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Zinc in PDB 5aba: Structure of the P53 Cancer Mutant Y220C with Bound Small-Molecule Stabilizer PHIKAN5149

Protein crystallography data

The structure of Structure of the P53 Cancer Mutant Y220C with Bound Small-Molecule Stabilizer PHIKAN5149, PDB code: 5aba was solved by A.C.Joerger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.44 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.893, 71.114, 104.939, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 20.3

Other elements in 5aba:

The structure of Structure of the P53 Cancer Mutant Y220C with Bound Small-Molecule Stabilizer PHIKAN5149 also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the P53 Cancer Mutant Y220C with Bound Small-Molecule Stabilizer PHIKAN5149 (pdb code 5aba). 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 Cancer Mutant Y220C with Bound Small-Molecule Stabilizer PHIKAN5149, PDB code: 5aba:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5aba

Go back to Zinc Binding Sites List in 5aba
Zinc binding site 1 out of 2 in the Structure of the P53 Cancer Mutant Y220C with Bound Small-Molecule Stabilizer PHIKAN5149


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 Cancer Mutant Y220C with Bound Small-Molecule Stabilizer PHIKAN5149 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn313

b:12.7
occ:1.00
ND1 A:HIS179 2.0 11.7 1.0
SG A:CYS238 2.3 14.4 1.0
SG A:CYS242 2.3 13.5 1.0
SG A:CYS176 2.3 11.1 1.0
CE1 A:HIS179 2.9 11.5 1.0
CG A:HIS179 3.0 11.5 1.0
CB A:CYS242 3.1 14.9 1.0
CB A:CYS176 3.4 12.2 1.0
CB A:HIS179 3.4 9.1 1.0
CB A:CYS238 3.4 12.0 1.0
CA A:CYS238 3.9 12.0 1.0
N A:CYS176 4.0 9.8 1.0
NE2 A:HIS179 4.1 11.8 1.0
O A:HOH2209 4.1 29.6 1.0
CD2 A:HIS179 4.1 12.9 1.0
CA A:CYS176 4.3 13.5 1.0
N A:HIS179 4.3 14.2 1.0
N A:TYR239 4.4 8.1 1.0
CA A:HIS179 4.5 14.6 1.0
CA A:CYS242 4.5 15.0 1.0
O A:HOH2130 4.6 14.9 1.0
C A:CYS238 4.7 11.7 1.0
O A:MET237 4.7 10.2 1.0
C A:CYS176 5.0 10.1 1.0

Zinc binding site 2 out of 2 in 5aba

Go back to Zinc Binding Sites List in 5aba
Zinc binding site 2 out of 2 in the Structure of the P53 Cancer Mutant Y220C with Bound Small-Molecule Stabilizer PHIKAN5149


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 Cancer Mutant Y220C with Bound Small-Molecule Stabilizer PHIKAN5149 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn313

b:12.1
occ:1.00
ND1 B:HIS179 2.0 12.2 1.0
SG B:CYS176 2.3 10.1 1.0
SG B:CYS238 2.3 10.5 1.0
SG B:CYS242 2.3 13.2 1.0
CE1 B:HIS179 3.0 11.7 1.0
CG B:HIS179 3.0 11.2 1.0
CB B:CYS242 3.1 12.6 1.0
CB B:CYS238 3.4 8.9 1.0
CB B:CYS176 3.4 11.5 1.0
CB B:HIS179 3.4 10.7 1.0
CA B:CYS238 3.9 9.1 1.0
N B:CYS176 4.0 9.1 1.0
O B:HOH2143 4.0 24.5 1.0
NE2 B:HIS179 4.1 15.5 1.0
CD2 B:HIS179 4.2 16.5 1.0
CA B:CYS176 4.3 9.4 1.0
N B:HIS179 4.3 13.3 1.0
N B:TYR239 4.5 10.4 1.0
CA B:CYS242 4.5 13.5 1.0
CA B:HIS179 4.5 10.0 1.0
O B:MET237 4.6 10.4 1.0
C B:CYS238 4.7 14.1 1.0
O B:HOH2135 4.7 11.3 1.0
C B:CYS176 5.0 11.4 1.0

Reference:

A.C.Joerger, M.R.Bauer, R.Wilcken, M.G.J.Baud, H.Harbrecht, T.E.Exner, F.M.Boeckler, J.Spencer, A.R.Fersht. Exploiting Transient Protein States For the Design of Small-Molecule Stabilizers of Mutant P53. Structure V. 23 2246 2015.
ISSN: ISSN 0969-2126
PubMed: 26636255
DOI: 10.1016/J.STR.2015.10.016
Page generated: Wed Dec 16 06:02:15 2020

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