Fluorine in PDB 7uk2: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390

Protein crystallography data

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390, PDB code: 7uk2 was solved by F.Erdogan, H.-S.Seo, S.Dhe-Paganon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.06 / 1.60
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.263, 83.135, 93.276, 90, 90, 90
R / Rfree (%) 19.9 / 22.2

Other elements in 7uk2:

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390 also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Potassium (K) 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 Nn-390 (pdb code 7uk2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390, PDB code: 7uk2:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7uk2

Go back to Fluorine Binding Sites List in 7uk2
Fluorine binding site 1 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390


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 Nn-390 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:38.8
occ:1.00
F01 A:O2L801 0.0 38.8 1.0
C02 A:O2L801 1.4 34.9 1.0
C03 A:O2L801 2.4 34.2 1.0
C27 A:O2L801 2.4 32.8 1.0
F04 A:O2L801 2.8 38.6 1.0
F28 A:O2L801 2.8 33.8 1.0
C26 A:O2L801 3.7 31.2 1.0
C05 A:O2L801 3.7 34.0 1.0
C07 A:O2L801 4.1 27.7 1.0
O A:HOH1231 4.6 32.9 1.0
O A:HOH918 4.6 36.8 1.0
F06 A:O2L801 4.8 37.0 1.0
O A:HOH1175 5.0 17.4 1.0

Fluorine binding site 2 out of 4 in 7uk2

Go back to Fluorine Binding Sites List in 7uk2
Fluorine binding site 2 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390


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 Nn-390 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:38.6
occ:1.00
F04 A:O2L801 0.0 38.6 1.0
C03 A:O2L801 1.4 34.2 1.0
C05 A:O2L801 2.4 34.0 1.0
C02 A:O2L801 2.4 34.9 1.0
F06 A:O2L801 2.8 37.0 1.0
F01 A:O2L801 2.8 38.8 1.0
O A:HOH918 3.4 36.8 1.0
C07 A:O2L801 3.6 27.7 1.0
C27 A:O2L801 3.7 32.8 1.0
C26 A:O2L801 4.2 31.2 1.0
F28 A:O2L801 4.8 33.8 1.0

Fluorine binding site 3 out of 4 in 7uk2

Go back to Fluorine Binding Sites List in 7uk2
Fluorine binding site 3 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390


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 Nn-390 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:37.0
occ:1.00
F06 A:O2L801 0.0 37.0 1.0
C05 A:O2L801 1.4 34.0 1.0
C07 A:O2L801 2.4 27.7 1.0
C03 A:O2L801 2.4 34.2 1.0
F04 A:O2L801 2.8 38.6 1.0
S08 A:O2L801 3.0 16.6 1.0
C11 A:O2L801 3.1 24.9 1.0
C10 A:O2L801 3.2 23.0 1.0
N09 A:O2L801 3.2 18.7 1.0
O24 A:O2L801 3.4 25.1 1.0
O A:HOH918 3.6 36.8 1.0
C26 A:O2L801 3.6 31.2 1.0
C02 A:O2L801 3.7 34.9 1.0
C27 A:O2L801 4.1 32.8 1.0
C13 A:O2L801 4.2 16.7 1.0
O25 A:O2L801 4.4 22.2 1.0
C12 A:O2L801 4.7 21.6 1.0
F01 A:O2L801 4.8 38.8 1.0

Fluorine binding site 4 out of 4 in 7uk2

Go back to Fluorine Binding Sites List in 7uk2
Fluorine binding site 4 out of 4 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 Complexed with Nn-390


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 Nn-390 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:33.8
occ:1.00
F28 A:O2L801 0.0 33.8 1.0
C27 A:O2L801 1.4 32.8 1.0
C26 A:O2L801 2.3 31.2 1.0
C02 A:O2L801 2.4 34.9 1.0
F01 A:O2L801 2.8 38.8 1.0
CD2 A:HIS463 3.3 11.4 1.0
NE2 A:HIS463 3.6 19.5 1.0
C07 A:O2L801 3.6 27.7 1.0
C03 A:O2L801 3.7 34.2 1.0
O A:HOH1231 3.7 32.9 1.0
O A:HOH1175 3.7 17.4 1.0
C05 A:O2L801 4.1 34.0 1.0
CG A:HIS463 4.4 15.8 1.0
CE1 A:HIS463 4.8 16.3 1.0
F04 A:O2L801 4.8 38.6 1.0
O25 A:O2L801 4.9 22.2 1.0
OD2 A:ASP460 4.9 27.5 1.0

Reference:

H.K.Garcha, N.Nawar, H.Sorger, F.Erdogan, M.M.K.Aung, A.Sedighi, P.Manaswiyoungkul, H.S.Seo, S.Schonefeldt, D.Poloske, S.Dhe-Paganon, H.A.Neubauer, S.M.Mustjoki, M.Herling, E.D.De Araujo, R.Moriggl, P.T.Gunning. High Efficacy and Drug Synergy of HDAC6-Selective Inhibitor Nn-429 in Natural Killer (Nk)/T-Cell Lymphoma. Pharmaceuticals V. 15 2022.
ISSN: ESSN 1424-8247
PubMed: 36355493
DOI: 10.3390/PH15111321
Page generated: Wed Apr 5 01:30:28 2023

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