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Fluorine in PDB 2x0v: Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine

Protein crystallography data

The structure of Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine, PDB code: 2x0v was solved by N.Basse, J.L.Kaar, A.C.Joerger, A.R.Fersht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.03 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.226, 71.088, 105.389, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.9

Other elements in 2x0v:

The structure of Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine (pdb code 2x0v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine, PDB code: 2x0v:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2x0v

Go back to Fluorine Binding Sites List in 2x0v
Fluorine binding site 1 out of 6 in the Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1290

b:30.5
occ:1.00
 F1 B:X0V1290 0.0 30.5 1.0
C1 B:X0V1290 1.4 28.2 1.0
F3 B:X0V1290 2.3 32.2 1.0
F2 B:X0V1290 2.3 29.6 1.0
C2 B:X0V1290 2.4 30.1 1.0
C7 B:X0V1290 3.0 23.6 1.0
F1 B:X0V1291 3.1 35.4 1.0
C B:GLU221 3.3 20.4 1.0
C B:CYS220 3.3 25.9 1.0
C4 B:X0V1290 3.3 26.8 1.0
N B:PRO222 3.4 21.8 1.0
O B:CYS220 3.4 20.2 1.0
N B:GLU221 3.4 20.0 1.0
CA B:GLU221 3.4 22.0 1.0
CB B:CYS220 3.4 20.4 1.0
CD B:PRO222 3.6 28.3 1.0
O B:GLU221 3.7 15.4 1.0
C7 B:X0V1291 3.7 24.7 1.0
CG B:PRO222 4.0 32.5 1.0
CA B:CYS220 4.0 17.0 1.0
C1 B:X0V1291 4.0 36.7 1.0
CA B:PRO222 4.1 21.3 1.0
F3 B:X0V1291 4.1 33.5 1.0
C8 B:X0V1290 4.3 30.8 1.0
C2 B:X0V1291 4.3 28.2 1.0
C3 B:X0V1290 4.5 26.2 1.0
CB B:PRO222 4.7 26.3 1.0
C8 B:X0V1291 4.7 29.8 1.0
O B:HOH2092 4.8 16.6 1.0
C6 B:X0V1290 4.9 31.7 1.0
CB B:GLU221 4.9 26.3 1.0
SG B:CYS220 5.0 20.9 1.0
O B:PRO151 5.0 12.7 1.0

Fluorine binding site 2 out of 6 in 2x0v

Go back to Fluorine Binding Sites List in 2x0v
Fluorine binding site 2 out of 6 in the Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1290

b:29.6
occ:1.00
 F2 B:X0V1290 0.0 29.6 1.0
C1 B:X0V1290 1.4 28.2 1.0
F3 B:X0V1290 2.3 32.2 1.0
F1 B:X0V1290 2.3 30.5 1.0
C2 B:X0V1290 2.4 30.1 1.0
C7 B:X0V1290 2.9 23.6 1.0
CB B:CYS220 3.3 20.4 1.0
O B:PRO152 3.3 12.2 1.0
O B:HOH2092 3.3 16.6 1.0
O B:CYS220 3.4 20.2 1.0
C4 B:X0V1290 3.5 26.8 1.0
CB B:THR155 3.6 11.3 1.0
F1 B:X0V1291 3.8 35.4 1.0
C B:CYS220 3.8 25.9 1.0
O B:THR155 3.9 8.0 1.0
N B:THR155 4.0 8.1 1.0
CA B:CYS220 4.1 17.0 1.0
C B:PRO152 4.2 13.3 1.0
OG1 B:THR155 4.2 10.6 1.0
C8 B:X0V1290 4.2 30.8 1.0
CA B:THR155 4.2 7.7 1.0
O B:PRO151 4.3 12.7 1.0
CA B:PRO153 4.4 12.5 1.0
C B:THR155 4.4 9.1 1.0
N B:GLY154 4.4 10.2 1.0
CG2 B:THR155 4.5 9.8 1.0
SG B:CYS220 4.5 20.9 1.0
N B:CYS220 4.6 11.7 1.0
N B:GLU221 4.6 20.0 1.0
N B:PRO153 4.6 13.1 1.0
C3 B:X0V1290 4.7 26.2 1.0
C B:PRO151 4.7 9.8 1.0
C B:PRO153 4.8 13.4 1.0
CB B:PRO151 4.9 12.9 1.0
C6 B:X0V1290 4.9 31.7 1.0
CA B:GLU221 5.0 22.0 1.0
CG B:PRO151 5.0 16.7 1.0

