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

Go back to Fluorine Binding Sites List in 5wgm
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: Sun Dec 13 12:41:52 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy