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Zinc in PDB 2vuk: Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small-Molecule Drug PHIKAN083

Protein crystallography data

The structure of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small-Molecule Drug PHIKAN083, PDB code: 2vuk was solved by A.C.Joerger, F.M.Boeckler, A.R.Fersht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.10 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.093, 71.234, 105.207, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 20.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small-Molecule Drug PHIKAN083 (pdb code 2vuk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small-Molecule Drug PHIKAN083, PDB code: 2vuk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2vuk

Go back to Zinc Binding Sites List in 2vuk
Zinc binding site 1 out of 2 in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small-Molecule Drug PHIKAN083


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small-Molecule Drug PHIKAN083 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1300

b:10.1
occ:1.00
ND1 A:HIS179 2.0 8.9 1.0
SG A:CYS242 2.3 11.6 1.0
SG A:CYS176 2.3 8.7 1.0
SG A:CYS238 2.3 12.7 1.0
CE1 A:HIS179 3.0 10.0 1.0
CG A:HIS179 3.0 9.5 1.0
CB A:CYS242 3.1 10.2 1.0
CB A:CYS176 3.4 10.1 1.0
CB A:HIS179 3.4 7.7 1.0
CB A:CYS238 3.4 8.5 1.0
CA A:CYS238 3.8 8.8 1.0
O A:HOH2118 3.9 34.8 1.0
N A:CYS176 4.0 8.9 1.0
NE2 A:HIS179 4.1 10.9 1.0
CD2 A:HIS179 4.2 9.0 1.0
N A:HIS179 4.3 9.4 1.0
CA A:CYS176 4.3 7.6 1.0
N A:TYR239 4.4 9.3 1.0
CA A:HIS179 4.5 8.3 1.0
CA A:CYS242 4.5 9.7 1.0
C A:CYS238 4.6 9.5 1.0
O A:HOH2104 4.7 13.1 1.0
O A:MET237 4.8 8.3 1.0

Zinc binding site 2 out of 2 in 2vuk

Go back to Zinc Binding Sites List in 2vuk
Zinc binding site 2 out of 2 in the Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small-Molecule Drug PHIKAN083


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the P53 Core Domain Mutant Y220C Bound to the Stabilizing Small-Molecule Drug PHIKAN083 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1300

b:9.8
occ:1.00
ND1 B:HIS179 2.0 9.5 1.0
SG B:CYS176 2.3 8.8 1.0
SG B:CYS242 2.3 10.4 1.0
SG B:CYS238 2.3 9.4 1.0
CE1 B:HIS179 2.9 11.5 1.0
CG B:HIS179 3.0 9.3 1.0
CB B:CYS242 3.1 9.2 1.0
CB B:CYS238 3.3 8.1 1.0
CB B:CYS176 3.4 10.2 1.0
CB B:HIS179 3.4 9.8 1.0
CA B:CYS238 3.8 6.2 1.0
O B:HOH2102 3.9 33.7 1.0
N B:CYS176 4.0 9.4 1.0
NE2 B:HIS179 4.1 12.3 1.0
CD2 B:HIS179 4.1 9.8 1.0
CA B:CYS176 4.3 10.2 1.0
N B:HIS179 4.4 10.1 1.0
N B:TYR239 4.5 9.1 1.0
CA B:CYS242 4.5 10.3 1.0
CA B:HIS179 4.5 9.9 1.0
O B:HOH2091 4.6 12.2 1.0
O B:MET237 4.6 8.8 1.0
C B:CYS238 4.7 7.9 1.0
N B:CYS238 5.0 8.4 1.0

Reference:

F.M.Boeckler, A.C.Joerger, G.Jaggi, T.J.Rutherford, D.B.Veprintsev, A.R.Fersht. Targeted Rescue of A Destabilized Mutant of P53 By An in Silico Screened Drug. Proc.Natl.Acad.Sci.Usa V. 105 10360 2008.
ISSN: ISSN 0027-8424
PubMed: 18650397
DOI: 10.1073/PNAS.0805326105
Page generated: Wed Dec 16 03:56:12 2020

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