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Fluorine in PDB 5wgm: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083, PDB code: 5wgm was solved by N.J.Porter, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.95 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.813, 174.304, 149.064, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 18.5

Other elements in 5wgm:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083 also contains other interesting chemical elements:

Potassium (K) 6 atoms
Zinc (Zn) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083 (pdb code 5wgm). 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 in Complex with Acy-1083, PDB code: 5wgm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5wgm

Go back to Fluorine Binding Sites List in 5wgm
Fluorine binding site 1 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 in Complex with Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F804

b:27.6
occ:1.00
 F20 A:AH7804 0.0 27.6 1.0
C19 A:AH7804 1.4 28.8 1.0
F21 A:AH7804 2.1 29.0 1.0
C18 A:AH7804 2.4 28.3 1.0
C22 A:AH7804 2.5 24.1 1.0
C17 A:AH7804 3.1 23.4 1.0
C23 A:AH7804 3.1 23.8 1.0
C10 A:AH7804 3.7 16.5 1.0
O A:HOH1154 4.1 25.3 1.0
O A:HOH1160 4.5 16.4 1.0
C11 A:AH7804 4.6 18.7 1.0
N09 A:AH7804 4.7 16.9 1.0
O1 A:EDO807 4.9 40.9 1.0
C16 A:AH7804 4.9 18.8 1.0

Fluorine binding site 2 out of 6 in 5wgm

Go back to Fluorine Binding Sites List in 5wgm
Fluorine binding site 2 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 in Complex with Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F804

b:29.0
occ:1.00
 F21 A:AH7804 0.0 29.0 1.0
C19 A:AH7804 1.4 28.8 1.0
F20 A:AH7804 2.1 27.6 1.0
C22 A:AH7804 2.3 24.1 1.0
C18 A:AH7804 2.3 28.3 1.0
O A:HOH1154 3.0 25.3 1.0
O1 A:EDO807 3.4 40.9 1.0
C1 A:EDO807 3.5 32.7 1.0
CD1 A:PHE643 3.6 17.7 1.0
C17 A:AH7804 3.6 23.4 1.0
C23 A:AH7804 3.6 23.8 1.0
CB A:PHE643 4.0 13.3 1.0
OD1 A:ASN645 4.1 31.0 1.0
C10 A:AH7804 4.1 16.5 1.0
O A:HOH1160 4.1 16.4 1.0
CG A:PHE643 4.2 13.7 1.0
N09 A:AH7804 4.5 16.9 1.0
CE1 A:PHE643 4.5 18.1 1.0
C2 A:EDO807 4.8 36.4 1.0
CA A:PHE643 4.9 11.9 1.0

Fluorine binding site 3 out of 6 in 5wgm

Go back to Fluorine Binding Sites List in 5wgm
Fluorine binding site 3 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 in Complex with Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F804

b:26.7
occ:1.00
 F20 B:AH7804 0.0 26.7 1.0
C19 B:AH7804 1.4 29.0 1.0
F21 B:AH7804 2.2 30.0 1.0
C22 B:AH7804 2.4 23.6 1.0
C18 B:AH7804 2.4 24.5 1.0
C23 B:AH7804 3.0 24.5 1.0
C17 B:AH7804 3.0 25.7 1.0
C10 B:AH7804 3.6 21.0 1.0
O B:HOH968 4.1 31.0 1.0
N09 B:AH7804 4.5 19.2 1.0
C11 B:AH7804 4.6 17.0 1.0
O B:HOH1104 4.7 18.7 1.0
C16 B:AH7804 4.9 18.8 1.0
O B:HOH964 5.0 40.7 1.0

Fluorine binding site 4 out of 6 in 5wgm

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Fluorine binding site 4 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 in Complex with Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F804

b:30.0
occ:1.00
 F21 B:AH7804 0.0 30.0 1.0
C19 B:AH7804 1.4 29.0 1.0
F20 B:AH7804 2.2 26.7 1.0
C18 B:AH7804 2.4 24.5 1.0
C22 B:AH7804 2.4 23.6 1.0
O B:HOH968 3.0 31.0 1.0
CD1 B:PHE643 3.6 15.6 1.0
O B:HOH964 3.6 40.7 1.0
C17 B:AH7804 3.6 25.7 1.0
C23 B:AH7804 3.7 24.5 1.0
OD1 B:ASN645 4.1 23.7 1.0
CB B:PHE643 4.1 12.4 1.0
C10 B:AH7804 4.1 21.0 1.0
O B:HOH923 4.2 30.4 1.0
CG B:PHE643 4.3 12.6 1.0
N09 B:AH7804 4.3 19.2 1.0
O B:HOH1104 4.4 18.7 1.0
CE1 B:PHE643 4.5 14.5 1.0
ND2 B:ASN645 4.8 28.5 1.0
CG B:ASN645 4.9 21.7 1.0
CA B:PHE643 4.9 14.5 1.0

Fluorine binding site 5 out of 6 in 5wgm

Go back to Fluorine Binding Sites List in 5wgm
Fluorine binding site 5 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 in Complex with Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F804

b:27.9
occ:1.00
 F20 C:AH7804 0.0 27.9 1.0
C19 C:AH7804 1.4 27.0 1.0
F21 C:AH7804 2.1 33.0 1.0
C22 C:AH7804 2.4 25.4 1.0
C18 C:AH7804 2.4 25.3 1.0
NH1 B:ARG562 2.6 30.5 1.0
C17 C:AH7804 2.9 22.8 1.0
C23 C:AH7804 3.0 24.2 1.0
O B:HOH1065 3.4 32.6 1.0
C10 C:AH7804 3.6 17.0 1.0
CZ B:ARG562 3.8 41.0 1.0
CD B:PRO442 3.8 22.9 1.0
O B:SER440 4.1 17.5 1.0
CG B:PRO442 4.1 28.4 1.0
O C:HOH1119 4.2 27.1 1.0
CB B:PRO442 4.3 24.6 1.0
N B:PRO442 4.5 21.3 1.0
O C:HOH1143 4.5 16.7 1.0
NE B:ARG562 4.5 38.1 1.0
C11 C:AH7804 4.6 17.2 1.0
NH2 B:ARG562 4.6 35.3 1.0
N09 C:AH7804 4.6 19.8 1.0
O B:HOH1133 4.7 24.9 1.0
CA B:PRO442 4.8 20.6 1.0
C16 C:AH7804 4.9 17.3 1.0

Fluorine binding site 6 out of 6 in 5wgm

Go back to Fluorine Binding Sites List in 5wgm
Fluorine binding site 6 out of 6 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Acy-1083


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 in Complex with Acy-1083 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F804

b:33.0
occ:1.00
 F21 C:AH7804 0.0 33.0 1.0
C19 C:AH7804 1.4 27.0 1.0
F20 C:AH7804 2.1 27.9 1.0
C22 C:AH7804 2.4 25.4 1.0
C18 C:AH7804 2.4 25.3 1.0
O C:HOH1119 2.8 27.1 1.0
NH1 B:ARG562 2.8 30.5 1.0
O1 C:EDO813 3.3 38.1 0.8
C17 C:AH7804 3.7 22.8 1.0
C23 C:AH7804 3.7 24.2 1.0
CD1 C:PHE643 3.7 16.0 1.0
O C:HOH1143 4.0 16.7 1.0
CB C:PHE643 4.1 13.7 1.0
OD1 C:ASN645 4.1 28.7 1.0
CZ B:ARG562 4.1 41.0 1.0
C10 C:AH7804 4.2 17.0 1.0
CG C:PHE643 4.3 18.4 1.0
C1 C:EDO813 4.5 32.2 0.8
N09 C:AH7804 4.6 19.8 1.0
CE1 C:PHE643 4.6 17.8 1.0
C2 C:EDO813 4.7 24.6 0.8
NH2 B:ARG562 4.8 35.3 1.0
CA C:PHE643 4.9 12.8 1.0
NE B:ARG562 5.0 38.1 1.0

Reference:

N.J.Porter, A.Mahendran, R.Breslow, D.W.Christianson. Unusual Zinc-Binding Mode of HDAC6-Selective Hydroxamate Inhibitors. Proc. Natl. Acad. Sci. V. 114 13459 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29203661
DOI: 10.1073/PNAS.1718823114
Page generated: Tue Jul 15 08:59:46 2025

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