Fluorine in PDB 6pzo: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153

Enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153, PDB code: 6pzo was solved by J.D.Osko, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.88 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.810, 92.580, 96.730, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 6pzo:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153 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 Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153 (pdb code 6pzo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153, PDB code: 6pzo:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6pzo

Go back to Fluorine Binding Sites List in 6pzo
Fluorine binding site 1 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F804

b:24.0
occ:1.00
F20 A:P6Y804 0.0 24.0 1.0
C19 A:P6Y804 1.3 27.2 1.0
F21 A:P6Y804 2.1 21.9 1.0
F22 A:P6Y804 2.1 29.0 1.0
C18 A:P6Y804 2.3 20.6 1.0
N17 A:P6Y804 2.7 29.4 1.0
CD2 A:LEU712 3.4 17.8 1.0
CG A:PRO464 3.5 12.7 1.0
C13 A:P6Y804 3.5 24.6 1.0
C16 A:P6Y804 4.0 24.3 1.0
CD1 A:LEU712 4.0 25.8 1.0
CD A:PRO464 4.0 11.6 1.0
C11 A:P6Y804 4.1 32.3 1.0
O12 A:P6Y804 4.2 38.5 1.0
CG A:LEU712 4.3 11.3 1.0
C14 A:P6Y804 4.6 34.6 1.0
CB A:PRO464 4.7 11.2 1.0
C15 A:P6Y804 4.8 32.8 1.0
N10 A:P6Y804 5.0 25.2 1.0

Fluorine binding site 2 out of 6 in 6pzo

Go back to Fluorine Binding Sites List in 6pzo
Fluorine binding site 2 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F804

b:21.9
occ:1.00
F21 A:P6Y804 0.0 21.9 1.0
C19 A:P6Y804 1.3 27.2 1.0
F22 A:P6Y804 2.1 29.0 1.0
F20 A:P6Y804 2.1 24.0 1.0
C18 A:P6Y804 2.4 20.6 1.0
C11 A:P6Y804 2.7 32.3 1.0
C13 A:P6Y804 2.9 24.6 1.0
O12 A:P6Y804 2.9 38.5 1.0
N10 A:P6Y804 3.3 25.2 1.0
C07 A:P6Y804 3.5 16.7 1.0
CD1 A:LEU712 3.5 25.8 1.0
N17 A:P6Y804 3.6 29.4 1.0
CZ A:PHE583 3.6 10.1 1.0
C08 A:P6Y804 4.0 20.9 1.0
CD2 A:LEU712 4.0 17.8 1.0
C09 A:P6Y804 4.1 20.8 1.0
C06 A:P6Y804 4.2 14.4 1.0
C14 A:P6Y804 4.3 34.6 1.0
CE2 A:PHE583 4.4 13.7 1.0
CG A:LEU712 4.4 11.3 1.0
CG A:PRO464 4.5 12.7 1.0
CE1 A:PHE583 4.6 12.9 1.0
O A:HOH1094 4.7 17.1 1.0
C16 A:P6Y804 4.7 24.3 1.0
C23 A:P6Y804 5.0 16.8 1.0

Fluorine binding site 3 out of 6 in 6pzo

Go back to Fluorine Binding Sites List in 6pzo
Fluorine binding site 3 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F804

b:29.0
occ:1.00
F22 A:P6Y804 0.0 29.0 1.0
C19 A:P6Y804 1.3 27.2 1.0
F21 A:P6Y804 2.1 21.9 1.0
F20 A:P6Y804 2.1 24.0 1.0
C18 A:P6Y804 2.4 20.6 1.0
N17 A:P6Y804 2.9 29.4 1.0
NE2 A:HIS463 3.4 12.0 1.0
O A:HOH1094 3.4 17.1 1.0
C13 A:P6Y804 3.5 24.6 1.0
CD A:PRO464 3.6 11.6 1.0
CG A:PRO464 3.6 12.7 1.0
CZ A:PHE583 3.8 10.1 1.0
CE1 A:HIS463 3.8 8.0 1.0
O A:HOH1137 3.8 26.0 1.0
CD2 A:HIS463 4.0 12.6 1.0
C11 A:P6Y804 4.0 32.3 1.0
C16 A:P6Y804 4.1 24.3 1.0
CE1 A:PHE583 4.3 12.9 1.0
N10 A:P6Y804 4.4 25.2 1.0
ND1 A:HIS463 4.5 11.7 1.0
CG A:HIS463 4.6 8.5 1.0
C14 A:P6Y804 4.6 34.6 1.0
O12 A:P6Y804 4.7 38.5 1.0
CE2 A:PHE583 4.7 13.7 1.0
C15 A:P6Y804 4.9 32.8 1.0
CB A:PRO464 4.9 11.2 1.0
CD1 A:LEU712 4.9 25.8 1.0
N A:PRO464 5.0 8.8 1.0

