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Fluorine in PDB 2xzk: The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights

Enzymatic activity of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights

All present enzymatic activity of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights:
3.2.1.18;

Protein crystallography data

The structure of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights, PDB code: 2xzk was solved by J.C.Telford, J.H.F.Yeung, M.J.Kiefel, A.G.Watts, S.Hader, J.Chan, A.J.Bennet, M.M.Moore, G.L.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.01 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.680, 58.080, 94.450, 90.00, 100.05, 90.00
R / Rfree (%) 17.923 / 21.375

Other elements in 2xzk:

The structure of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights (pdb code 2xzk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights, PDB code: 2xzk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 2xzk

Go back to Fluorine Binding Sites List in 2xzk
Fluorine binding site 1 out of 12 in the The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F500

b:13.2
occ:1.00
 F1 A:FKD500 0.0 13.2 1.0
C3 A:FKD500 1.4 9.1 1.0
C2 A:FKD500 2.3 9.2 1.0
C4 A:FKD500 2.4 8.5 1.0
OD1 A:ASP84 2.7 13.8 0.7
O1A A:FKD500 2.7 9.2 1.0
O4 A:FKD500 2.8 9.7 1.0
OD2 A:ASP84 2.8 14.4 0.7
C1 A:FKD500 2.8 9.6 1.0
CG A:ASP84 2.9 12.3 0.7
O6 A:FKD500 3.0 8.3 1.0
O A:HOH2153 3.0 30.7 1.0
NH1 A:ARG59 3.0 6.9 1.0
C5 A:FKD500 3.1 8.3 1.0
OD2 A:ASP84 3.5 10.6 0.3
C6 A:FKD500 3.6 8.3 1.0
O1B A:FKD500 3.9 9.6 1.0
CB A:ASP84 3.9 10.8 0.3
OH A:TYR358 3.9 7.8 1.0
CZ A:ARG59 3.9 9.3 1.0
O A:HOH2551 4.0 15.5 1.0
NH2 A:ARG59 4.1 10.6 1.0
NH2 A:ARG78 4.1 7.4 1.0
CG A:ASP84 4.2 10.5 0.3
CB A:ASP84 4.2 11.4 0.7
O5 A:FKD500 4.4 7.8 1.0
O A:HOH2548 4.4 22.6 1.0
NH1 A:ARG78 4.4 10.1 1.0
CZ A:TYR358 4.5 8.3 1.0
O7 A:FKD500 4.6 8.8 1.0
CD1 A:ILE60 4.6 7.6 1.0
CZ A:ARG78 4.7 8.5 1.0
C7 A:FKD500 4.8 9.3 1.0
O A:HOH2146 4.9 11.9 1.0
CE1 A:TYR358 5.0 9.0 1.0

Fluorine binding site 2 out of 12 in 2xzk

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Fluorine binding site 2 out of 12 in the The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:21.4
occ:1.00
 F1 A:K99501 0.0 21.4 1.0
C3 A:K99501 1.4 20.1 1.0
C2 A:K99501 2.4 20.2 1.0
C4 A:K99501 2.4 19.0 1.0
F2 A:K99501 2.6 20.6 1.0
O4 A:K99501 2.8 17.6 1.0
O6 A:K99501 2.9 19.8 1.0
C5 A:K99501 2.9 18.7 1.0
NH2 A:ARG323 3.1 17.8 1.0
CE1 A:PHE378 3.1 17.6 1.0
O A:HOH2465 3.3 36.0 1.0
NE A:ARG323 3.4 15.4 1.0
C6 A:K99501 3.5 19.4 1.0
CZ A:ARG323 3.5 18.1 1.0
CZ A:PHE378 3.6 16.5 1.0
CD1 A:PHE378 3.6 16.6 1.0
C1 A:K99501 3.7 20.3 1.0
O1B A:K99501 4.1 19.2 1.0
O A:HOH2461 4.2 25.6 1.0
O5 A:K99501 4.3 16.6 1.0
CE2 A:PHE378 4.3 17.1 1.0
CG A:PHE378 4.4 16.1 1.0
O7 A:K99501 4.5 20.4 1.0
CD A:ARG323 4.5 14.0 1.0
NH1 A:ARG323 4.6 16.9 1.0
C7 A:K99501 4.6 21.9 1.0
CD2 A:PHE378 4.7 16.8 1.0
O1A A:K99501 4.7 20.1 1.0
CG A:ARG323 4.9 11.0 1.0

