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Fluorine in PDB 5in4: Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor

Enzymatic activity of Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor

All present enzymatic activity of Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor:
4.2.1.47;

Protein crystallography data

The structure of Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor, PDB code: 5in4 was solved by E.A.Sickmier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.58 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.028, 140.077, 85.953, 90.00, 106.24, 90.00
R / Rfree (%) 14.6 / 17.6

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor (pdb code 5in4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor, PDB code: 5in4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5in4

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Fluorine binding site 1 out of 12 in the Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor


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 Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:16.1
occ:1.00
 F35 A:6CK1003 0.0 16.1 1.0
C34 A:6CK1003 1.3 13.0 1.0
F37 A:6CK1003 2.2 16.2 1.0
F36 A:6CK1003 2.2 15.4 1.0
C27 A:6CK1003 2.4 9.8 1.0
C28 A:6CK1003 2.9 13.6 1.0
CD1 A:LEU82 3.1 12.9 1.0
CB A:LEU82 3.2 10.4 1.0
O29 A:6CK1003 3.4 15.5 1.0
O26 A:6CK1003 3.6 11.8 1.0
OH A:TYR69 3.7 13.6 1.0
CG A:LEU82 3.8 8.9 1.0
CG2 A:THR62 4.0 12.1 1.0
CG2 A:VAL54 4.2 13.8 1.0
C30 A:6CK1003 4.3 13.2 1.0
CB A:VAL54 4.4 13.6 1.0
CG1 A:VAL54 4.4 21.5 1.0
CA A:LEU82 4.6 11.0 1.0
C25 A:6CK1003 4.8 11.5 1.0
C A:LEU82 4.9 11.9 1.0
CE1 A:PHE60 4.9 18.9 1.0
O10 A:6CK1003 4.9 13.7 1.0
CZ A:TYR69 4.9 15.8 1.0
OE2 A:GLU77 4.9 20.1 1.0
CD2 A:LEU82 4.9 11.7 1.0
O A:HOH1104 5.0 39.2 1.0

Fluorine binding site 2 out of 12 in 5in4

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Fluorine binding site 2 out of 12 in the Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor


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 Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:15.4
occ:1.00
 F36 A:6CK1003 0.0 15.4 1.0
C34 A:6CK1003 1.4 13.0 1.0
F35 A:6CK1003 2.2 16.1 1.0
F37 A:6CK1003 2.2 16.2 1.0
C27 A:6CK1003 2.4 9.8 1.0
O26 A:6CK1003 2.7 11.8 1.0
O29 A:6CK1003 2.9 15.5 1.0
C28 A:6CK1003 3.1 13.6 1.0
CB A:LEU82 3.5 10.4 1.0
O A:LEU82 3.8 13.6 1.0
C A:LEU82 3.9 11.9 1.0
CE2 A:TYR84 4.1 12.3 1.0
CZ A:TYR84 4.1 12.6 1.0
C25 A:6CK1003 4.2 11.5 1.0
N A:HIS83 4.2 8.1 1.0
CA A:LEU82 4.3 11.0 1.0
CD2 A:TYR84 4.4 11.1 1.0
CE1 A:TYR84 4.4 10.9 1.0
OH A:TYR84 4.4 12.8 1.0
C30 A:6CK1003 4.5 13.2 1.0
N A:TYR84 4.6 9.8 1.0
CA A:HIS83 4.6 11.0 1.0
C A:HIS83 4.6 9.9 1.0
CD1 A:TYR84 4.7 10.3 1.0
CG A:TYR84 4.7 9.8 1.0
O24 A:6CK1003 4.7 12.8 1.0
CD1 A:LEU82 4.7 12.9 1.0
CG A:LEU82 4.7 8.9 1.0
C32 A:6CK1003 4.7 13.5 1.0
OE2 A:GLU77 4.8 20.1 1.0
CB A:VAL54 4.8 13.6 1.0
O A:HOH1294 4.9 22.9 1.0
CG2 A:VAL54 5.0 13.8 1.0

Fluorine binding site 3 out of 12 in 5in4

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Fluorine binding site 3 out of 12 in the Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor


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 Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:16.2
occ:1.00
 F37 A:6CK1003 0.0 16.2 1.0
C34 A:6CK1003 1.3 13.0 1.0
F35 A:6CK1003 2.2 16.1 1.0
F36 A:6CK1003 2.2 15.4 1.0
C27 A:6CK1003 2.4 9.8 1.0
O26 A:6CK1003 2.9 11.8 1.0
OH A:TYR84 3.0 12.8 1.0
CZ A:TYR84 3.1 12.6 1.0
CE1 A:TYR84 3.4 10.9 1.0
CE1 A:PHE60 3.5 18.9 1.0
C28 A:6CK1003 3.8 13.6 1.0
CE2 A:TYR84 3.9 12.3 1.0
CD1 A:PHE60 4.0 18.0 1.0
C25 A:6CK1003 4.1 11.5 1.0
O A:HOH1104 4.1 39.2 1.0
CD1 A:TYR84 4.2 10.3 1.0
O29 A:6CK1003 4.3 15.5 1.0
CG1 A:VAL54 4.3 21.5 1.0
O23 A:6CK1003 4.6 13.5 1.0
O A:HOH1334 4.6 26.6 1.0
CD2 A:TYR84 4.6 11.1 1.0
CB A:VAL54 4.6 13.6 1.0
CZ A:PHE60 4.7 19.6 1.0
O A:HOH1315 4.7 25.2 1.0
CG A:TYR84 4.8 9.8 1.0
O24 A:6CK1003 4.8 12.8 1.0
C30 A:6CK1003 4.8 13.2 1.0
CG2 A:THR62 4.9 12.1 1.0

Fluorine binding site 4 out of 12 in 5in4

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Fluorine binding site 4 out of 12 in the Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor


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 Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:14.9
occ:1.00
 F35 B:6CK401 0.0 14.9 1.0
C34 B:6CK401 1.3 14.9 1.0
F36 B:6CK401 2.2 15.3 1.0
F37 B:6CK401 2.2 15.2 1.0
C27 B:6CK401 2.4 9.8 1.0
C28 B:6CK401 2.8 13.3 1.0
CD1 B:LEU82 3.2 12.3 1.0
CB B:LEU82 3.2 10.5 1.0
O29 B:6CK401 3.3 15.0 1.0
O26 B:6CK401 3.6 12.5 1.0
OH B:TYR69 3.6 13.4 1.0
CG B:LEU82 3.8 11.0 1.0
CG2 B:VAL54 3.8 21.3 1.0
CG2 B:THR62 4.0 12.7 1.0
C30 B:6CK401 4.2 15.4 1.0
CG1 B:VAL54 4.3 14.4 1.0
CB B:VAL54 4.6 15.5 1.0
CA B:LEU82 4.6 12.7 1.0
C25 B:6CK401 4.7 11.0 1.0
O10 B:6CK401 4.7 13.7 1.0
CE1 B:PHE60 4.8 18.4 1.0
C B:LEU82 4.8 13.4 1.0
CZ B:TYR69 4.8 13.9 1.0
OE2 B:GLU77 4.9 20.9 1.0
O B:HOH518 5.0 36.1 1.0
CD2 B:LEU82 5.0 12.9 1.0

Fluorine binding site 5 out of 12 in 5in4

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Fluorine binding site 5 out of 12 in the Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor


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 Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:15.3
occ:1.00
 F36 B:6CK401 0.0 15.3 1.0
C34 B:6CK401 1.4 14.9 1.0
F37 B:6CK401 2.2 15.2 1.0
F35 B:6CK401 2.2 14.9 1.0
C27 B:6CK401 2.4 9.8 1.0
O26 B:6CK401 2.7 12.5 1.0
O29 B:6CK401 2.7 15.0 1.0
C28 B:6CK401 3.0 13.3 1.0
O B:HOH746 3.2 32.6 1.0
CB B:LEU82 3.5 10.5 1.0
CG2 B:VAL54 3.7 21.3 1.0
O B:LEU82 3.8 13.6 1.0
C B:LEU82 3.9 13.4 1.0
CE2 B:TYR84 4.0 11.5 1.0
CZ B:TYR84 4.1 11.7 1.0
C25 B:6CK401 4.1 11.0 1.0
N B:HIS83 4.2 10.3 1.0
CA B:LEU82 4.3 12.7 1.0
CD2 B:TYR84 4.4 12.2 1.0
C30 B:6CK401 4.4 15.4 1.0
CE1 B:TYR84 4.4 10.8 1.0
OH B:TYR84 4.4 13.1 1.0
N B:TYR84 4.6 10.3 1.0
CA B:HIS83 4.6 10.2 1.0
C32 B:6CK401 4.7 12.9 1.0
O24 B:6CK401 4.7 12.4 1.0
C B:HIS83 4.7 7.9 1.0
CG B:TYR84 4.7 9.8 1.0
CD1 B:TYR84 4.7 12.1 1.0
CG B:LEU82 4.7 11.0 1.0
CD1 B:LEU82 4.8 12.3 1.0
OE2 B:GLU77 4.8 20.9 1.0
O B:HOH721 4.9 26.3 1.0

Fluorine binding site 6 out of 12 in 5in4

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Fluorine binding site 6 out of 12 in the Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor


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 Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:15.2
occ:1.00
 F37 B:6CK401 0.0 15.2 1.0
C34 B:6CK401 1.3 14.9 1.0
F36 B:6CK401 2.2 15.3 1.0
F35 B:6CK401 2.2 14.9 1.0
C27 B:6CK401 2.4 9.8 1.0
O26 B:6CK401 2.9 12.5 1.0
OH B:TYR84 3.0 13.1 1.0
CZ B:TYR84 3.1 11.7 1.0
CE1 B:TYR84 3.3 10.8 1.0
CE1 B:PHE60 3.5 18.4 1.0
CG2 B:VAL54 3.6 21.3 1.0
C28 B:6CK401 3.7 13.3 1.0
CE2 B:TYR84 3.8 11.5 1.0
C25 B:6CK401 4.1 11.0 1.0
CD1 B:PHE60 4.1 17.8 1.0
O B:HOH518 4.1 36.1 1.0
CD1 B:TYR84 4.1 12.1 1.0
O29 B:6CK401 4.2 15.0 1.0
CD2 B:TYR84 4.5 12.2 1.0
O23 B:6CK401 4.5 15.5 1.0
CZ B:PHE60 4.6 19.2 1.0
O B:HOH669 4.7 22.1 1.0
CG B:TYR84 4.7 9.8 1.0
CB B:VAL54 4.7 15.5 1.0
O24 B:6CK401 4.8 12.4 1.0
O B:HOH627 4.8 28.3 1.0
C30 B:6CK401 4.8 15.4 1.0
O B:HOH746 4.8 32.6 1.0
CG2 B:THR62 5.0 12.7 1.0
CB B:LEU82 5.0 10.5 1.0

Fluorine binding site 7 out of 12 in 5in4

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Fluorine binding site 7 out of 12 in the Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor


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 Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1003

b:14.6
occ:1.00
 F35 C:6CK1003 0.0 14.6 1.0
C34 C:6CK1003 1.3 15.2 1.0
F36 C:6CK1003 2.1 14.7 1.0
F37 C:6CK1003 2.2 17.2 1.0
C27 C:6CK1003 2.4 12.6 1.0
C28 C:6CK1003 2.8 16.8 1.0
CD1 C:LEU82 3.2 16.8 1.0
CB C:LEU82 3.3 11.6 1.0
O29 C:6CK1003 3.4 13.8 1.0
O26 C:6CK1003 3.6 12.8 1.0
OH C:TYR69 3.6 14.7 1.0
CG C:LEU82 3.8 12.7 1.0
CG2 C:THR62 4.0 14.8 1.0
C30 C:6CK1003 4.2 16.5 1.0
CG2 C:VAL54 4.2 11.9 1.0
CG1 C:VAL54 4.4 20.3 1.0
CB C:VAL54 4.5 15.8 1.0
CA C:LEU82 4.7 13.1 1.0
C25 C:6CK1003 4.7 11.6 1.0
O10 C:6CK1003 4.8 13.6 1.0
CE1 C:PHE60 4.8 15.1 1.0
CZ C:TYR69 4.8 12.9 1.0
OE2 C:GLU77 4.9 19.4 1.0
C C:LEU82 4.9 15.4 1.0
CD2 C:LEU82 5.0 12.4 1.0

Fluorine binding site 8 out of 12 in 5in4

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Fluorine binding site 8 out of 12 in the Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor


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 Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1003

b:14.7
occ:1.00
 F36 C:6CK1003 0.0 14.7 1.0
C34 C:6CK1003 1.4 15.2 1.0
F35 C:6CK1003 2.1 14.6 1.0
F37 C:6CK1003 2.1 17.2 1.0
C27 C:6CK1003 2.4 12.6 1.0
O26 C:6CK1003 2.7 12.8 1.0
O29 C:6CK1003 2.8 13.8 1.0
C28 C:6CK1003 3.0 16.8 1.0
O C:HOH1352 3.3 27.6 1.0
CB C:LEU82 3.6 11.6 1.0
O C:LEU82 3.9 15.0 1.0
C C:LEU82 4.0 15.4 1.0
CZ C:TYR84 4.0 8.9 1.0
CE2 C:TYR84 4.0 12.1 1.0
C25 C:6CK1003 4.2 11.6 1.0
N C:HIS83 4.3 12.1 1.0
CE1 C:TYR84 4.3 11.6 1.0
CD2 C:TYR84 4.4 11.7 1.0
OH C:TYR84 4.4 12.1 1.0
CA C:LEU82 4.4 13.1 1.0
C30 C:6CK1003 4.4 16.5 1.0
N C:TYR84 4.6 9.9 1.0
CD1 C:TYR84 4.6 10.8 1.0
O C:HOH1251 4.6 33.8 1.0
CG C:TYR84 4.7 11.4 1.0
C C:HIS83 4.7 10.6 1.0
C32 C:6CK1003 4.7 13.4 1.0
CD1 C:LEU82 4.7 16.8 1.0
O24 C:6CK1003 4.7 11.2 1.0
CA C:HIS83 4.7 11.2 1.0
CB C:VAL54 4.8 15.8 1.0
CG C:LEU82 4.8 12.7 1.0
OE2 C:GLU77 4.8 19.4 1.0
O C:HOH1323 4.8 23.5 1.0
CG2 C:VAL54 4.9 11.9 1.0