Fluorine binding site 4 out of 6 in 6pzo

Go back to Fluorine Binding Sites List in 6pzo
Fluorine binding site 4 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F804

b:21.6
occ:1.00
F20 B:P6Y804 0.0 21.6 1.0
C19 B:P6Y804 1.3 27.0 1.0
F22 B:P6Y804 2.1 23.8 1.0
F21 B:P6Y804 2.2 29.9 1.0
C18 B:P6Y804 2.4 17.5 1.0
N10 B:P6Y804 2.8 16.6 1.0
C11 B:P6Y804 2.8 28.9 1.0
C13 B:P6Y804 2.9 25.0 1.0
C23 B:P6Y804 3.3 14.6 1.0
N17 B:P6Y804 3.4 22.2 1.0
O12 B:P6Y804 3.6 25.8 1.0
CD1 B:LEU712 3.6 9.3 1.0
C09 B:P6Y804 3.7 16.6 1.0
CZ B:PHE583 3.7 7.2 1.0
C08 B:P6Y804 3.8 14.5 1.0
CD2 B:LEU712 4.2 14.6 1.0
C24 B:P6Y804 4.2 12.9 1.0
C14 B:P6Y804 4.3 33.9 1.0
CE2 B:PHE583 4.5 10.7 1.0
CG B:LEU712 4.6 9.5 1.0
O B:HOH925 4.6 17.1 1.0
C16 B:P6Y804 4.6 22.5 1.0
CG B:PRO464 4.6 9.9 1.0
CE1 B:PHE583 4.7 9.5 1.0
C07 B:P6Y804 4.9 13.9 1.0
C15 B:P6Y804 4.9 30.1 1.0

Fluorine binding site 5 out of 6 in 6pzo

Go back to Fluorine Binding Sites List in 6pzo
Fluorine binding site 5 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F804

b:29.9
occ:1.00
F21 B:P6Y804 0.0 29.9 1.0
C19 B:P6Y804 1.3 27.0 1.0
F22 B:P6Y804 2.1 23.8 1.0
F20 B:P6Y804 2.2 21.6 1.0
C18 B:P6Y804 2.4 17.5 1.0
N17 B:P6Y804 3.1 22.2 1.0
C13 B:P6Y804 3.2 25.0 1.0
O B:HOH925 3.3 17.1 1.0
O B:HOH1184 3.4 27.8 1.0
NE2 B:HIS463 3.5 9.4 1.0
C11 B:P6Y804 3.5 28.9 1.0
CG B:PRO464 3.6 9.9 1.0
O12 B:P6Y804 3.7 25.8 1.0
CZ B:PHE583 3.8 7.2 1.0
CD B:PRO464 3.8 9.0 1.0
CE1 B:HIS463 3.9 10.5 1.0
CD2 B:HIS463 4.0 7.2 1.0
N10 B:P6Y804 4.2 16.6 1.0
C16 B:P6Y804 4.3 22.5 1.0
C14 B:P6Y804 4.4 33.9 1.0
CE1 B:PHE583 4.4 9.5 1.0
ND1 B:HIS463 4.6 8.4 1.0
CG B:HIS463 4.7 9.3 1.0
CE2 B:PHE583 4.8 10.7 1.0
C15 B:P6Y804 4.8 30.1 1.0
CD1 B:LEU712 4.9 9.3 1.0

Fluorine binding site 6 out of 6 in 6pzo

Go back to Fluorine Binding Sites List in 6pzo
Fluorine binding site 6 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Yx-153 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F804

b:23.8
occ:1.00
F22 B:P6Y804 0.0 23.8 1.0
C19 B:P6Y804 1.3 27.0 1.0
F20 B:P6Y804 2.1 21.6 1.0
F21 B:P6Y804 2.1 29.9 1.0
C18 B:P6Y804 2.4 17.5 1.0
N17 B:P6Y804 2.6 22.2 1.0
CD2 B:LEU712 3.4 14.6 1.0
CG B:PRO464 3.6 9.9 1.0
C13 B:P6Y804 3.7 25.0 1.0
CD1 B:LEU712 3.8 9.3 1.0
C16 B:P6Y804 3.9 22.5 1.0
CD B:PRO464 4.2 9.0 1.0
CG B:LEU712 4.2 9.5 1.0
C11 B:P6Y804 4.3 28.9 1.0
N10 B:P6Y804 4.7 16.6 1.0
C14 B:P6Y804 4.7 33.9 1.0
O B:HOH1184 4.8 27.8 1.0
C15 B:P6Y804 4.8 30.1 1.0
CB B:PRO464 4.9 9.6 1.0

Reference:

J.D.Osko, N.J.Porter, P.A.Narayana Reddy, Y.C.Xiao, J.Rokka, M.Jung, J.M.Hooker, J.M.Salvino, D.W.Christianson. Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. J.Med.Chem. V. 63 295 2020.
ISSN: ISSN 0022-2623
PubMed: 31793776
DOI: 10.1021/ACS.JMEDCHEM.9B01540
Page generated: Sun Dec 13 13:07:27 2020

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