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Fluorine in PDB 2igo: Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose

Enzymatic activity of Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose

All present enzymatic activity of Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose:
1.1.3.10;

Protein crystallography data

The structure of Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose, PDB code: 2igo was solved by C.Divne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.90 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 168.590, 103.080, 169.040, 90.00, 106.30, 90.00
R / Rfree (%) 18.4 / 22.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose (pdb code 2igo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose, PDB code: 2igo:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 2igo

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Fluorine binding site 1 out of 8 in the Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose


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 Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:25.0
occ:1.00
 F2 A:SHG801 0.0 25.0 1.0
C2 A:SHG801 1.4 29.3 1.0
C1 A:SHG801 2.5 35.1 1.0
C3 A:SHG801 2.5 30.0 1.0
O4 A:FAD701 2.9 17.8 1.0
NE2 A:GLN448 2.9 22.4 1.0
O1 A:SHG801 2.9 38.1 1.0
O3 A:SHG801 3.0 33.9 1.0
ND2 A:ASN593 3.2 19.4 1.0
OE1 A:GLN448 3.4 23.7 1.0
CB A:THR169 3.5 23.4 1.0
CD A:GLN448 3.6 23.4 1.0
C4 A:FAD701 3.6 20.3 1.0
CG2 A:THR169 3.6 24.9 1.0
O5 A:SHG801 3.8 38.5 1.0
C4 A:SHG801 3.9 35.7 1.0
CB A:ALA171 4.0 18.5 1.0
N5 A:FAD701 4.0 18.5 1.0
OG1 A:THR169 4.1 26.0 1.0
C4X A:FAD701 4.2 18.6 1.0
C5 A:SHG801 4.4 36.5 1.0
CZ A:PHE474 4.5 19.6 1.0
CG A:ASN593 4.5 22.5 1.0
N3 A:FAD701 4.6 18.3 1.0
CA A:THR169 4.8 21.9 1.0
N A:ALA171 4.8 17.7 1.0
O4 A:SHG801 5.0 37.8 1.0

Fluorine binding site 2 out of 8 in 2igo

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Fluorine binding site 2 out of 8 in the Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose


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 Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:24.9
occ:1.00
 F2 B:SHG802 0.0 24.9 1.0
C2 B:SHG802 1.4 29.8 1.0
C3 B:SHG802 2.5 29.1 1.0
C1 B:SHG802 2.5 28.4 1.0
O3 B:SHG802 2.8 28.1 1.0
NE2 B:GLN448 2.9 22.7 1.0
O4 B:FAD702 2.9 17.6 1.0
O1 B:SHG802 3.0 29.9 1.0
ND2 B:ASN593 3.2 18.9 1.0
CB B:THR169 3.4 19.7 1.0
OE1 B:GLN448 3.5 20.3 1.0
CG2 B:THR169 3.5 25.8 1.0
CD B:GLN448 3.6 21.4 1.0
C4 B:FAD702 3.6 20.4 1.0
O5 B:SHG802 3.8 32.3 1.0
C4 B:SHG802 3.8 31.8 1.0
OG1 B:THR169 4.0 25.7 1.0
CB B:ALA171 4.0 17.8 1.0
N5 B:FAD702 4.1 18.1 1.0
C4X B:FAD702 4.2 17.6 1.0
C5 B:SHG802 4.3 33.1 1.0
CG B:ASN593 4.4 18.7 1.0
CZ B:PHE474 4.5 20.6 1.0
N3 B:FAD702 4.5 17.8 1.0
CA B:THR169 4.8 20.5 1.0
O4 B:SHG802 4.9 31.0 1.0
N B:ALA171 4.9 17.3 1.0
CE2 B:PHE474 5.0 17.9 1.0

Fluorine binding site 3 out of 8 in 2igo

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Fluorine binding site 3 out of 8 in the Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose


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 Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:30.3
occ:1.00
 F2 D:SHG803 0.0 30.3 1.0
C2 D:SHG803 1.4 30.7 1.0
C3 D:SHG803 2.4 30.7 1.0
C1 D:SHG803 2.5 33.8 1.0
O3 D:SHG803 2.9 39.4 1.0
O4 D:FAD703 2.9 21.2 1.0
NE2 D:GLN448 3.0 23.1 1.0
O1 D:SHG803 3.0 36.5 1.0
ND2 D:ASN593 3.2 24.0 1.0
CB D:THR169 3.4 23.0 1.0
OE1 D:GLN448 3.5 22.8 1.0
C4 D:FAD703 3.6 22.5 1.0
CG2 D:THR169 3.6 27.0 1.0
CD D:GLN448 3.6 24.2 1.0
O5 D:SHG803 3.8 37.6 1.0
C4 D:SHG803 3.8 35.4 1.0
CB D:ALA171 3.9 19.8 1.0
N5 D:FAD703 3.9 18.2 1.0
OG1 D:THR169 4.0 23.9 1.0
C4X D:FAD703 4.1 19.9 1.0
C5 D:SHG803 4.3 34.6 1.0
CG D:ASN593 4.4 23.7 1.0
N3 D:FAD703 4.5 20.5 1.0
CZ D:PHE474 4.5 19.3 1.0
CA D:THR169 4.7 21.1 1.0
O4 D:SHG803 4.8 37.1 1.0
N D:ALA171 4.9 19.7 1.0