Fluorine binding site 3 out of 6 in 2x0v

Go back to Fluorine Binding Sites List in 2x0v
Fluorine binding site 3 out of 6 in the Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1290

b:32.2
occ:1.00
 F3 B:X0V1290 0.0 32.2 1.0
C1 B:X0V1290 1.4 28.2 1.0
F2 B:X0V1290 2.3 29.6 1.0
F1 B:X0V1290 2.3 30.5 1.0
C2 B:X0V1290 2.4 30.1 1.0
C4 B:X0V1290 2.7 26.8 1.0
O B:PRO151 2.8 12.7 1.0
CD B:PRO151 3.3 16.5 1.0
F1 B:X0V1291 3.4 35.4 1.0
C B:PRO151 3.5 9.8 1.0
CG2 B:THR150 3.6 16.8 1.0
C7 B:X0V1290 3.7 23.6 1.0
CG B:PRO151 3.8 16.7 1.0
N B:PRO151 3.8 13.2 1.0
C7 B:X0V1291 3.8 24.7 1.0
CB B:PRO151 3.9 12.9 1.0
O B:PRO152 3.9 12.2 1.0
CA B:PRO151 4.0 11.6 1.0
C3 B:X0V1290 4.1 26.2 1.0
C B:PRO152 4.4 13.3 1.0
N B:PRO152 4.4 10.2 1.0
C B:THR150 4.5 16.2 1.0
C1 B:X0V1291 4.6 36.7 1.0
CB B:CYS220 4.6 20.4 1.0
C8 B:X0V1291 4.6 29.8 1.0
C2 B:X0V1291 4.7 28.2 1.0
CB B:THR155 4.7 11.3 1.0
C8 B:X0V1290 4.8 30.8 1.0
OG1 B:THR155 4.8 10.6 1.0
CB B:THR150 4.9 17.7 1.0
CA B:PRO152 4.9 13.2 1.0
N1 B:X0V1290 4.9 37.7 1.0
CA B:THR150 4.9 13.4 1.0
N B:PRO153 4.9 13.1 1.0
C6 B:X0V1290 4.9 31.7 1.0

Fluorine binding site 4 out of 6 in 2x0v

Go back to Fluorine Binding Sites List in 2x0v
Fluorine binding site 4 out of 6 in the Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1291

b:35.4
occ:1.00
 F1 B:X0V1291 0.0 35.4 1.0
C1 B:X0V1291 1.4 36.7 1.0
F2 B:X0V1291 2.3 37.1 1.0
F3 B:X0V1291 2.3 33.5 1.0
C2 B:X0V1291 2.4 28.2 1.0
C7 B:X0V1291 2.7 24.7 1.0
CB B:CYS220 3.0 20.4 1.0
F1 B:X0V1290 3.1 30.5 1.0
F3 B:X0V1290 3.4 32.2 1.0
SG B:CYS220 3.5 20.9 1.0
C1 B:X0V1290 3.6 28.2 1.0
C4 B:X0V1291 3.7 27.1 1.0
CG B:PRO151 3.7 16.7 1.0
F2 B:X0V1290 3.8 29.6 1.0
CD B:PRO151 3.9 16.5 1.0
C8 B:X0V1291 4.1 29.8 1.0
CA B:CYS220 4.3 17.0 1.0
O B:GLU221 4.6 15.4 1.0
C B:CYS220 4.7 25.9 1.0
CB B:PRO151 4.7 12.9 1.0
CD1 B:LEU257 4.7 12.6 1.0
N B:GLU221 4.8 20.0 1.0
C3 B:X0V1291 4.8 26.6 1.0
CG2 B:THR155 4.8 9.8 1.0
C6 B:X0V1291 5.0 32.9 1.0
C B:GLU221 5.0 20.4 1.0

