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Fluorine in PDB 5m7u: Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor

Enzymatic activity of Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor

All present enzymatic activity of Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor:
3.2.1.169;

Protein crystallography data

The structure of Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor, PDB code: 5m7u was solved by C.Roth, S.Chan, W.A.Offen, G.R.Hemsworth, L.I.Willems, D.King, V.Varghese, R.Britton, D.J.Vocadlo, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 95.56 / 2.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.230, 101.230, 284.673, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor (pdb code 5m7u). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor, PDB code: 5m7u:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5m7u

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Fluorine binding site 1 out of 9 in the Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:69.7
occ:0.20
 F1 A:XHA1001 0.0 69.7 0.2
C17 A:XHA1001 1.3 70.6 0.2
F2 A:XHA1001 2.1 71.8 0.2
F3 A:XHA1001 2.1 68.3 0.2
C16 A:XHA1001 2.4 69.8 0.2
C15 A:XHA1001 2.8 70.2 0.2
C14 A:XHA1001 3.3 72.0 0.8
C18 A:XHA1001 3.6 70.8 0.2
C15 A:XHA1001 3.8 71.7 0.8
C14 A:XHA1001 4.1 70.1 0.2
C13 A:XHA1001 4.3 70.9 0.8
NZ B:LYS648 4.5 74.9 1.0
C12 A:XHA1001 4.7 71.1 0.2
CE B:LYS648 4.8 73.7 1.0
C13 A:XHA1001 4.9 70.4 0.2

Fluorine binding site 2 out of 9 in 5m7u

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Fluorine binding site 2 out of 9 in the Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:82.2
occ:0.80
 F1 A:XHA1001 0.0 82.2 0.8
C17 A:XHA1001 1.3 77.3 0.8
F2 A:XHA1001 2.1 74.9 0.8
F3 A:XHA1001 2.1 84.0 0.8
C16 A:XHA1001 2.4 71.6 0.8
C14 A:XHA1001 2.4 70.1 0.2
C15 A:XHA1001 2.8 71.7 0.8
OG B:SER649 3.1 69.5 1.0
C13 A:XHA1001 3.2 70.4 0.2
C15 A:XHA1001 3.3 70.2 0.2
C18 A:XHA1001 3.6 69.5 0.8
CB B:SER649 4.0 62.8 1.0
C14 A:XHA1001 4.2 72.0 0.8
CZ2 B:TRP645 4.3 63.9 1.0
NZ B:LYS648 4.3 74.9 1.0
C12 A:XHA1001 4.5 71.1 0.2
NE1 B:TRP645 4.5 65.9 1.0
C16 A:XHA1001 4.6 69.8 0.2
CE2 B:TRP645 4.6 62.7 1.0
C12 A:XHA1001 4.7 68.4 0.8
CA B:SER649 4.7 62.3 1.0
CD1 B:TRP679 4.9 77.5 1.0
C13 A:XHA1001 4.9 70.9 0.8

Fluorine binding site 3 out of 9 in 5m7u

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Fluorine binding site 3 out of 9 in the Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:71.8
occ:0.20
 F2 A:XHA1001 0.0 71.8 0.2
C17 A:XHA1001 1.3 70.6 0.2
F1 A:XHA1001 2.1 69.7 0.2
F3 A:XHA1001 2.1 68.3 0.2
C16 A:XHA1001 2.4 69.8 0.2
C14 A:XHA1001 3.1 72.0 0.8
C15 A:XHA1001 3.2 70.2 0.2
C18 A:XHA1001 3.3 70.8 0.2
OH A:TYR69 3.3 62.4 1.0
CZ A:TYR69 3.8 60.6 1.0
C13 A:XHA1001 3.9 70.9 0.8
C15 A:XHA1001 4.0 71.7 0.8
CH2 B:TRP645 4.2 63.2 1.0
CE1 A:TYR69 4.3 58.8 1.0
C14 A:XHA1001 4.4 70.1 0.2
C12 A:XHA1001 4.5 71.1 0.2
CE2 A:TYR69 4.5 59.3 1.0
CZ3 B:TRP645 4.6 61.2 1.0
OD2 A:ASP175 4.6 64.0 1.0
CB A:ASP175 4.7 63.9 1.0
C13 A:XHA1001 4.9 70.4 0.2
CG A:ASP175 5.0 65.1 1.0

