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Fluorine in PDB 3k4m: Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG

Enzymatic activity of Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG

All present enzymatic activity of Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG:
1.1.3.10;

Protein crystallography data

The structure of Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG, PDB code: 3k4m was solved by C.Divne, T.C.Tan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 168.190, 103.140, 168.710, 90.00, 106.47, 90.00
R / Rfree (%) 20.7 / 26.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG (pdb code 3k4m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG, PDB code: 3k4m:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3k4m

Go back to Fluorine Binding Sites List in 3k4m
Fluorine binding site 1 out of 8 in the Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:36.5
occ:1.00
 F2 A:SHG901 0.0 36.5 1.0
C2 A:SHG901 1.4 34.2 1.0
C3 A:SHG901 2.4 34.4 1.0
C1 A:SHG901 2.4 35.1 1.0
O4 A:FAD801 2.6 24.2 1.0
NE2 A:GLN448 3.0 17.1 1.0
O3 A:SHG901 3.0 34.6 1.0
O1 A:SHG901 3.0 39.1 1.0
ND2 A:ASN593 3.3 16.8 1.0
CB A:THR169 3.4 17.6 1.0
C4 A:FAD801 3.5 25.3 1.0
CG2 A:THR169 3.5 18.3 1.0
OE1 A:GLN448 3.6 16.9 1.0
CD A:GLN448 3.7 16.5 1.0
O5 A:SHG901 3.7 32.4 1.0
C4 A:SHG901 3.7 35.6 1.0
CB A:ALA171 3.8 15.6 1.0
OG1 A:THR169 3.9 16.9 1.0
C4X A:FAD801 4.0 19.8 1.0
N5 A:FAD801 4.0 21.8 1.0
C5 A:SHG901 4.2 36.8 1.0
CG A:ASN593 4.6 18.9 1.0
CZ A:PHE474 4.6 14.4 1.0
CA A:THR169 4.6 16.2 1.0
O4 A:SHG901 4.7 43.6 1.0
N3 A:FAD801 4.7 26.2 1.0
OD2 A:ASP452 4.8 16.7 1.0
N A:ALA171 4.8 15.2 1.0
C5X A:FAD801 4.9 21.7 1.0
CE2 A:PHE474 4.9 18.5 1.0
C A:THR169 5.0 16.7 1.0
N A:THR169 5.0 15.6 1.0
CA A:ALA171 5.0 16.2 1.0

Fluorine binding site 2 out of 8 in 3k4m

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Fluorine binding site 2 out of 8 in the Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:42.0
occ:1.00
 F2 B:SHG901 0.0 42.0 1.0
C2 B:SHG901 1.3 37.6 1.0
C3 B:SHG901 2.4 38.8 1.0
C1 B:SHG901 2.5 36.8 1.0
O3 B:SHG901 2.8 39.0 1.0
ND2 B:ASN593 3.0 15.5 1.0
NE2 B:GLN448 3.0 10.8 1.0
O4 B:FAD801 3.0 21.3 1.0
O1 B:SHG901 3.0 36.5 1.0
OE1 B:GLN448 3.4 16.2 1.0
CG2 B:THR169 3.6 15.5 1.0
CD B:GLN448 3.6 12.4 1.0
CB B:THR169 3.6 14.3 1.0
O5 B:SHG901 3.6 34.5 1.0
C4 B:SHG901 3.7 38.0 1.0
C4 B:FAD801 3.8 26.0 1.0
CB B:ALA171 3.8 15.3 1.0
OG1 B:THR169 4.1 18.2 1.0
N5 B:FAD801 4.1 26.9 1.0
C5 B:SHG901 4.1 37.9 1.0
C4X B:FAD801 4.2 24.6 1.0
CG B:ASN593 4.3 14.4 1.0
N3 B:FAD801 4.5 28.3 1.0
CZ B:PHE474 4.5 13.8 1.0
O4 B:SHG901 4.6 43.0 1.0
C5X B:FAD801 4.9 27.2 1.0
OD2 B:ASP452 4.9 18.5 1.0
CE2 B:PHE474 4.9 12.6 1.0
CA B:THR169 4.9 14.4 1.0

Fluorine binding site 3 out of 8 in 3k4m

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Fluorine binding site 3 out of 8 in the Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F901

b:46.6
occ:1.00
 F2 C:SHG901 0.0 46.6 1.0
C2 C:SHG901 1.4 40.3 1.0
C3 C:SHG901 2.4 39.8 1.0
C1 C:SHG901 2.4 40.1 1.0
CB C:THR169 2.9 23.6 1.0
O3 C:SHG901 3.0 46.1 1.0
O4 C:FAD801 3.0 20.0 1.0
O1 C:SHG901 3.1 42.7 1.0
CG2 C:THR169 3.2 25.5 1.0
C4 C:FAD801 3.2 27.1 1.0
NE2 C:GLN448 3.3 21.3 1.0
OG1 C:THR169 3.4 27.3 1.0
ND2 C:ASN593 3.5 19.1 1.0
N5 C:FAD801 3.6 33.5 1.0
O5 C:SHG901 3.6 37.7 1.0
C4 C:SHG901 3.7 39.2 1.0
C4X C:FAD801 3.8 30.0 1.0
OE1 C:GLN448 3.8 24.1 1.0
CD C:GLN448 4.0 22.5 1.0
C5 C:SHG901 4.1 38.3 1.0
CB C:ALA171 4.2 20.8 1.0
CA C:THR169 4.3 23.3 1.0
N3 C:FAD801 4.5 29.9 1.0
C5X C:FAD801 4.5 28.6 1.0
O4 C:SHG901 4.6 38.6 1.0
CG C:ASN593 4.7 20.9 1.0
N C:THR169 4.7 22.0 1.0
C C:THR169 4.7 22.8 1.0
OD2 C:ASP452 4.9 33.9 1.0
C6 C:FAD801 4.9 25.7 1.0
CZ C:PHE474 4.9 17.6 1.0
N C:ALA171 4.9 21.4 1.0

Fluorine binding site 4 out of 8 in 3k4m

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Fluorine binding site 4 out of 8 in the Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F901

b:38.1
occ:1.00
 F2 D:SHG901 0.0 38.1 1.0
C2 D:SHG901 1.4 41.3 1.0
C1 D:SHG901 2.5 40.9 1.0
C3 D:SHG901 2.5 39.0 1.0
O4 D:FAD801 2.9 22.9 1.0
O3 D:SHG901 2.9 41.6 1.0
NE2 D:GLN448 2.9 13.4 1.0
O1 D:SHG901 2.9 40.6 1.0
ND2 D:ASN593 3.1 13.8 1.0
OE1 D:GLN448 3.4 19.3 1.0
CD D:GLN448 3.6 13.6 1.0
CB D:THR169 3.6 21.4 1.0
O5 D:SHG901 3.7 38.1 1.0
C4 D:SHG901 3.8 40.2 1.0
C4 D:FAD801 3.8 21.4 1.0
CG2 D:THR169 3.8 23.8 1.0
OG1 D:THR169 3.9 21.2 1.0
N5 D:FAD801 4.0 22.5 1.0
CB D:ALA171 4.0 20.1 1.0
C5 D:SHG901 4.2 39.0 1.0
C4X D:FAD801 4.2 16.7 1.0
CG D:ASN593 4.4 16.0 1.0
CZ D:PHE474 4.5 19.2 1.0
N3 D:FAD801 4.7 21.5 1.0
OD2 D:ASP452 4.8 32.3 1.0
O4 D:SHG901 4.8 42.0 1.0
CE2 D:PHE474 4.8 19.1 1.0
C5X D:FAD801 4.9 22.3 1.0
CA D:THR169 5.0 21.4 1.0

Fluorine binding site 5 out of 8 in 3k4m

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Fluorine binding site 5 out of 8 in the Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F901

b:47.4
occ:1.00
 F2 E:SHG901 0.0 47.4 1.0
C2 E:SHG901 1.4 46.5 1.0
C1 E:SHG901 2.5 47.6 1.0
C3 E:SHG901 2.5 46.7 1.0
NE2 E:GLN448 2.8 19.9 1.0
O1 E:SHG901 3.0 50.1 1.0
O3 E:SHG901 3.1 46.4 1.0
ND2 E:ASN593 3.3 13.0 1.0
CB E:THR169 3.4 20.1 1.0
OE1 E:GLN448 3.5 22.8 1.0
O4 E:FAD801 3.5 29.1 1.0
CD E:GLN448 3.5 20.3 1.0
CG2 E:THR169 3.6 21.0 1.0
C4 E:FAD801 3.7 25.9 1.0
OG1 E:THR169 3.7 23.5 1.0
O5 E:SHG901 3.7 45.2 1.0
C4 E:SHG901 3.8 43.6 1.0
CB E:ALA171 3.9 21.0 1.0
N5 E:FAD801 4.0 29.7 1.0
C4X E:FAD801 4.2 27.3 1.0
C5 E:SHG901 4.3 45.2 1.0
CZ E:PHE474 4.4 19.4 1.0
CG E:ASN593 4.6 20.6 1.0
N3 E:FAD801 4.6 26.7 1.0
O4 E:SHG901 4.8 48.2 1.0
CA E:THR169 4.8 19.5 1.0
CE2 E:PHE474 4.9 21.5 1.0
CG E:GLN448 5.0 19.1 1.0

