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Fluorine in PDB 6kd9: Binding Pose 1 of 2-CF3 Bound Asqj Complex

Protein crystallography data

The structure of Binding Pose 1 of 2-CF3 Bound Asqj Complex, PDB code: 6kd9 was solved by H.J.Liao, N.L.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.47 / 2.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.755, 73.352, 121.434, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 28.6

Other elements in 6kd9:

The structure of Binding Pose 1 of 2-CF3 Bound Asqj Complex also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Binding Pose 1 of 2-CF3 Bound Asqj Complex (pdb code 6kd9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Binding Pose 1 of 2-CF3 Bound Asqj Complex, PDB code: 6kd9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6kd9

Go back to Fluorine Binding Sites List in 6kd9
Fluorine binding site 1 out of 6 in the Binding Pose 1 of 2-CF3 Bound Asqj Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Binding Pose 1 of 2-CF3 Bound Asqj Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:96.1
occ:1.00
 F81 B:CV3402 0.0 96.1 1.0
C08 B:CV3402 1.0 95.4 1.0
F83 B:CV3402 1.6 94.4 1.0
F82 B:CV3402 1.6 95.9 1.0
C21 B:CV3402 2.0 87.0 1.0
C23 B:CV3402 3.0 75.1 1.0
C05 B:CV3402 3.0 78.9 1.0
CB B:GLN131 3.1 54.4 1.0
H231 B:CV3402 3.1 90.1 1.0
H051 B:CV3402 3.1 94.6 1.0
NE2 B:GLN131 3.4 64.9 1.0
CG B:GLN131 3.5 56.0 1.0
CD B:PRO132 3.5 63.4 1.0
CD B:GLN131 3.6 61.5 1.0
CG B:PRO132 3.8 61.8 1.0
CA B:GLN131 3.8 61.2 1.0
N B:PRO132 3.9 71.5 1.0
ND1 B:HIS134 4.2 52.3 1.0
CE1 B:HIS134 4.3 50.7 1.0
O B:PRO132 4.3 54.8 1.0
C B:GLN131 4.4 69.7 1.0
C04 B:CV3402 4.4 72.8 1.0
C20 B:CV3402 4.4 69.0 1.0
OE1 B:GLN131 4.4 58.6 1.0
CG1 B:VAL72 4.7 56.0 1.0
O B:VAL72 4.8 61.8 1.0
CB B:PRO132 4.8 62.8 1.0
CA B:PRO132 4.9 67.5 1.0
C19 B:CV3402 4.9 66.8 1.0

Fluorine binding site 2 out of 6 in 6kd9

Go back to Fluorine Binding Sites List in 6kd9
Fluorine binding site 2 out of 6 in the Binding Pose 1 of 2-CF3 Bound Asqj Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Binding Pose 1 of 2-CF3 Bound Asqj Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:95.9
occ:1.00
 F82 B:CV3402 0.0 95.9 1.0
C08 B:CV3402 1.0 95.4 1.0
F83 B:CV3402 1.6 94.4 1.0
F81 B:CV3402 1.6 96.1 1.0
C21 B:CV3402 2.0 87.0 1.0
H051 B:CV3402 2.6 94.6 1.0
C05 B:CV3402 2.7 78.9 1.0
O B:VAL72 3.2 61.8 1.0
C23 B:CV3402 3.3 75.1 1.0
H231 B:CV3402 3.5 90.1 1.0
CG1 B:VAL72 3.6 56.0 1.0
NE2 B:GLN131 3.6 64.9 1.0
C B:VAL72 4.0 58.3 1.0
C20 B:CV3402 4.2 69.0 1.0
CG B:GLN131 4.3 56.0 1.0
CD B:GLN131 4.3 61.5 1.0
CB B:GLN131 4.3 54.4 1.0
CD B:PRO132 4.5 63.4 1.0
CA B:LEU73 4.5 58.0 1.0
C04 B:CV3402 4.6 72.8 1.0
N B:LEU73 4.6 60.9 1.0
CB B:VAL72 4.7 68.5 1.0
CG B:PRO132 4.8 61.8 1.0
H201 B:CV3402 4.9 82.8 1.0
CD2 B:LEU73 4.9 55.0 1.0
CA B:VAL72 4.9 60.9 1.0
C19 B:CV3402 4.9 66.8 1.0
CA B:GLN131 5.0 61.2 1.0