Fluorine binding site 5 out of 6 in 2x0v

Go back to Fluorine Binding Sites List in 2x0v
Fluorine binding site 5 out of 6 in the Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1291

b:37.1
occ:1.00
 F2 B:X0V1291 0.0 37.1 1.0
C1 B:X0V1291 1.4 36.7 1.0
F3 B:X0V1291 2.3 33.5 1.0
F1 B:X0V1291 2.3 35.4 1.0
C2 B:X0V1291 2.4 28.2 1.0
C4 B:X0V1291 2.8 27.1 1.0
C7 B:X0V1291 3.5 24.7 1.0
CB B:LEU145 4.0 9.6 1.0
CG1 B:VAL147 4.0 11.4 1.0
CD1 B:LEU257 4.1 12.6 1.0
CD1 B:LEU145 4.1 16.5 1.0
C3 B:X0V1291 4.1 26.6 1.0
SG B:CYS220 4.1 20.9 1.0
CB B:CYS220 4.5 20.4 1.0
CG B:PRO151 4.5 16.7 1.0
C8 B:X0V1291 4.7 29.8 1.0
CG B:LEU145 4.7 11.0 1.0
CD B:PRO151 4.8 16.5 1.0
CE1 B:PHE109 4.8 11.2 1.0
CD1 B:PHE109 4.9 8.3 1.0
CG2 B:VAL147 4.9 11.5 1.0
C6 B:X0V1291 4.9 32.9 1.0
O B:LEU145 5.0 12.6 1.0

Fluorine binding site 6 out of 6 in 2x0v

Go back to Fluorine Binding Sites List in 2x0v
Fluorine binding site 6 out of 6 in the Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the P53 Core Domain Mutant Y220C Bound to 4- (Trifluoromethyl)Benzene-1,2-Diamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1291

b:33.5
occ:1.00
 F3 B:X0V1291 0.0 33.5 1.0
C1 B:X0V1291 1.4 36.7 1.0
F2 B:X0V1291 2.3 37.1 1.0
F1 B:X0V1291 2.3 35.4 1.0
C2 B:X0V1291 2.4 28.2 1.0
C4 B:X0V1291 3.0 27.1 1.0
C7 B:X0V1291 3.4 24.7 1.0
O B:GLU221 3.5 15.4 1.0
CB B:CYS220 3.5 20.4 1.0
OG1 B:THR230 3.6 26.0 1.0
CB B:THR230 3.7 18.3 1.0
CD1 B:LEU145 3.9 16.5 1.0
SG B:CYS220 3.9 20.9 1.0
CG2 B:THR230 4.1 15.9 1.0
F1 B:X0V1290 4.1 30.5 1.0
N B:GLU221 4.2 20.0 1.0
CA B:CYS220 4.2 17.0 1.0
C3 B:X0V1291 4.3 26.6 1.0
O B:HOH2212 4.3 36.0 1.0
C B:GLU221 4.3 20.4 1.0
CB B:LEU145 4.4 9.6 1.0
C8 B:X0V1291 4.5 29.8 1.0
C B:CYS220 4.6 25.9 1.0
CG B:LEU145 4.8 11.0 1.0
C6 B:X0V1291 4.9 32.9 1.0
CA B:GLU221 4.9 22.0 1.0

Reference:

N.Basse, J.L.Kaar, G.Settanni, A.C.Joerger, T.J.Rutherford, A.R.Fersht. Toward the Rational Design of P53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant. Chem.Biol. V. 17 46 2010.
ISSN: ISSN 1074-5521
PubMed: 20142040
DOI: 10.1016/J.CHEMBIOL.2009.12.011
Page generated: Wed Jul 31 16:32:00 2024

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