Fluorine binding site 3 out of 12 in 2xzk

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Fluorine binding site 3 out of 12 in the The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:20.6
occ:1.00
 F2 A:K99501 0.0 20.6 1.0
C2 A:K99501 1.3 20.2 1.0
O6 A:K99501 2.3 19.8 1.0
C1 A:K99501 2.3 20.3 1.0
C3 A:K99501 2.3 20.1 1.0
F1 A:K99501 2.6 21.4 1.0
O1B A:K99501 3.0 19.2 1.0
O1A A:K99501 3.1 20.1 1.0
O A:HOH2461 3.5 25.6 1.0
C6 A:K99501 3.6 19.4 1.0
C4 A:K99501 3.7 19.0 1.0
O A:HOH2465 4.0 36.0 1.0
C5 A:K99501 4.1 18.7 1.0
O A:HOH2460 4.5 36.6 1.0
C7 A:K99501 4.6 21.9 1.0
CE1 A:PHE378 4.6 17.6 1.0
C8 A:K99501 4.7 24.6 1.0
CZ A:PHE378 4.7 16.5 1.0
O4 A:K99501 4.8 17.6 1.0
O8 A:K99501 4.8 24.9 1.0
O7 A:K99501 4.9 20.4 1.0

Fluorine binding site 4 out of 12 in 2xzk

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Fluorine binding site 4 out of 12 in the The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:21.5
occ:1.00
 F1 A:K99502 0.0 21.5 1.0
C3 A:K99502 1.4 20.2 1.0
C2 A:K99502 2.4 21.8 1.0
C4 A:K99502 2.4 20.0 1.0
F2 A:K99502 2.6 21.6 1.0
O4 A:K99502 2.8 16.2 1.0
O6 A:K99502 2.9 22.2 1.0
O A:LYS337 2.9 11.3 1.0
C5 A:K99502 3.0 20.9 1.0
C A:PHE338 3.0 11.4 1.0
C A:LYS337 3.1 12.0 1.0
O A:PHE338 3.2 11.9 1.0
N A:PHE338 3.3 11.9 1.0
N A:ASN339 3.4 10.3 1.0
CB A:LYS337 3.4 13.8 1.0
CA A:PHE338 3.4 11.3 1.0
C6 A:K99502 3.5 23.0 1.0
O A:HOH2478 3.6 27.5 1.0
C1 A:K99502 3.8 23.2 1.0
CA A:LYS337 3.9 13.0 1.0
CA A:ASN339 4.0 10.8 1.0
O1A A:K99502 4.1 22.7 1.0
O5 A:K99502 4.3 21.1 1.0
CB A:ASN339 4.6 10.4 1.0
O A:ILE329 4.6 10.4 1.0
O7 A:K99502 4.7 26.5 1.0
C7 A:K99502 4.8 25.8 1.0
O1B A:K99502 4.8 25.7 1.0
CG A:LYS337 4.8 17.6 1.0
OD2 A:ASP332 4.8 15.9 1.0
N A:LYS337 4.9 12.9 1.0
CB A:PHE338 4.9 11.1 1.0

Fluorine binding site 5 out of 12 in 2xzk

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Fluorine binding site 5 out of 12 in the The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:21.6
occ:1.00
 F2 A:K99502 0.0 21.6 1.0
C2 A:K99502 1.3 21.8 1.0
O6 A:K99502 2.3 22.2 1.0
C3 A:K99502 2.3 20.2 1.0
C1 A:K99502 2.4 23.2 1.0
F1 A:K99502 2.6 21.5 1.0
O1B A:K99502 2.9 25.7 1.0
O1A A:K99502 3.2 22.7 1.0
CA A:ASN339 3.4 10.8 1.0
O A:HOH2478 3.6 27.5 1.0
C6 A:K99502 3.6 23.0 1.0
CB A:ASN339 3.6 10.4 1.0
C4 A:K99502 3.7 20.0 1.0
N A:ASN339 3.8 10.3 1.0
O A:PHE338 3.9 11.9 1.0
C A:PHE338 4.0 11.4 1.0
C5 A:K99502 4.1 20.9 1.0
O A:HOH2480 4.2 21.8 1.0
O8 A:K99502 4.6 29.8 1.0
C A:ASN339 4.7 10.1 1.0
C7 A:K99502 4.8 25.8 1.0
O4 A:K99502 4.8 16.2 1.0
O7 A:K99502 4.8 26.5 1.0