Fluorine binding site 3 out of 6 in 6kd9

Go back to Fluorine Binding Sites List in 6kd9
Fluorine binding site 3 out of 6 in the Binding Pose 1 of 2-CF3 Bound Asqj Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Binding Pose 1 of 2-CF3 Bound Asqj Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:94.4
occ:1.00
 F83 B:CV3402 0.0 94.4 1.0
C08 B:CV3402 1.0 95.4 1.0
F81 B:CV3402 1.6 96.1 1.0
F82 B:CV3402 1.6 95.9 1.0
C21 B:CV3402 2.0 87.0 1.0
H231 B:CV3402 2.4 90.1 1.0
C23 B:CV3402 2.5 75.1 1.0
C05 B:CV3402 3.4 78.9 1.0
CG1 B:VAL72 3.5 56.0 1.0
H051 B:CV3402 3.7 94.6 1.0
CG B:PRO132 3.7 61.8 1.0
CD B:PRO132 3.9 63.4 1.0
O B:VAL72 4.0 61.8 1.0
C04 B:CV3402 4.0 72.8 1.0
CB B:GLN131 4.6 54.4 1.0
N B:PRO132 4.6 71.5 1.0
H041 B:CV3402 4.6 87.3 1.0
C20 B:CV3402 4.7 69.0 1.0
NE2 B:GLN131 4.7 64.9 1.0
C B:VAL72 4.8 58.3 1.0
CB B:PRO132 4.9 62.8 1.0
C19 B:CV3402 4.9 66.8 1.0
CB B:VAL72 4.9 68.5 1.0
ND1 B:HIS134 4.9 52.3 1.0

Fluorine binding site 4 out of 6 in 6kd9

Go back to Fluorine Binding Sites List in 6kd9
Fluorine binding site 4 out of 6 in the Binding Pose 1 of 2-CF3 Bound Asqj Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Binding Pose 1 of 2-CF3 Bound Asqj Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F402

b:90.2
occ:1.00
 F81 F:CV3402 0.0 90.2 1.0
C08 F:CV3402 1.0 88.7 1.0
F83 F:CV3402 1.6 87.8 1.0
F82 F:CV3402 1.6 89.5 1.0
C21 F:CV3402 2.0 81.6 1.0
H231 F:CV3402 2.8 84.2 1.0
C23 F:CV3402 2.8 70.2 1.0
O F:VAL72 3.0 64.7 1.0
C05 F:CV3402 3.2 71.5 1.0
CG1 F:VAL72 3.3 55.1 1.0
H051 F:CV3402 3.4 85.8 1.0
C F:VAL72 3.9 62.0 1.0
NE2 F:GLN131 4.0 56.9 1.0
C04 F:CV3402 4.3 63.1 1.0
CD F:PRO132 4.4 53.5 1.0
C20 F:CV3402 4.5 69.4 1.0
CG F:GLN131 4.5 56.4 1.0
CB F:VAL72 4.5 57.0 1.0
CG F:PRO132 4.6 51.3 1.0
N F:LEU73 4.6 61.2 1.0
CA F:LEU73 4.6 59.6 1.0
CD F:GLN131 4.6 60.8 1.0
CB F:GLN131 4.7 60.9 1.0
CA F:VAL72 4.7 57.3 1.0
C19 F:CV3402 4.9 60.4 1.0
H041 F:CV3402 4.9 75.7 1.0

