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Fluorine in PDB 2vqq: Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor

Protein crystallography data

The structure of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor, PDB code: 2vqq was solved by M.J.Bottomley, P.Lo Surdo, P.Di Giovine, A.Cirillo, R.Scarpelli, F.Ferrigno, P.Jones, P.Neddermann, R.De Francesco, C.Steinkuhler, P.Gallinari, A.Carfi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.00 / 1.9
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.605, 70.673, 88.201, 90.00, 108.08, 90.00
R / Rfree (%) 19.4 / 22.1

Other elements in 2vqq:

The structure of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor also contains other interesting chemical elements:

Potassium (K) 4 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor (pdb code 2vqq). 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 HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor, PDB code: 2vqq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2vqq

Go back to Fluorine Binding Sites List in 2vqq
Fluorine binding site 1 out of 6 in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1410

b:17.1
occ:1.00
 F1 A:TFG1410 0.0 17.1 1.0
C6 A:TFG1410 1.3 18.8 1.0
F3 A:TFG1410 2.2 20.0 1.0
F2 A:TFG1410 2.2 19.2 1.0
C5 A:TFG1410 2.3 18.7 1.0
O3 A:TFG1410 2.6 20.0 1.0
O2 A:TFG1410 2.7 17.0 1.0
N A:GLY330 3.0 13.7 1.0
CA A:GLY330 3.1 14.5 1.0
OD1 A:ASP196 3.4 9.8 1.0
NE2 A:HIS158 3.6 14.5 1.0
ZN A:ZN1411 3.6 13.6 1.0
CB A:PRO156 3.7 13.8 1.0
C1 A:TFG1410 3.7 17.9 1.0
CG A:PRO156 3.7 14.8 1.0
C A:GLU329 3.8 13.8 1.0
CD2 A:HIS158 4.1 13.9 1.0
CG A:ASP196 4.1 10.9 1.0
O A:HOH2270 4.2 13.8 1.0
OD2 A:ASP196 4.3 11.0 1.0
CB A:GLU329 4.3 13.6 1.0
O A:GLU329 4.4 13.4 1.0
C2 A:TFG1410 4.4 18.5 1.0
CA A:GLU329 4.5 13.6 1.0
C A:GLY330 4.5 14.9 1.0
NE2 A:HIS159 4.6 12.7 1.0
CD2 A:HIS159 4.7 14.2 1.0
CE1 A:HIS158 4.7 13.4 1.0
OD2 A:ASP290 4.8 10.9 1.0

Fluorine binding site 2 out of 6 in 2vqq

Go back to Fluorine Binding Sites List in 2vqq
Fluorine binding site 2 out of 6 in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1410

b:19.2
occ:1.00
 F2 A:TFG1410 0.0 19.2 1.0
C6 A:TFG1410 1.3 18.8 1.0
F1 A:TFG1410 2.2 17.1 1.0
F3 A:TFG1410 2.2 20.0 1.0
C5 A:TFG1410 2.4 18.7 1.0
O3 A:TFG1410 2.9 20.0 1.0
O A:GLY167 3.0 15.1 1.0
C2 A:TFG1410 3.0 18.5 1.0
C1 A:TFG1410 3.0 17.9 1.0
CD2 A:HIS159 3.2 14.2 1.0
CG A:PRO156 3.4 14.8 1.0
O2 A:TFG1410 3.6 17.0 1.0
NE2 A:HIS159 3.7 12.7 1.0
SG A:CYS169 3.8 14.3 1.0
CB A:PRO156 3.9 13.8 1.0
C A:GLY167 4.1 15.5 1.0
NE2 A:HIS158 4.1 14.5 1.0
CD2 A:HIS158 4.3 13.9 1.0
CD1 A:PHE168 4.3 19.5 1.0
C3 A:TFG1410 4.3 18.7 1.0
CG A:HIS159 4.5 13.9 1.0
CB A:PHE168 4.6 16.1 1.0
S1 A:TFG1410 4.7 17.9 1.0
CD A:PRO156 4.8 14.4 1.0
ZN A:ZN1411 4.8 13.6 1.0
CA A:GLY167 4.9 15.9 1.0
CE1 A:HIS159 4.9 14.2 1.0
CG A:PHE168 5.0 17.8 1.0