Fluorine binding site 4 out of 9 in 5m7u

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Fluorine binding site 4 out of 9 in the Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:74.9
occ:0.80
 F2 A:XHA1001 0.0 74.9 0.8
C17 A:XHA1001 1.3 77.3 0.8
F3 A:XHA1001 2.1 84.0 0.8
F1 A:XHA1001 2.1 82.2 0.8
C16 A:XHA1001 2.4 71.6 0.8
C18 A:XHA1001 2.8 69.5 0.8
C13 A:XHA1001 3.1 70.4 0.2
C14 A:XHA1001 3.2 70.1 0.2
CG B:TRP679 3.2 77.4 1.0
CD2 B:TRP679 3.2 77.3 1.0
CD1 B:TRP679 3.5 77.5 1.0
CE2 B:TRP679 3.6 78.3 1.0
C15 A:XHA1001 3.6 71.7 0.8
CB B:TRP679 3.7 77.4 1.0
NE1 B:TRP679 3.7 78.4 1.0
CE3 B:TRP679 3.8 76.9 1.0
CB A:TYR286 3.9 59.0 1.0
C12 A:XHA1001 4.1 68.4 0.8
C12 A:XHA1001 4.3 71.1 0.2
OG B:SER649 4.4 69.5 1.0
CZ2 B:TRP679 4.4 79.7 1.0
O A:TYR286 4.4 60.7 1.0
C15 A:XHA1001 4.5 70.2 0.2
CA A:TYR286 4.5 59.0 1.0
CZ3 B:TRP679 4.5 79.1 1.0
C14 A:XHA1001 4.7 72.0 0.8
CH2 B:TRP679 4.8 80.3 1.0
C11 A:XHA1001 4.9 71.2 0.2
C A:TYR286 4.9 60.4 1.0
C13 A:XHA1001 4.9 70.9 0.8

Fluorine binding site 5 out of 9 in 5m7u

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Fluorine binding site 5 out of 9 in the Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:68.3
occ:0.20
 F3 A:XHA1001 0.0 68.3 0.2
C17 A:XHA1001 1.3 70.6 0.2
F2 A:XHA1001 2.1 71.8 0.2
F1 A:XHA1001 2.1 69.7 0.2
C16 A:XHA1001 2.4 69.8 0.2
C18 A:XHA1001 2.8 70.8 0.2
C14 A:XHA1001 3.2 72.0 0.8
C13 A:XHA1001 3.6 70.9 0.8
C15 A:XHA1001 3.6 70.2 0.2
CB A:ASP175 4.1 63.9 1.0
C12 A:XHA1001 4.1 71.1 0.2
CG A:ASP175 4.3 65.1 1.0
OH A:TYR69 4.3 62.4 1.0
C15 A:XHA1001 4.3 71.7 0.8
OD2 A:ASP175 4.4 64.0 1.0
O A:ASP175 4.5 65.9 1.0
CA A:ASP175 4.7 65.0 1.0
C14 A:XHA1001 4.7 70.1 0.2
OD1 A:ASP175 4.8 66.3 1.0
C12 A:XHA1001 4.9 68.4 0.8
C A:ASP175 4.9 65.3 1.0
C13 A:XHA1001 4.9 70.4 0.2

Fluorine binding site 6 out of 9 in 5m7u

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Fluorine binding site 6 out of 9 in the Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:84.0
occ:0.80
 F3 A:XHA1001 0.0 84.0 0.8
C17 A:XHA1001 1.3 77.3 0.8
F2 A:XHA1001 2.1 74.9 0.8
F1 A:XHA1001 2.1 82.2 0.8
C16 A:XHA1001 2.4 71.6 0.8
C14 A:XHA1001 2.8 70.1 0.2
C13 A:XHA1001 3.1 70.4 0.2
C15 A:XHA1001 3.1 71.7 0.8
CZ2 B:TRP645 3.2 63.9 1.0
NE1 B:TRP645 3.3 65.9 1.0
C18 A:XHA1001 3.3 69.5 0.8
CA A:TYR286 3.5 59.0 1.0
CE2 B:TRP645 3.5 62.7 1.0
CB A:TYR286 3.5 59.0 1.0
O A:TYR286 3.8 60.7 1.0
C15 A:XHA1001 4.0 70.2 0.2
OG B:SER649 4.0 69.5 1.0
C A:TYR286 4.1 60.4 1.0
CH2 B:TRP645 4.4 63.2 1.0
C14 A:XHA1001 4.4 72.0 0.8
C12 A:XHA1001 4.5 71.1 0.2
CD1 B:TRP645 4.5 60.2 1.0
C12 A:XHA1001 4.5 68.4 0.8
N A:TYR286 4.6 57.2 1.0
O A:ASP285 4.7 58.7 1.0
CB B:SER649 4.8 62.8 1.0
CD2 B:TRP645 4.9 59.3 1.0
NZ B:LYS648 5.0 74.9 1.0
C13 A:XHA1001 5.0 70.9 0.8