Fluorine binding site 4 out of 8 in 2igo

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Fluorine binding site 4 out of 8 in the Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose


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 Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F804

b:29.2
occ:1.00
 F2 C:SHG804 0.0 29.2 1.0
C2 C:SHG804 1.4 32.0 1.0
C1 C:SHG804 2.4 37.8 1.0
C3 C:SHG804 2.5 36.1 1.0
O1 C:SHG804 2.8 37.8 1.0
NE2 C:GLN448 2.8 25.8 1.0
O3 C:SHG804 3.0 37.3 1.0
O4 C:FAD704 3.1 20.7 1.0
ND2 C:ASN593 3.3 19.2 1.0
OE1 C:GLN448 3.4 26.9 1.0
CB C:THR169 3.5 24.7 1.0
CD C:GLN448 3.5 27.2 1.0
CG2 C:THR169 3.6 28.5 1.0
C4 C:FAD704 3.7 25.1 1.0
O5 C:SHG804 3.8 37.1 1.0
C4 C:SHG804 3.9 38.4 1.0
OG1 C:THR169 3.9 29.8 1.0
CB C:ALA171 4.1 21.4 1.0
N5 C:FAD704 4.1 24.7 1.0
C4X C:FAD704 4.3 21.0 1.0
C5 C:SHG804 4.3 39.2 1.0
CZ C:PHE474 4.5 23.2 1.0
CG C:ASN593 4.5 24.3 1.0
N3 C:FAD704 4.6 22.3 1.0
CA C:THR169 4.8 23.8 1.0
O4 C:SHG804 4.9 41.4 1.0
CE2 C:PHE474 5.0 24.2 1.0
CG C:GLN448 5.0 23.1 1.0
CE1 C:HIS450 5.0 23.2 1.0

Fluorine binding site 5 out of 8 in 2igo

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Fluorine binding site 5 out of 8 in the Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose


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 Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F805

b:35.0
occ:1.00
 F2 E:SHG805 0.0 35.0 1.0
C2 E:SHG805 1.4 36.4 1.0
C3 E:SHG805 2.5 31.9 1.0
C1 E:SHG805 2.5 37.5 1.0
NE2 E:GLN448 2.8 25.4 1.0
O1 E:SHG805 2.9 41.1 1.0
O3 E:SHG805 3.0 34.2 1.0
O4 E:FAD705 3.2 22.9 1.0
ND2 E:ASN593 3.2 22.0 1.0
OE1 E:GLN448 3.5 26.8 1.0
CB E:THR169 3.5 26.1 1.0
CD E:GLN448 3.6 25.8 1.0
CG2 E:THR169 3.6 31.3 1.0
C4 E:FAD705 3.8 20.7 1.0
O5 E:SHG805 3.9 40.7 1.0
C4 E:SHG805 3.9 36.2 1.0
CB E:ALA171 4.1 19.9 1.0
OG1 E:THR169 4.1 28.3 1.0
N5 E:FAD705 4.1 18.3 1.0
C4X E:FAD705 4.3 19.1 1.0
C5 E:SHG805 4.4 38.7 1.0
CZ E:PHE474 4.4 24.1 1.0
CG E:ASN593 4.5 24.0 1.0
N3 E:FAD705 4.7 15.3 1.0
O4 E:SHG805 4.9 38.7 1.0
CE1 E:HIS450 4.9 18.9 1.0
CA E:THR169 4.9 24.6 1.0
CE2 E:PHE474 4.9 22.0 1.0

Fluorine binding site 6 out of 8 in 2igo

Go back to Fluorine Binding Sites List in 2igo
Fluorine binding site 6 out of 8 in the Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose


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 Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F806

b:32.3
occ:1.00
 F2 F:SHG806 0.0 32.3 1.0
C2 F:SHG806 1.4 31.8 1.0
C1 F:SHG806 2.4 33.2 1.0
C3 F:SHG806 2.5 33.4 1.0
O4 F:FAD706 2.8 20.4 1.0
O1 F:SHG806 2.9 33.6 1.0
O3 F:SHG806 3.0 34.0 1.0
NE2 F:GLN448 3.1 24.4 1.0
ND2 F:ASN593 3.2 21.9 1.0
CB F:THR169 3.4 24.2 1.0
C4 F:FAD706 3.5 21.1 1.0
OE1 F:GLN448 3.6 24.4 1.0
CG2 F:THR169 3.6 24.5 1.0
O5 F:SHG806 3.8 35.5 1.0
CD F:GLN448 3.8 26.4 1.0
OG1 F:THR169 3.8 26.6 1.0
C4 F:SHG806 3.9 34.3 1.0
N5 F:FAD706 3.9 23.1 1.0
CB F:ALA171 4.0 21.0 1.0
C4X F:FAD706 4.1 21.0 1.0
C5 F:SHG806 4.3 35.9 1.0
CG F:ASN593 4.4 25.8 1.0
N3 F:FAD706 4.4 17.6 1.0
CZ F:PHE474 4.6 21.9 1.0
CA F:THR169 4.7 22.4 1.0
O4 F:SHG806 4.8 38.0 1.0
N F:ALA171 4.9 22.4 1.0