Fluorine binding site 6 out of 8 in 3k4m

Go back to Fluorine Binding Sites List in 3k4m
Fluorine binding site 6 out of 8 in the Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F901

b:31.8
occ:1.00
 F2 F:SHG901 0.0 31.8 1.0
C2 F:SHG901 1.4 28.0 1.0
C3 F:SHG901 2.4 29.3 1.0
C1 F:SHG901 2.4 29.4 1.0
O3 F:SHG901 2.9 35.7 1.0
O4 F:FAD801 3.0 27.1 1.0
O1 F:SHG901 3.0 33.3 1.0
NE2 F:GLN448 3.1 16.9 1.0
CB F:THR169 3.2 21.2 1.0
CG2 F:THR169 3.4 20.8 1.0
ND2 F:ASN593 3.5 16.6 1.0
OG1 F:THR169 3.6 20.2 1.0
O5 F:SHG901 3.6 32.3 1.0
OE1 F:GLN448 3.7 17.5 1.0
C4 F:SHG901 3.7 30.9 1.0
CD F:GLN448 3.8 15.7 1.0
C4 F:FAD801 3.9 27.1 1.0
N5 F:FAD801 4.0 25.0 1.0
C4X F:FAD801 4.1 20.7 1.0
C5 F:SHG901 4.2 33.7 1.0
CB F:ALA171 4.2 22.4 1.0
OD2 F:ASP452 4.6 38.3 1.0
CA F:THR169 4.6 19.8 1.0
O4 F:SHG901 4.7 31.7 1.0
N3 F:FAD801 4.7 23.2 1.0
CZ F:PHE474 4.7 13.0 1.0
CG F:ASN593 4.7 19.1 1.0
C5X F:FAD801 4.9 17.8 1.0
N F:ALA171 4.9 22.8 1.0
C F:THR169 5.0 20.2 1.0

Fluorine binding site 7 out of 8 in 3k4m

Go back to Fluorine Binding Sites List in 3k4m
Fluorine binding site 7 out of 8 in the Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F901

b:48.5
occ:1.00
 F2 G:SHG901 0.0 48.5 1.0
C2 G:SHG901 1.4 45.2 1.0
C1 G:SHG901 2.5 43.8 1.0
C3 G:SHG901 2.5 45.0 1.0
NE2 G:GLN448 2.8 20.0 1.0
O3 G:SHG901 2.9 42.5 1.0
O1 G:SHG901 2.9 44.3 1.0
O4 G:FAD801 3.0 30.1 1.0
ND2 G:ASN593 3.2 14.8 1.0
OE1 G:GLN448 3.3 26.2 1.0
CD G:GLN448 3.5 24.8 1.0
CB G:THR169 3.5 21.6 1.0
CG2 G:THR169 3.6 22.1 1.0
O5 G:SHG901 3.7 41.2 1.0
C4 G:SHG901 3.8 45.2 1.0
C4 G:FAD801 3.9 27.2 1.0
OG1 G:THR169 3.9 23.7 1.0
CB G:ALA171 4.0 20.3 1.0
N5 G:FAD801 4.1 30.2 1.0
C4X G:FAD801 4.2 24.9 1.0
C5 G:SHG901 4.2 44.5 1.0
CZ G:PHE474 4.4 18.2 1.0
CG G:ASN593 4.5 16.2 1.0
N3 G:FAD801 4.7 25.9 1.0
CA G:THR169 4.8 21.2 1.0
CE2 G:PHE474 4.8 20.7 1.0
O4 G:SHG901 4.9 48.7 1.0
OD2 G:ASP452 4.9 22.6 1.0
CG G:GLN448 5.0 21.5 1.0
CE1 G:HIS450 5.0 15.8 1.0

Fluorine binding site 8 out of 8 in 3k4m

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Fluorine binding site 8 out of 8 in the Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Pyranose 2-Oxidase Y456W Mutant in Complex with 2FG within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F901

b:39.7
occ:1.00
 F2 H:SHG901 0.0 39.7 1.0
C2 H:SHG901 1.4 41.2 1.0
C3 H:SHG901 2.4 41.3 1.0
C1 H:SHG901 2.5 41.6 1.0
O3 H:SHG901 2.8 42.6 1.0
NE2 H:GLN448 2.8 14.7 1.0
O1 H:SHG901 2.9 45.4 1.0
ND2 H:ASN593 3.1 13.0 1.0
O4 H:FAD801 3.1 28.0 1.0
OE1 H:GLN448 3.5 23.4 1.0
CB H:THR169 3.6 17.6 1.0
CD H:GLN448 3.6 17.2 1.0
C4 H:SHG901 3.7 42.2 1.0
O5 H:SHG901 3.7 41.1 1.0
CG2 H:THR169 3.8 21.1 1.0
OG1 H:THR169 3.9 18.1 1.0
C4 H:FAD801 3.9 25.8 1.0
CB H:ALA171 4.0 17.6 1.0
N5 H:FAD801 4.1 25.4 1.0
C5 H:SHG901 4.2 42.3 1.0
CZ H:PHE474 4.3 16.8 1.0
C4X H:FAD801 4.3 24.3 1.0
CG H:ASN593 4.4 15.7 1.0
O4 H:SHG901 4.7 49.0 1.0
CE2 H:PHE474 4.8 17.2 1.0
N3 H:FAD801 4.8 25.6 1.0
CA H:THR169 4.9 16.7 1.0

Reference:

O.Spadiut, T.C.Tan, I.Pisanelli, D.Haltrich, C.Divne. Importance of the Gating Segment in the Substrate-Recognition Loop of Pyranose 2-Oxidase. Febs J. V. 277 2892 2010.
ISSN: ISSN 1742-464X
PubMed: 20528921
DOI: 10.1111/J.1742-4658.2010.07705.X
Page generated: Wed Jul 31 19:47:33 2024

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