Fluorine binding site 6 out of 12 in 2xzk

Go back to Fluorine Binding Sites List in 2xzk
Fluorine binding site 6 out of 12 in the The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F500

b:12.1
occ:1.00
 F1 B:FKD500 0.0 12.1 1.0
C3 B:FKD500 1.4 9.4 1.0
C2 B:FKD500 2.3 9.0 1.0
C4 B:FKD500 2.4 7.2 1.0
O4 B:FKD500 2.7 8.0 1.0
OD1 B:ASP84 2.7 10.3 0.7
O1A B:FKD500 2.8 8.8 1.0
C1 B:FKD500 2.8 9.2 1.0
OD2 B:ASP84 2.9 10.7 0.7
O6 B:FKD500 3.0 8.4 1.0
CG B:ASP84 3.0 10.5 0.7
C5 B:FKD500 3.0 7.2 1.0
NH1 B:ARG59 3.0 6.8 1.0
O B:HOH2130 3.1 27.9 1.0
OD2 B:ASP84 3.5 8.4 0.3
C6 B:FKD500 3.6 7.1 1.0
OH B:TYR358 3.8 6.5 1.0
O1B B:FKD500 3.8 8.5 1.0
CZ B:ARG59 3.9 7.4 1.0
CB B:ASP84 3.9 9.9 0.3
O B:HOH2513 4.0 16.4 1.0
NH2 B:ARG59 4.1 10.1 1.0
NH2 B:ARG78 4.2 7.6 1.0
CG B:ASP84 4.2 9.9 0.3
CB B:ASP84 4.3 10.2 0.7
O5 B:FKD500 4.3 8.6 1.0
NH1 B:ARG78 4.4 7.1 1.0
CZ B:TYR358 4.4 5.4 1.0
O B:HOH2512 4.4 24.4 1.0
O7 B:FKD500 4.5 9.3 1.0
CD1 B:ILE60 4.6 6.8 1.0
C7 B:FKD500 4.7 7.2 1.0
CZ B:ARG78 4.8 8.2 1.0
O B:HOH2124 5.0 11.5 1.0
CE1 B:TYR358 5.0 6.0 1.0

Fluorine binding site 7 out of 12 in 2xzk

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Fluorine binding site 7 out of 12 in the The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:15.0
occ:1.00
 F1 B:K99501 0.0 15.0 1.0
C3 B:K99501 1.4 14.6 1.0
C2 B:K99501 2.4 15.8 1.0
C4 B:K99501 2.4 12.9 1.0
F2 B:K99501 2.6 16.5 1.0
O4 B:K99501 2.8 11.3 1.0
O6 B:K99501 2.9 15.8 1.0
NH2 B:ARG323 3.0 13.6 1.0
C5 B:K99501 3.0 14.0 1.0
CE1 B:PHE378 3.2 9.2 1.0
NE B:ARG323 3.4 10.1 1.0
CZ B:ARG323 3.4 12.8 1.0
CZ B:PHE378 3.4 10.9 1.0
C6 B:K99501 3.5 15.9 1.0
CD1 B:PHE378 3.7 11.2 1.0
C1 B:K99501 3.7 16.2 1.0
O1B B:K99501 4.1 14.7 1.0
CE2 B:PHE378 4.1 10.3 1.0
O B:HOH2515 4.2 23.3 1.0
O5 B:K99501 4.3 12.8 1.0
CG B:PHE378 4.3 10.7 1.0
O7 B:K99501 4.5 16.1 1.0
CD B:ARG323 4.5 10.9 1.0
CD2 B:PHE378 4.5 10.4 1.0
NH1 B:ARG323 4.6 14.2 1.0
C7 B:K99501 4.7 18.1 1.0
O1A B:K99501 4.7 17.2 1.0
CG B:ARG323 4.9 9.8 1.0

Fluorine binding site 8 out of 12 in 2xzk

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Fluorine binding site 8 out of 12 in the The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:16.5
occ:1.00
 F2 B:K99501 0.0 16.5 1.0
C2 B:K99501 1.4 15.8 1.0
O6 B:K99501 2.2 15.8 1.0
C1 B:K99501 2.3 16.2 1.0
C3 B:K99501 2.4 14.6 1.0
F1 B:K99501 2.6 15.0 1.0
O1B B:K99501 3.0 14.7 1.0
O1A B:K99501 3.1 17.2 1.0
O B:HOH2515 3.5 23.3 1.0
C6 B:K99501 3.6 15.9 1.0
C4 B:K99501 3.7 12.9 1.0
C5 B:K99501 4.1 14.0 1.0
C7 B:K99501 4.6 18.1 1.0
CZ B:PHE378 4.6 10.9 1.0
CE1 B:PHE378 4.6 9.2 1.0
C8 B:K99501 4.7 20.4 1.0
O8 B:K99501 4.7 23.3 1.0
O7 B:K99501 4.8 16.1 1.0
O4 B:K99501 4.8 11.3 1.0
O B:HOH2423 5.0 17.2 1.0