Fluorine binding site 7 out of 8 in 2igo

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Fluorine binding site 7 out of 8 in the Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F807

b:28.3
occ:1.00
 F2 H:SHG807 0.0 28.3 1.0
C2 H:SHG807 1.4 31.0 1.0
C3 H:SHG807 2.5 34.0 1.0
C1 H:SHG807 2.5 33.5 1.0
NE2 H:GLN448 2.8 22.1 1.0
O1 H:SHG807 2.8 38.9 1.0
O3 H:SHG807 2.9 35.2 1.0
O4 H:FAD707 3.1 18.7 1.0
ND2 H:ASN593 3.3 20.6 1.0
CB H:THR169 3.4 22.5 1.0
CG2 H:THR169 3.5 25.9 1.0
OE1 H:GLN448 3.5 22.6 1.0
CD H:GLN448 3.6 21.0 1.0
C4 H:FAD707 3.7 21.0 1.0
O5 H:SHG807 3.8 33.9 1.0
C4 H:SHG807 3.8 35.8 1.0
OG1 H:THR169 4.0 26.9 1.0
CB H:ALA171 4.0 19.1 1.0
N5 H:FAD707 4.1 19.2 1.0
C5 H:SHG807 4.3 35.1 1.0
C4X H:FAD707 4.3 19.6 1.0
CG H:ASN593 4.5 19.6 1.0
CZ H:PHE474 4.5 21.6 1.0
N3 H:FAD707 4.6 19.6 1.0
CA H:THR169 4.8 22.5 1.0
O4 H:SHG807 4.9 35.9 1.0
N H:ALA171 5.0 18.6 1.0
CE1 H:HIS450 5.0 19.7 1.0

Fluorine binding site 8 out of 8 in 2igo

Go back to Fluorine Binding Sites List in 2igo
Fluorine binding site 8 out of 8 in the Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Pyranose 2-Oxidase H167A Mutant with 2-Fluoro-2- Deoxy-D-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F808

b:27.9
occ:1.00
 F2 G:SHG808 0.0 27.9 1.0
C2 G:SHG808 1.4 30.3 1.0
C1 G:SHG808 2.4 32.4 1.0
C3 G:SHG808 2.5 31.1 1.0
O1 G:SHG808 2.8 35.4 1.0
O4 G:FAD708 2.8 24.9 1.0
NE2 G:GLN448 2.9 23.1 1.0
O3 G:SHG808 3.0 34.9 1.0
ND2 G:ASN593 3.2 27.5 1.0
CB G:THR169 3.4 24.0 1.0
CG2 G:THR169 3.5 26.5 1.0
OE1 G:GLN448 3.5 25.4 1.0
C4 G:FAD708 3.6 27.1 1.0
CD G:GLN448 3.6 27.1 1.0
O5 G:SHG808 3.7 37.1 1.0
OG1 G:THR169 3.9 28.4 1.0
C4 G:SHG808 3.9 35.8 1.0
N5 G:FAD708 3.9 21.6 1.0
CB G:ALA171 4.1 18.9 1.0
C4X G:FAD708 4.1 25.2 1.0
C5 G:SHG808 4.3 37.5 1.0
N3 G:FAD708 4.5 20.9 1.0
CZ G:PHE474 4.5 21.9 1.0
CG G:ASN593 4.5 24.0 1.0
CA G:THR169 4.7 23.2 1.0
O4 G:SHG808 4.9 37.9 1.0
N G:ALA171 4.9 20.9 1.0
CE1 G:HIS450 5.0 24.3 1.0

Reference:

M.Kujawa, H.Ebner, C.Leitner, B.M.Hallberg, M.Prongjit, J.Sucharitakul, R.Ludwig, U.Rudsander, C.Peterbauer, P.Chaiyen, D.Haltrich, C.Divne. Structural Basis For Substrate Binding and Regioselective Oxidation of Monosaccharides at C3 By Pyranose 2-Oxidase. J.Biol.Chem. V. 281 35104 2006.
ISSN: ISSN 0021-9258
PubMed: 16984920
DOI: 10.1074/JBC.M604718200
Page generated: Wed Jul 31 14:51:31 2024

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