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Zinc in PDB 7b48: Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273H Mutant Bound to Mq: R273H-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-R273H Mutant Bound to Mq: R273H-Mq (II), PDB code: 7b48 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) 36.67 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.249, 72.003, 85.233, 90, 90.07, 90
R / Rfree (%) 17.6 / 22.8

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-R273H Mutant Bound to Mq: R273H-Mq (II) (pdb code 7b48). 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-R273H Mutant Bound to Mq: R273H-Mq (II), PDB code: 7b48:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7b48

Go back to Zinc Binding Sites List in 7b48
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-R273H Mutant Bound to Mq: R273H-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-R273H Mutant Bound to Mq: R273H-Mq (II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:30.1
occ:1.00
ND1 A:HIS179 1.9 44.3 1.0
SG A:CYS242 2.0 35.6 1.0
SG A:CYS238 2.5 29.6 1.0
SG A:CYS176 2.6 43.3 1.0
CE1 A:HIS179 2.8 46.1 1.0
CG A:HIS179 2.9 43.3 1.0
CB A:CYS242 3.3 38.2 1.0
CB A:CYS238 3.3 28.5 1.0
CB A:CYS176 3.4 45.9 1.0
CB A:HIS179 3.4 43.1 1.0
CA A:CYS238 3.8 28.3 1.0
N A:CYS176 3.9 48.1 1.0
NE2 A:HIS179 3.9 45.4 1.0
CD2 A:HIS179 4.0 43.9 1.0
CA A:CYS176 4.2 46.4 1.0
N A:ASN239 4.4 30.9 1.0
N A:HIS179 4.5 44.1 1.0
O A:MET237 4.5 26.7 1.0
CA A:HIS179 4.5 44.0 1.0
O A:HOH498 4.6 37.0 1.0
CA A:CYS242 4.6 40.9 1.0
C A:CYS238 4.7 28.6 1.0
C A:CYS176 4.9 45.0 1.0
O A:CYS176 4.9 44.6 1.0
N A:CYS238 4.9 26.2 1.0

Zinc binding site 2 out of 4 in 7b48

Go back to Zinc Binding Sites List in 7b48
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-R273H Mutant Bound to Mq: R273H-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-R273H Mutant Bound to Mq: R273H-Mq (II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:28.0
occ:1.00
ND1 B:HIS179 1.9 35.4 1.0
SG B:CYS242 2.3 28.6 1.0
SG B:CYS238 2.4 27.1 1.0
SG B:CYS176 2.5 34.3 1.0
CG B:HIS179 2.9 35.6 1.0
CE1 B:HIS179 3.0 36.0 1.0
CB B:CYS242 3.1 29.9 1.0
CB B:HIS179 3.2 35.7 1.0
CB B:CYS238 3.3 25.6 1.0
CB B:CYS176 3.5 35.0 1.0
CA B:CYS238 3.8 26.2 1.0
CD2 B:HIS179 4.1 35.5 1.0
NE2 B:HIS179 4.1 35.8 1.0
N B:CYS176 4.1 34.5 1.0
O B:HOH473 4.3 30.0 1.0
CA B:CYS176 4.3 34.9 1.0
N B:HIS179 4.3 36.3 1.0
CA B:HIS179 4.4 36.3 1.0
CA B:CYS242 4.5 32.8 1.0
N B:ASN239 4.6 29.4 1.0
C B:CYS238 4.7 26.8 1.0
O B:MET237 4.7 23.5 1.0
N B:CYS238 4.9 24.3 1.0

Zinc binding site 3 out of 4 in 7b48

Go back to Zinc Binding Sites List in 7b48
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-R273H Mutant Bound to Mq: R273H-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-R273H Mutant Bound to Mq: R273H-Mq (II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:27.4
occ:1.00
ND1 C:HIS179 1.9 23.3 1.0
SG C:CYS176 2.3 28.3 1.0
SG C:CYS242 2.4 33.6 1.0
SG C:CYS238 2.4 26.6 1.0
CE1 C:HIS179 2.8 23.4 1.0
CB C:CYS242 2.9 35.1 1.0
CG C:HIS179 3.0 24.7 1.0
CB C:CYS238 3.1 26.0 1.0
CB C:CYS176 3.4 29.1 1.0
CB C:HIS179 3.4 25.9 1.0
CA C:CYS238 3.8 25.5 1.0
N C:CYS176 4.0 28.4 1.0
NE2 C:HIS179 4.0 23.7 1.0
CD2 C:HIS179 4.1 24.2 1.0
CA C:CYS176 4.2 29.7 1.0
CA C:CYS242 4.3 37.0 1.0
N C:HIS179 4.4 28.9 1.0
N C:ASN239 4.5 27.6 1.0
CA C:HIS179 4.5 28.2 1.0
O C:HOH475 4.5 40.3 1.0
C C:CYS238 4.7 25.8 1.0
O C:MET237 4.8 26.7 1.0
N C:CYS238 5.0 24.4 1.0

Zinc binding site 4 out of 4 in 7b48

Go back to Zinc Binding Sites List in 7b48
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-R273H Mutant Bound to Mq: R273H-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-R273H Mutant Bound to Mq: R273H-Mq (II) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:34.6
occ:1.00
ND1 D:HIS179 2.2 37.0 1.0
SG D:CYS242 2.3 34.4 1.0
SG D:CYS176 2.3 34.3 1.0
SG D:CYS238 2.4 28.9 1.0
CB D:CYS242 3.1 35.8 1.0
CG D:HIS179 3.2 37.4 1.0
CE1 D:HIS179 3.2 39.3 1.0
CB D:HIS179 3.4 36.5 1.0
CB D:CYS176 3.4 33.3 1.0
CB D:CYS238 3.5 28.0 1.0
CA D:CYS238 3.8 27.3 1.0
N D:CYS176 4.0 32.0 1.0
CA D:CYS176 4.2 33.8 1.0
CD2 D:HIS179 4.3 39.1 1.0
NE2 D:HIS179 4.4 38.5 1.0
N D:HIS179 4.4 38.4 1.0
N D:ASN239 4.4 28.8 1.0
CA D:CYS242 4.5 36.9 1.0
CA D:HIS179 4.5 38.8 1.0
C D:CYS238 4.7 27.5 1.0
O D:CYS176 4.7 35.3 1.0
O D:MET237 4.7 27.5 1.0
O D:HOH477 4.7 34.2 1.0
C D:CYS176 4.8 35.3 1.0
N D:CYS238 5.0 25.9 1.0

Reference:

O.Degtjarik, D.Golovenko, Y.Diskin-Posner, L.Abrahmsen, H.Rozenberg, Z.Shakked. P53 Structure 2 To Be Published.
Page generated: Fri Dec 17 11:45:58 2021

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