Fluorine binding site 3 out of 6 in 2vqq

Go back to Fluorine Binding Sites List in 2vqq
Fluorine binding site 3 out of 6 in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1410

b:20.0
occ:1.00
 F3 A:TFG1410 0.0 20.0 1.0
C6 A:TFG1410 1.3 18.8 1.0
F1 A:TFG1410 2.2 17.1 1.0
F2 A:TFG1410 2.2 19.2 1.0
C5 A:TFG1410 2.4 18.7 1.0
O2 A:TFG1410 2.8 17.0 1.0
C1 A:TFG1410 3.1 17.9 1.0
O A:HOH2270 3.3 13.8 1.0
CG A:PRO156 3.4 14.8 1.0
C2 A:TFG1410 3.6 18.5 1.0
O3 A:TFG1410 3.6 20.0 1.0
CA A:GLY330 3.7 14.5 1.0
CD1 A:PHE168 3.8 19.5 1.0
O A:HOH2218 3.9 31.0 1.0
CB A:PRO156 4.2 13.8 1.0
N A:GLY330 4.3 13.7 1.0
O A:GLY167 4.3 15.1 1.0
S1 A:TFG1410 4.4 17.9 1.0
CD A:PRO156 4.5 14.4 1.0
CE1 A:PHE168 4.5 20.4 1.0
ZN A:ZN1411 4.6 13.6 1.0
CB A:PHE168 4.7 16.1 1.0
CG A:PHE168 4.7 17.8 1.0
C3 A:TFG1410 4.8 18.7 1.0
C A:GLU329 4.8 13.8 1.0
O A:HOH2104 4.8 30.7 1.0
O A:GLU329 4.9 13.4 1.0
C A:GLY330 4.9 14.9 1.0

Fluorine binding site 4 out of 6 in 2vqq

Go back to Fluorine Binding Sites List in 2vqq
Fluorine binding site 4 out of 6 in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1409

b:19.4
occ:1.00
 F1 B:TFG1409 0.0 19.4 1.0
C6 B:TFG1409 1.3 19.7 1.0
F2 B:TFG1409 2.2 18.4 1.0
F3 B:TFG1409 2.2 21.9 1.0
C5 B:TFG1409 2.3 18.2 1.0
O3 B:TFG1409 2.5 20.7 1.0
O2 B:TFG1409 2.7 15.5 1.0
N B:GLY330 3.1 12.9 1.0
CA B:GLY330 3.1 13.4 1.0
OD1 B:ASP196 3.5 9.6 1.0
CB B:PRO156 3.6 14.0 1.0
CG B:PRO156 3.6 14.8 1.0
C1 B:TFG1409 3.7 16.6 1.0
NE2 B:HIS158 3.7 13.1 1.0
ZN B:ZN1410 3.7 14.6 1.0
C B:GLU329 3.7 12.6 1.0
CD2 B:HIS158 4.1 14.0 1.0
CG B:ASP196 4.2 11.2 1.0
O B:HOH2338 4.3 15.6 1.0
O B:GLU329 4.3 12.4 1.0
C2 B:TFG1409 4.3 17.6 1.0
CB B:GLU329 4.4 12.9 1.0
OD2 B:ASP196 4.4 12.8 1.0
CA B:GLU329 4.5 12.6 1.0
C B:GLY330 4.6 13.7 1.0
NE2 B:HIS159 4.7 13.1 1.0
CD2 B:HIS159 4.7 14.9 1.0
CE1 B:HIS158 4.8 13.7 1.0
OD2 B:ASP290 4.9 12.4 1.0
CD B:PRO156 5.0 14.6 1.0

