Zinc in PDB 7b4b: Structural Basis of Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (I)

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 (I), PDB code: 7b4b 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) 36.46 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.73, 70.686, 85.107, 90, 90.29, 90
R / Rfree (%) 18 / 21.8

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-R273C Mutant Bound to Mq: R273C-Mq (I) (pdb code 7b4b). 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 (I), PDB code: 7b4b:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7b4b

Go back to Zinc Binding Sites List in 7b4b
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 (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 Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:29.3
occ:1.00
ND1 A:HIS179 2.1 30.6 1.0
SG A:CYS238 2.3 20.9 0.7
SG A:CYS176 2.3 25.6 1.0
SG A:CYS242 2.3 30.3 1.0
SG A:CYS238 2.6 15.9 0.3
CE1 A:HIS179 3.0 37.8 1.0
CB A:CYS242 3.0 24.6 1.0
CG A:HIS179 3.1 22.2 1.0
CB A:CYS176 3.5 39.3 1.0
CB A:HIS179 3.5 29.0 1.0
CB A:CYS238 3.5 73.1 0.3
CB A:CYS238 3.6 15.9 0.7
CA A:CYS238 3.8 14.4 0.7
CA A:CYS238 3.9 43.8 0.3
N A:CYS176 4.0 21.0 1.0
N A:ASN239 4.1 26.0 1.0
NE2 A:HIS179 4.1 37.8 1.0
CD2 A:HIS179 4.2 50.2 1.0
CA A:CYS176 4.3 22.0 1.0
N A:HIS179 4.4 33.2 1.0
C A:CYS238 4.5 18.0 0.7
CA A:CYS242 4.5 30.2 1.0
C A:CYS238 4.5 52.9 0.3
CA A:HIS179 4.6 26.6 1.0
O A:MET237 4.8 28.3 1.0
O A:CYS176 5.0 29.6 1.0
C A:CYS176 5.0 29.1 1.0

Zinc binding site 2 out of 4 in 7b4b

Go back to Zinc Binding Sites List in 7b4b
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 (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 Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:25.7
occ:1.00
ND1 B:HIS179 2.1 30.1 1.0
SG B:CYS242 2.3 21.3 1.0
SG B:CYS176 2.4 22.1 1.0
SG B:CYS238 2.4 14.2 0.5
SG B:CYS238 2.4 30.2 0.5
CE1 B:HIS179 3.1 21.9 1.0
CB B:CYS242 3.1 17.6 1.0
CG B:HIS179 3.1 18.2 1.0
CB B:CYS238 3.3 14.3 0.5
CB B:CYS176 3.4 19.5 1.0
CB B:HIS179 3.4 21.7 1.0
CB B:CYS238 3.6 42.6 0.5
CA B:CYS238 3.9 51.6 0.5
CA B:CYS238 3.9 9.7 0.5
N B:CYS176 4.0 17.7 1.0
O B:HOH549 4.1 27.6 1.0
NE2 B:HIS179 4.2 25.6 1.0
CD2 B:HIS179 4.2 31.3 1.0
CA B:CYS176 4.3 20.5 1.0
N B:ASN239 4.3 22.9 1.0
N B:HIS179 4.4 20.0 1.0
O B:HOH511 4.4 22.3 0.7
CA B:CYS242 4.5 23.8 1.0
CA B:HIS179 4.5 20.0 1.0
C B:CYS238 4.6 55.7 0.5
C B:CYS238 4.7 10.1 0.5
O B:MET237 4.8 19.9 1.0
O B:CYS176 5.0 22.6 1.0

Zinc binding site 3 out of 4 in 7b4b

Go back to Zinc Binding Sites List in 7b4b
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 (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 Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (I) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:29.4
occ:1.00
ND1 C:HIS179 2.0 31.4 1.0
SG C:CYS238 2.3 31.0 0.6
SG C:CYS176 2.3 23.8 1.0
SG C:CYS242 2.3 26.6 1.0
SG C:CYS238 2.4 17.3 0.4
CE1 C:HIS179 2.9 27.1 1.0
CG C:HIS179 3.0 31.1 1.0
CB C:CYS242 3.1 23.1 1.0
CB C:CYS238 3.3 21.4 0.4
CB C:CYS176 3.4 27.2 1.0
CB C:HIS179 3.4 22.9 1.0
CB C:CYS238 3.6 37.9 0.6
CA C:CYS238 3.8 16.7 0.4
CA C:CYS238 3.8 15.8 0.6
N C:CYS176 4.0 24.6 1.0
NE2 C:HIS179 4.0 25.3 1.0
CD2 C:HIS179 4.1 24.5 1.0
N C:ASN239 4.3 26.6 1.0
CA C:CYS176 4.3 23.1 1.0
N C:HIS179 4.3 23.3 1.0
CA C:CYS242 4.5 25.9 1.0
CA C:HIS179 4.5 25.4 1.0
C C:CYS238 4.5 28.7 0.6
C C:CYS238 4.6 29.6 0.4
O C:HOH492 4.7 32.7 1.0
O C:MET237 4.8 22.1 1.0
O C:CYS176 4.8 27.6 1.0
C C:CYS176 4.9 27.2 1.0

Zinc binding site 4 out of 4 in 7b4b

Go back to Zinc Binding Sites List in 7b4b
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 (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 Reactivation of Oncogenic P53 Mutants By A Small Molecule: Methylene Quinuclidinone (Mq). Human P53DBD-R273C Mutant Bound to Mq: R273C-Mq (I) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:32.5
occ:1.00
ND1 D:HIS179 2.0 34.1 1.0
SG D:CYS238 2.3 19.7 0.5
SG D:CYS176 2.3 28.8 1.0
SG D:CYS242 2.4 37.5 1.0
SG D:CYS238 2.5 38.4 0.5
CE1 D:HIS179 2.8 53.3 1.0
CG D:HIS179 3.1 25.6 1.0
CB D:CYS242 3.2 29.9 1.0
CB D:CYS176 3.3 26.9 1.0
CB D:CYS238 3.5 37.3 0.5
CB D:CYS238 3.5 32.1 0.5
CB D:HIS179 3.6 26.9 1.0
CA D:CYS238 3.8 24.0 0.5
CA D:CYS238 3.9 20.6 0.5
N D:CYS176 3.9 24.5 1.0
NE2 D:HIS179 4.0 52.9 1.0
N D:ASN239 4.1 24.8 1.0
CD2 D:HIS179 4.1 55.4 1.0
CA D:CYS176 4.2 29.7 1.0
N D:HIS179 4.4 35.7 1.0
C D:CYS238 4.5 48.4 0.5
C D:CYS238 4.6 15.9 0.5
CA D:CYS242 4.6 38.3 1.0
CA D:HIS179 4.7 25.8 1.0
O D:HOH501 4.8 45.5 0.8
O D:MET237 4.8 25.1 1.0
O D:CYS176 4.9 23.6 1.0
C D:CYS176 4.9 26.8 1.0
O D:ASN239 5.0 25.3 1.0

Reference:

O.Degtjarik, D.Golovenko, Y.Diskin-Posner, L.Abrahmsen, H.Rozenberg, Z.Shakked. P53 Structure 5 To Be Published.
Page generated: Fri Dec 17 11:45:59 2021

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