Fluorine binding site 7 out of 9 in 5m7u

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Fluorine binding site 7 out of 9 in the Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:0.1
occ:1.00
 F1 B:XHA1001 0.0 0.1 1.0
C17 B:XHA1001 1.3 94.1 1.0
F2 B:XHA1001 2.1 0.1 1.0
F3 B:XHA1001 2.1 0.5 1.0
C16 B:XHA1001 2.4 78.4 1.0
C18 B:XHA1001 2.8 68.9 1.0
CD2 A:TRP679 3.2 70.3 1.0
CG A:TRP679 3.3 68.9 1.0
CB B:TYR286 3.4 48.7 1.0
CB A:TRP679 3.6 67.7 1.0
CE3 A:TRP679 3.6 68.6 1.0
C15 B:XHA1001 3.6 75.2 1.0
CD1 A:TRP679 3.7 70.1 1.0
CE2 A:TRP679 3.8 71.5 1.0
NE1 A:TRP679 4.0 70.3 1.0
CA B:TYR286 4.1 50.7 1.0
O B:TYR286 4.1 59.8 1.0
C12 B:XHA1001 4.2 64.0 1.0
CZ3 A:TRP679 4.4 69.0 1.0
NH2 A:ARG682 4.4 0.4 1.0
CZ2 A:TRP679 4.5 71.7 1.0
OG A:SER649 4.5 72.4 1.0
C B:TYR286 4.6 53.1 1.0
CG B:TYR286 4.6 45.4 1.0
CH2 A:TRP679 4.8 70.7 1.0
C14 B:XHA1001 4.8 73.6 1.0
CZ2 A:TRP645 4.9 66.2 1.0
C13 B:XHA1001 5.0 68.1 1.0

Fluorine binding site 8 out of 9 in 5m7u

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Fluorine binding site 8 out of 9 in the Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:0.1
occ:1.00
 F2 B:XHA1001 0.0 0.1 1.0
C17 B:XHA1001 1.3 94.1 1.0
F1 B:XHA1001 2.1 0.1 1.0
F3 B:XHA1001 2.1 0.5 1.0
C16 B:XHA1001 2.4 78.4 1.0
C15 B:XHA1001 2.9 75.2 1.0
CZ2 A:TRP645 3.2 66.2 1.0
NE1 A:TRP645 3.3 64.8 1.0
CE2 A:TRP645 3.5 63.8 1.0
OG A:SER649 3.5 72.4 1.0
C18 B:XHA1001 3.5 68.9 1.0
O B:TYR286 4.1 59.8 1.0
CA B:TYR286 4.1 50.7 1.0
CB B:TYR286 4.2 48.7 1.0
CB A:SER649 4.2 65.8 1.0
C14 B:XHA1001 4.3 73.6 1.0
CH2 A:TRP645 4.3 65.5 1.0
NZ A:LYS648 4.3 75.9 1.0
NH2 A:ARG682 4.3 0.4 1.0
CD1 A:TRP645 4.5 63.6 1.0
C B:TYR286 4.6 53.1 1.0
CD2 A:TRP645 4.7 61.7 1.0
C12 B:XHA1001 4.7 64.0 1.0
C13 B:XHA1001 5.0 68.1 1.0

Fluorine binding site 9 out of 9 in 5m7u

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Fluorine binding site 9 out of 9 in the Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of Human O-Glcnac Hydrolase with New Iminocyclitol Type Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:0.5
occ:1.00
 F3 B:XHA1001 0.0 0.5 1.0
C17 B:XHA1001 1.3 94.1 1.0
F2 B:XHA1001 2.1 0.1 1.0
F1 B:XHA1001 2.1 0.1 1.0
C16 B:XHA1001 2.4 78.4 1.0
C15 B:XHA1001 3.1 75.2 1.0
C18 B:XHA1001 3.4 68.9 1.0
OG A:SER649 3.5 72.4 1.0
CD1 A:TRP679 4.2 70.1 1.0
C14 B:XHA1001 4.4 73.6 1.0
CG A:TRP679 4.4 68.9 1.0
NE1 A:TRP679 4.4 70.3 1.0
NH2 A:ARG682 4.5 0.4 1.0
CB A:SER649 4.5 65.8 1.0
C12 B:XHA1001 4.6 64.0 1.0
CD2 A:TRP679 4.6 70.3 1.0
CE2 A:TRP679 4.6 71.5 1.0
CB A:TRP679 4.9 67.7 1.0
C13 B:XHA1001 5.0 68.1 1.0
CZ2 A:TRP645 5.0 66.2 1.0

Reference:

C.Roth, S.Chan, W.A.Offen, G.R.Hemsworth, L.I.Willems, D.T.King, V.Varghese, R.Britton, D.J.Vocadlo, G.J.Davies. Structural and Functional Insight Into Human O-Glcnacase. Nat. Chem. Biol. V. 13 610 2017.
ISSN: ESSN 1552-4469
PubMed: 28346405
DOI: 10.1038/NCHEMBIO.2358
Page generated: Thu Aug 1 11:38:08 2024

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