Fluorine binding site 5 out of 6 in 2vqq

Go back to Fluorine Binding Sites List in 2vqq
Fluorine binding site 5 out of 6 in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1409

b:18.4
occ:1.00
 F2 B:TFG1409 0.0 18.4 1.0
C6 B:TFG1409 1.3 19.7 1.0
F1 B:TFG1409 2.2 19.4 1.0
F3 B:TFG1409 2.2 21.9 1.0
C5 B:TFG1409 2.4 18.2 1.0
O3 B:TFG1409 2.8 20.7 1.0
C2 B:TFG1409 2.9 17.6 1.0
C1 B:TFG1409 3.0 16.6 1.0
O B:GLY167 3.0 14.7 1.0
CD2 B:HIS159 3.2 14.9 1.0
CG B:PRO156 3.5 14.8 1.0
O2 B:TFG1409 3.6 15.5 1.0
NE2 B:HIS159 3.6 13.1 1.0
SG B:CYS169 3.8 14.0 1.0
CB B:PRO156 3.9 14.0 1.0
C B:GLY167 4.1 15.6 1.0
NE2 B:HIS158 4.2 13.1 1.0
C3 B:TFG1409 4.3 17.1 1.0
CD1 B:PHE168 4.3 20.7 1.0
CD2 B:HIS158 4.3 14.0 1.0
CG B:HIS159 4.4 14.2 1.0
S1 B:TFG1409 4.6 16.2 1.0
CB B:PHE168 4.7 16.6 1.0
CA B:GLY167 4.8 15.8 1.0
ZN B:ZN1410 4.8 14.6 1.0
CE1 B:HIS159 4.9 13.7 1.0
CD B:PRO156 4.9 14.6 1.0
CG B:PHE168 5.0 18.8 1.0

Fluorine binding site 6 out of 6 in 2vqq

Go back to Fluorine Binding Sites List in 2vqq
Fluorine binding site 6 out of 6 in the Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of HDAC4 Catalytic Domain (A Double Cysteine-to- Alanine Mutant) Bound to A Trifluoromethylketone Inhbitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1409

b:21.9
occ:1.00
 F3 B:TFG1409 0.0 21.9 1.0
C6 B:TFG1409 1.3 19.7 1.0
F1 B:TFG1409 2.2 19.4 1.0
F2 B:TFG1409 2.2 18.4 1.0
C5 B:TFG1409 2.4 18.2 1.0
O2 B:TFG1409 2.8 15.5 1.0
C1 B:TFG1409 3.0 16.6 1.0
CG B:PRO156 3.4 14.8 1.0
C2 B:TFG1409 3.5 17.6 1.0
O B:HOH2338 3.5 15.6 1.0
O B:HOH2274 3.5 28.7 1.0
O3 B:TFG1409 3.6 20.7 1.0
CD1 B:PHE168 3.7 20.7 1.0
CA B:GLY330 3.9 13.4 1.0
O B:GLY167 4.2 14.7 1.0
CB B:PRO156 4.2 14.0 1.0
S1 B:TFG1409 4.4 16.2 1.0
CE1 B:PHE168 4.4 21.7 1.0
N B:GLY330 4.5 12.9 1.0
CD B:PRO156 4.5 14.6 1.0
CG B:PHE168 4.6 18.8 1.0
CB B:PHE168 4.6 16.6 1.0
C3 B:TFG1409 4.6 17.1 1.0
ZN B:ZN1410 4.7 14.6 1.0
C B:GLU329 5.0 12.6 1.0
O B:GLU329 5.0 12.4 1.0

Reference:

M.J.Bottomley, P.Lo Surdo, P.Di Giovine, A.Cirillo, R.Scarpelli, F.Ferrigno, P.Jones, P.Neddermann, R.De Francesco, C.Steinkuhler, P.Gallinari, A.Carfi. Structural and Functional Analysis of the Human HDAC4 Catalytic Domain Reveals A Regulatory Zinc-Binding Domain. J.Biol.Chem. V. 283 26694 2008.
ISSN: ISSN 0021-9258
PubMed: 18614528
DOI: 10.1074/JBC.M803514200
Page generated: Wed Jul 31 16:17:11 2024

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