Fluorine binding site 9 out of 12 in 2xzk

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Fluorine binding site 9 out of 12 in the The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:20.4
occ:1.00
 F1 B:K99502 0.0 20.4 1.0
C3 B:K99502 1.4 21.2 1.0
C4 B:K99502 2.4 20.0 1.0
C2 B:K99502 2.4 23.5 1.0
F2 B:K99502 2.7 23.4 1.0
O4 B:K99502 2.8 18.2 1.0
O6 B:K99502 2.9 23.0 1.0
O B:LYS337 2.9 12.8 1.0
C5 B:K99502 3.0 20.8 1.0
C B:PHE338 3.0 11.9 1.0
C B:LYS337 3.1 13.3 1.0
O B:PHE338 3.2 13.1 1.0
N B:ASN339 3.3 11.4 1.0
N B:PHE338 3.4 12.2 1.0
CA B:PHE338 3.4 12.3 1.0
CB B:LYS337 3.4 15.2 1.0
O B:HOH2523 3.5 39.0 1.0
C6 B:K99502 3.6 22.5 1.0
C1 B:K99502 3.8 25.6 1.0
CA B:LYS337 3.9 14.5 1.0
CA B:ASN339 3.9 11.0 1.0
O1B B:K99502 4.1 27.5 1.0
O B:HOH2439 4.1 48.5 1.0
O5 B:K99502 4.3 19.7 1.0
O B:ILE329 4.5 7.9 1.0
O7 B:K99502 4.5 25.4 1.0
CB B:ASN339 4.6 10.7 1.0
C7 B:K99502 4.7 25.2 1.0
O1A B:K99502 4.8 27.1 1.0
CG B:LYS337 4.8 19.0 1.0
CB B:PHE338 4.9 11.8 1.0
N B:LYS337 5.0 14.3 1.0

Fluorine binding site 10 out of 12 in 2xzk

Go back to Fluorine Binding Sites List in 2xzk
Fluorine binding site 10 out of 12 in the The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:23.4
occ:1.00
 F2 B:K99502 0.0 23.4 1.0
C2 B:K99502 1.3 23.5 1.0
O6 B:K99502 2.2 23.0 1.0
C3 B:K99502 2.3 21.2 1.0
C1 B:K99502 2.3 25.6 1.0
F1 B:K99502 2.7 20.4 1.0
O1A B:K99502 2.9 27.1 1.0
O B:HOH2221 3.1 37.1 1.0
O1B B:K99502 3.2 27.5 1.0
CA B:ASN339 3.4 11.0 1.0
O B:HOH2439 3.6 48.5 1.0
O B:HOH2523 3.6 39.0 1.0
C6 B:K99502 3.6 22.5 1.0
CB B:ASN339 3.6 10.7 1.0
C4 B:K99502 3.7 20.0 1.0
N B:ASN339 3.8 11.4 1.0
O B:HOH2510 3.9 33.9 1.0
O B:HOH2443 4.0 16.5 1.0
O B:PHE338 4.0 13.1 1.0
C5 B:K99502 4.1 20.8 1.0
C B:PHE338 4.1 11.9 1.0
C7 B:K99502 4.7 25.2 1.0
C B:ASN339 4.7 11.2 1.0
O4 B:K99502 4.8 18.2 1.0
O7 B:K99502 4.8 25.4 1.0
O B:HOH2519 4.9 19.0 1.0

Reference:

J.C.Telford, J.H.F.Yeung, G.Xu, M.J.Kiefel, A.G.Watts, S.Hader, J.Chan, A.J.Bennet, M.M.Moore, G.L.Taylor. The Aspergillus Fumigatus Sialidase Is A Kdnase: Structural and Mechanistic Insights. J.Biol.Chem. V. 286 10783 2011.
ISSN: ISSN 0021-9258
PubMed: 21247893
DOI: 10.1074/JBC.M110.207043
Page generated: Wed Jul 31 16:42:59 2024

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