c
Zinc binding site 3 out of 4 in the Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (II)


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 Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:27.0
occ:1.00
 ND1 C:HIS179 1.8 21.9 1.0
SG C:CYS242 2.2 31.7 1.0
SG C:CYS238 2.3 24.1 0.5
SG C:CYS176 2.4 24.9 1.0
SG C:CYS238 2.6 27.2 0.5
CE1 C:HIS179 2.6 23.2 1.0
CG C:HIS179 2.9 23.7 1.0
CB C:CYS238 3.0 24.6 0.5
CB C:CYS242 3.0 32.4 1.0
CB C:HIS179 3.4 24.3 1.0
CB C:CYS176 3.5 25.4 1.0
CB C:CYS238 3.7 25.8 0.5
CA C:CYS238 3.8 24.1 0.5
CA C:CYS238 3.8 25.0 0.5
NE2 C:HIS179 3.8 24.1 1.0
CD2 C:HIS179 4.0 23.9 1.0
N C:CYS176 4.1 25.1 1.0
O C:HOH530 4.1 33.1 1.0
N C:ASN239 4.3 26.6 1.0
CA C:CYS176 4.4 26.0 1.0
CA C:CYS242 4.4 35.6 1.0
C C:CYS238 4.5 25.3 0.5
N C:HIS179 4.6 26.8 1.0
CA C:HIS179 4.6 26.3 1.0
C C:CYS238 4.6 24.6 0.5
O C:MET237 4.8 26.1 1.0
O C:HOH465 4.8 28.9 1.0
O C:CYS176 4.9 26.4 1.0
O C:ASN239 4.9 29.4 1.0

Zinc binding site 4 out of 4 in 7b4c

Go back to Zinc Binding Sites List in 7b4c
Zinc binding site 4 out of 4 in the Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (II)


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 Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:30.4
occ:1.00
 ND1 D:HIS179 2.0 35.8 1.0
SG D:CYS238 2.2 25.0 0.5
SG D:CYS176 2.3 36.1 1.0
SG D:CYS238 2.4 26.0 0.5
SG D:CYS242 2.4 37.5 1.0
CE1 D:HIS179 3.0 37.4 1.0
CG D:HIS179 3.1 36.3 1.0
CB D:CYS242 3.1 36.2 1.0
CB D:CYS176 3.4 34.8 1.0
CB D:CYS238 3.4 24.1 0.5
CB D:HIS179 3.5 34.8 1.0
CB D:CYS238 3.5 24.9 0.5
CA D:CYS238 3.8 24.5 0.5
CA D:CYS238 3.8 24.9 0.5
N D:CYS176 4.0 31.7 1.0
O D:HOH522 4.0 46.5 1.0
NE2 D:HIS179 4.2 37.7 1.0
CD2 D:HIS179 4.2 38.0 1.0
N D:ASN239 4.2 26.7 1.0
CA D:CYS176 4.3 34.4 1.0
N D:HIS179 4.4 38.2 1.0
C D:CYS238 4.5 24.7 0.5
C D:CYS238 4.6 25.0 0.5
CA D:CYS242 4.6 37.4 1.0
CA D:HIS179 4.6 36.5 1.0
O D:HOH423 4.7 46.8 1.0
O D:HOH455 4.8 35.2 1.0
O D:MET237 4.9 25.4 1.0
C D:CYS176 5.0 36.4 1.0
O D:ASN239 5.0 27.2 1.0

Reference:

O.Degtjarik, D.Golovenko, Y.Diskin-Posner, L.Abrahmsen, H.Rozenberg, Z.Shakked. P53 Structure 6 To Be Published.
Page generated: Tue Oct 29 17:25:14 2024

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