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Fluorine in PDB 5abg: Structure of GH84 with Ligand

Enzymatic activity of Structure of GH84 with Ligand

All present enzymatic activity of Structure of GH84 with Ligand:
3.2.1.169; 3.2.1.52;

Protein crystallography data

The structure of Structure of GH84 with Ligand, PDB code: 5abg was solved by M.Bergeron-Brlek, J.Goodwin-Tindall, N.Cekic, V.Varghese, W.F.Zandberg, X.Shan, C.Roth, S.Chan, G.J.Davies, D.J.Vocadlo, R.Britton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.44 / 2.00
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.531, 161.184, 223.980, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 23.5

Other elements in 5abg:

The structure of Structure of GH84 with Ligand also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of GH84 with Ligand (pdb code 5abg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of GH84 with Ligand, PDB code: 5abg:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5abg

Go back to Fluorine Binding Sites List in 5abg
Fluorine binding site 1 out of 2 in the Structure of GH84 with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of GH84 with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1717

b:98.9
occ:1.00
F25 A:V0N1717 0.0 98.9 1.0
C22 A:V0N1717 1.3 92.7 1.0
C21 A:V0N1717 2.4 88.4 1.0
C23 A:V0N1717 2.4 84.4 1.0
H23 A:V0N1717 2.6 0.2 1.0
H21 A:V0N1717 2.6 0.1 1.0
C20 A:V0N1717 3.6 87.5 1.0
C24 A:V0N1717 3.6 80.1 1.0
C19 A:V0N1717 4.1 79.9 1.0
H20 A:V0N1717 4.5 1.0 1.0
H24 A:V0N1717 4.5 96.2 1.0
HH2 A:TRP286 4.9 85.0 1.0

Fluorine binding site 2 out of 2 in 5abg

Go back to Fluorine Binding Sites List in 5abg
Fluorine binding site 2 out of 2 in the Structure of GH84 with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of GH84 with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1718

b:98.7
occ:1.00
F25 B:V0N1718 0.0 98.7 1.0
C22 B:V0N1718 1.3 98.0 1.0
C21 B:V0N1718 2.4 95.9 1.0
C23 B:V0N1718 2.4 96.9 1.0
H21 B:V0N1718 2.6 0.1 1.0
H23 B:V0N1718 2.6 0.2 1.0
C20 B:V0N1718 3.6 92.5 1.0
C24 B:V0N1718 3.6 92.9 1.0
HH2 B:TRP286 3.7 0.3 1.0
C19 B:V0N1718 4.1 87.6 1.0
CH2 B:TRP286 4.3 86.9 1.0
HZ2 B:TRP286 4.4 0.5 1.0
H20 B:V0N1718 4.5 0.1 1.0
H24 B:V0N1718 4.5 0.5 1.0
CZ2 B:TRP286 4.6 86.2 1.0

Reference:

M.Bergeron-Brlek, J.Goodwin-Tindall, N.Cekic, C.Roth, W.F.Zandberg, X.Shan, V.Varghese, S.Chan, G.J.Davies, D.J.Vocadlo, R.Britton. A Convenient Approach to Stereoisomeric Iminocyclitols: Generation of Potent Brain-Permeable Oga Inhibitors. Angew.Chem.Int.Ed.Engl. V. 54 15429 2015.
ISSN: ISSN 1433-7851
PubMed: 26545827
DOI: 10.1002/ANIE.201507985
Page generated: Tue Jul 15 02:12:00 2025

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