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Zinc in PDB 5g4m: Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Monofluorinated Derivative of the Small Molecule Stabilizer PHIKAN083

Protein crystallography data

The structure of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Monofluorinated Derivative of the Small Molecule Stabilizer PHIKAN083, PDB code: 5g4m was solved by A.C.Joerger, M.Bauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.57 / 1.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.030, 71.144, 105.144, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 17

Other elements in 5g4m:

The structure of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Monofluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Monofluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 (pdb code 5g4m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Monofluorinated Derivative of the Small Molecule Stabilizer PHIKAN083, PDB code: 5g4m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5g4m

Go back to Zinc Binding Sites List in 5g4m
Zinc binding site 1 out of 2 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Monofluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Monofluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1291

b:17.1
occ:1.00
ND1 A:HIS179 2.0 16.2 1.0
SG A:CYS238 2.3 21.3 1.0
SG A:CYS242 2.3 18.2 1.0
SG A:CYS176 2.3 16.2 1.0
CE1 A:HIS179 2.9 17.4 1.0
CG A:HIS179 3.0 16.5 1.0
CB A:CYS242 3.1 18.2 1.0
CB A:CYS176 3.4 15.6 1.0
CB A:CYS238 3.4 17.8 1.0
CB A:HIS179 3.4 15.3 1.0
CA A:CYS238 3.8 15.1 1.0
N A:CYS176 4.0 15.0 1.0
NE2 A:HIS179 4.0 18.8 1.0
CD2 A:HIS179 4.1 18.8 1.0
O A:HOH2211 4.2 46.2 1.0
N A:HIS179 4.3 17.1 1.0
CA A:CYS176 4.3 15.5 1.0
N A:TYR239 4.4 16.2 1.0
CA A:HIS179 4.5 15.9 1.0
CA A:CYS242 4.5 18.1 1.0
C A:CYS238 4.7 15.4 1.0
O A:HOH2135 4.7 21.2 1.0
O A:MET237 4.8 14.1 1.0
C A:CYS176 5.0 16.8 1.0

Zinc binding site 2 out of 2 in 5g4m

Go back to Zinc Binding Sites List in 5g4m
Zinc binding site 2 out of 2 in the Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Monofluorinated Derivative of the Small Molecule Stabilizer PHIKAN083


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the P53 Cancer Mutant Y220C in Complex with A Monofluorinated Derivative of the Small Molecule Stabilizer PHIKAN083 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1291

b:16.9
occ:1.00
ND1 B:HIS179 2.0 16.8 1.0
SG B:CYS242 2.3 18.3 1.0
SG B:CYS176 2.3 16.4 1.0
SG B:CYS238 2.3 17.2 1.0
CE1 B:HIS179 3.0 18.3 1.0
CG B:HIS179 3.1 17.3 1.0
CB B:CYS242 3.1 18.1 1.0
CB B:CYS238 3.3 15.7 1.0
CB B:CYS176 3.4 15.4 1.0
CB B:HIS179 3.4 16.1 1.0
CA B:CYS238 3.8 14.9 1.0
N B:CYS176 4.0 14.4 1.0
NE2 B:HIS179 4.1 20.0 1.0
CD2 B:HIS179 4.2 19.5 1.0
O B:HOH2101 4.2 48.1 1.0
CA B:CYS176 4.3 16.1 1.0
N B:HIS179 4.4 17.5 1.0
N B:TYR239 4.5 15.9 1.0
CA B:HIS179 4.5 16.4 1.0
CA B:CYS242 4.5 17.0 1.0
O B:MET237 4.6 15.8 1.0
O B:HOH2127 4.6 18.9 1.0
C B:CYS238 4.7 15.7 1.0
N B:CYS238 5.0 14.8 1.0
C B:CYS176 5.0 17.6 1.0

Reference:

M.R.Bauer, R.N.Jones, M.G.J.Baud, R.Wilcken, F.M.Boeckler, A.R.Fersht, A.C.Joerger, J.Spencer. Harnessing Fluorine-Sulfur Contacts and Multipolar Interactions For the Design of P53 Mutant Y220C Rescue Drugs. Acs Chem.Biol. V. 11 2265 2016.
ISSN: ISSN 1554-8929
PubMed: 27267810
DOI: 10.1021/ACSCHEMBIO.6B00315
Page generated: Wed Dec 16 06:18:36 2020

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