Fluorine binding site 5 out of 6 in 6kd9

Go back to Fluorine Binding Sites List in 6kd9
Fluorine binding site 5 out of 6 in the Binding Pose 1 of 2-CF3 Bound Asqj Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Binding Pose 1 of 2-CF3 Bound Asqj Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F402

b:89.5
occ:1.00
 F82 F:CV3402 0.0 89.5 1.0
C08 F:CV3402 1.0 88.7 1.0
F81 F:CV3402 1.6 90.2 1.0
F83 F:CV3402 1.6 87.8 1.0
C21 F:CV3402 2.0 81.6 1.0
C23 F:CV3402 2.8 70.2 1.0
H231 F:CV3402 2.8 84.2 1.0
C05 F:CV3402 3.1 71.5 1.0
CB F:GLN131 3.2 60.9 1.0
NE2 F:GLN131 3.2 56.9 1.0
CG F:GLN131 3.3 56.4 1.0
H051 F:CV3402 3.3 85.8 1.0
CD F:GLN131 3.4 60.8 1.0
CD F:PRO132 3.5 53.5 1.0
CA F:GLN131 3.9 59.2 1.0
CG F:PRO132 3.9 51.3 1.0
N F:PRO132 4.0 54.5 1.0
C04 F:CV3402 4.3 63.1 1.0
OE1 F:GLN131 4.3 54.5 1.0
CE1 F:HIS134 4.4 61.0 1.0
ND1 F:HIS134 4.4 63.7 1.0
C20 F:CV3402 4.5 69.4 1.0
C F:GLN131 4.5 56.8 1.0
O F:VAL72 4.6 64.7 1.0
CG1 F:VAL72 4.6 55.1 1.0
O F:PRO132 4.6 55.1 1.0
C19 F:CV3402 4.9 60.4 1.0
H041 F:CV3402 4.9 75.7 1.0

Fluorine binding site 6 out of 6 in 6kd9

Go back to Fluorine Binding Sites List in 6kd9
Fluorine binding site 6 out of 6 in the Binding Pose 1 of 2-CF3 Bound Asqj Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Binding Pose 1 of 2-CF3 Bound Asqj Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F402

b:87.8
occ:1.00
 F83 F:CV3402 0.0 87.8 1.0
C08 F:CV3402 1.0 88.7 1.0
F81 F:CV3402 1.6 90.2 1.0
F82 F:CV3402 1.6 89.5 1.0
C21 F:CV3402 2.0 81.6 1.0
H051 F:CV3402 2.3 85.8 1.0
C05 F:CV3402 2.5 71.5 1.0
CG F:PRO132 3.3 51.3 1.0
C23 F:CV3402 3.4 70.2 1.0
CD F:PRO132 3.6 53.5 1.0
H231 F:CV3402 3.7 84.2 1.0
CG1 F:VAL72 3.8 55.1 1.0
C20 F:CV3402 4.0 69.4 1.0
N F:PRO132 4.3 54.5 1.0
O F:VAL72 4.3 64.7 1.0
CB F:GLN131 4.5 60.9 1.0
CB F:PRO132 4.6 49.0 1.0
H201 F:CV3402 4.6 83.2 1.0
ND1 F:HIS134 4.6 63.7 1.0
C04 F:CV3402 4.7 63.1 1.0
NE2 F:GLN131 4.7 56.9 1.0
O F:PRO132 4.7 55.1 1.0
CG F:GLN131 4.8 56.4 1.0
C19 F:CV3402 4.9 60.4 1.0
CA F:GLN131 4.9 59.2 1.0
CD F:GLN131 5.0 60.8 1.0
CE1 F:HIS134 5.0 61.0 1.0

Reference:

H.J.Liao, N.L.Chan. Binding Pose 1 of 2-CF3 Bound Asqj Complex J.Am.Chem.Soc. 2020.
ISSN: ESSN 1520-5126
Page generated: Tue Jul 15 12:47:26 2025

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