Fluorine binding site 9 out of 12 in 5in4

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Fluorine binding site 9 out of 12 in the Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1003

b:17.2
occ:1.00
 F37 C:6CK1003 0.0 17.2 1.0
C34 C:6CK1003 1.3 15.2 1.0
F36 C:6CK1003 2.1 14.7 1.0
F35 C:6CK1003 2.2 14.6 1.0
C27 C:6CK1003 2.4 12.6 1.0
O26 C:6CK1003 2.9 12.8 1.0
OH C:TYR84 3.0 12.1 1.0
CZ C:TYR84 3.1 8.9 1.0
CE1 C:TYR84 3.3 11.6 1.0
CE1 C:PHE60 3.5 15.1 1.0
C28 C:6CK1003 3.7 16.8 1.0
CE2 C:TYR84 3.8 12.1 1.0
CD1 C:PHE60 4.0 17.9 1.0
C25 C:6CK1003 4.1 11.6 1.0
CD1 C:TYR84 4.2 10.8 1.0
O29 C:6CK1003 4.3 13.8 1.0
CG1 C:VAL54 4.3 20.3 1.0
O23 C:6CK1003 4.5 16.2 1.0
CZ C:PHE60 4.6 21.1 1.0
CD2 C:TYR84 4.6 11.7 1.0
O C:HOH1292 4.6 22.1 1.0
CB C:VAL54 4.7 15.8 1.0
O C:HOH1350 4.7 25.2 1.0
O C:HOH1352 4.8 27.6 1.0
CG C:TYR84 4.8 11.4 1.0
C30 C:6CK1003 4.8 16.5 1.0
O24 C:6CK1003 4.8 11.2 1.0
CG2 C:THR62 4.9 14.8 1.0

Fluorine binding site 10 out of 12 in 5in4

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Fluorine binding site 10 out of 12 in the Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Gdp-Mannose 4,6 Dehydratase Bound to A Gdp-Fucose Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:12.9
occ:1.00
 F35 D:6CK401 0.0 12.9 1.0
C34 D:6CK401 1.3 13.4 1.0
F37 D:6CK401 2.1 13.9 1.0
F36 D:6CK401 2.2 13.5 1.0
C27 D:6CK401 2.4 8.8 1.0
C28 D:6CK401 2.9 11.3 1.0
CD1 D:LEU82 3.1 10.0 1.0
CB D:LEU82 3.3 8.5 1.0
O29 D:6CK401 3.4 12.1 1.0
O26 D:6CK401 3.6 11.5 1.0
OH D:TYR69 3.7 13.4 1.0
CG D:LEU82 3.8 8.9 1.0
CG2 D:THR62 4.0 10.9 1.0
CG2 D:VAL54 4.1 11.6 1.0
C30 D:6CK401 4.3 12.6 1.0
CG1 D:VAL54 4.3 16.7 1.0
CB D:VAL54 4.3 12.3 1.0
CA D:LEU82 4.7 10.1 1.0
C25 D:6CK401 4.8 8.8 1.0
O10 D:6CK401 4.8 12.3 1.0
CE1 D:PHE60 4.9 21.6 1.0
CZ D:TYR69 4.9 15.2 1.0
C D:LEU82 4.9 10.5 1.0
CD2 D:LEU82 4.9 11.9 1.0
OE2 D:GLU77 5.0 19.7 1.0

Reference:

J.G.Allen, M.Mujacic, M.J.Frohn, A.J.Pickrell, P.Kodama, D.Bagal, T.San Miguel, E.A.Sickmier, S.Osgood, A.Swietlow, V.Li, J.B.Jordan, K.W.Kim, A.C.Rousseau, Y.J.Kim, S.Caille, M.Achmatowicz, O.Thiel, C.H.Fotsch, P.Reddy, J.D.Mccarter. Facile Modulation of Antibody Fucosylation with Small Molecule Fucostatin Inhibitors and Cocrystal Structure with Gdp-Mannose 4,6-Dehydratase. Acs Chem.Biol. V. 11 2734 2016.
ISSN: ESSN 1554-8937
PubMed: 27434622
DOI: 10.1021/ACSCHEMBIO.6B00460
Page generated: Thu Aug 1 10:16:19 2024

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