Fluorine in PDB 7dfu: Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.

Enzymatic activity of Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.

All present enzymatic activity of Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.:
3.4.21.92;

Protein crystallography data

The structure of Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4., PDB code: 7dfu was solved by C.-G.Yang, T.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.69 / 1.90
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 132.498, 132.498, 187.833, 90, 90, 90
R / Rfree (%) 21.7 / 24.3

Other elements in 7dfu:

The structure of Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 7 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. (pdb code 7dfu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 14 binding sites of Fluorine where determined in the Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4., PDB code: 7dfu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 14 in 7dfu

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Fluorine binding site 1 out of 14 in the Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.


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 Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:24.6
occ:1.00
F1 A:EZA401 0.0 24.6 1.0
C12 A:EZA401 1.3 22.4 1.0
C13 A:EZA401 2.4 21.6 1.0
C11 A:EZA401 2.4 21.6 1.0
CD1 A:LEU122 3.1 27.6 1.0
CB B:TYR90 3.2 15.7 1.0
CA B:THR87 3.2 13.0 1.0
O B:ASP86 3.4 10.1 1.0
C14 A:EZA401 3.6 25.2 1.0
C10 A:EZA401 3.6 23.6 1.0
N B:THR87 3.7 12.3 1.0
C B:ASP86 3.8 12.3 1.0
CG B:TYR90 3.8 21.8 1.0
OG1 B:THR87 3.8 9.3 1.0
CG A:LEU122 3.9 20.2 1.0
CB B:THR87 3.9 11.1 1.0
CD2 B:TYR90 4.1 24.0 1.0
C15 A:EZA401 4.1 25.1 1.0
CG2 B:THR87 4.2 12.5 1.0
C B:THR87 4.2 14.1 1.0
O B:THR87 4.2 17.9 1.0
CD2 A:LEU122 4.5 22.1 1.0
CA B:TYR90 4.6 19.2 1.0
CD1 B:TYR90 4.7 23.6 1.0
F2 A:EZA401 4.7 27.4 1.0
O B:HOH524 4.8 14.7 1.0
N B:TYR90 4.8 18.1 1.0
CB B:ASP86 4.9 9.2 1.0
C9 A:EZA401 4.9 24.8 1.0
CA B:ASP86 4.9 11.7 1.0

Fluorine binding site 2 out of 14 in 7dfu

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Fluorine binding site 2 out of 14 in the Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.


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 Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:27.4
occ:1.00
F2 A:EZA401 0.0 27.4 1.0
C14 A:EZA401 1.3 25.2 1.0
C13 A:EZA401 2.4 21.6 1.0
C15 A:EZA401 2.4 25.1 1.0
CD2 A:TYR70 3.2 22.5 1.0
CE2 A:TYR70 3.2 23.0 1.0
CD1 B:LEU56 3.5 14.2 1.0
CG2 A:VAL100 3.5 21.5 1.0
C12 A:EZA401 3.6 22.4 1.0
C10 A:EZA401 3.6 23.6 1.0
CG1 B:VAL52 3.8 11.2 1.0
CG A:TYR70 4.0 21.3 1.0
CZ A:TYR70 4.0 22.1 1.0
C11 A:EZA401 4.1 21.6 1.0
CG B:LEU56 4.5 18.3 1.0
CD2 B:LEU56 4.5 19.5 1.0
CG1 A:VAL100 4.6 22.6 1.0
OG1 B:THR87 4.6 9.3 1.0
CB A:VAL100 4.6 21.6 1.0
CD1 A:TYR70 4.7 24.7 1.0
OH A:TYR70 4.7 22.0 1.0
CE1 A:TYR70 4.7 23.0 1.0
CB A:TYR70 4.7 13.5 1.0
CG2 A:ILE98 4.7 16.1 1.0
F1 A:EZA401 4.7 24.6 1.0
C9 A:EZA401 4.9 24.8 1.0

Fluorine binding site 3 out of 14 in 7dfu

Go back to Fluorine Binding Sites List in 7dfu
Fluorine binding site 3 out of 14 in the Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.


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 Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:41.5
occ:1.00
F1 B:EZA401 0.0 41.5 1.0
C12 B:EZA401 1.3 40.7 1.0
C13 B:EZA401 2.4 40.1 1.0
C11 B:EZA401 2.4 41.2 1.0
CB C:TYR90 3.1 25.4 1.0
CA C:THR87 3.3 14.9 1.0
O C:ASP86 3.6 14.7 1.0
C14 B:EZA401 3.6 41.9 1.0
C10 B:EZA401 3.6 41.0 1.0
CG C:TYR90 3.6 33.8 1.0
CD2 B:LEU122 3.7 17.8 1.0
CD1 B:LEU122 3.7 21.6 1.0
CD2 C:TYR90 3.8 38.3 1.0
N C:THR87 3.9 13.6 1.0
OG1 C:THR87 4.0 15.4 1.0
CB C:THR87 4.0 16.7 1.0
C C:ASP86 4.0 14.1 1.0
O C:THR87 4.0 18.4 1.0
CG2 C:THR87 4.1 16.8 1.0
C15 B:EZA401 4.1 41.8 1.0
C C:THR87 4.2 16.8 1.0
CG B:LEU122 4.3 16.2 1.0
CA C:TYR90 4.4 22.3 1.0
CD1 C:TYR90 4.7 36.8 1.0
N C:TYR90 4.7 19.8 1.0
F2 B:EZA401 4.7 43.3 1.0
CG2 C:ILE91 4.8 16.1 1.0
N C:ILE91 4.8 22.6 1.0
C9 B:EZA401 4.9 40.8 1.0
CE2 C:TYR90 4.9 41.8 1.0
C C:TYR90 5.0 21.6 1.0
O C:HOH522 5.0 13.1 1.0

Fluorine binding site 4 out of 14 in 7dfu

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Fluorine binding site 4 out of 14 in the Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.


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 Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:43.3
occ:1.00
F2 B:EZA401 0.0 43.3 1.0
C14 B:EZA401 1.3 41.9 1.0
C13 B:EZA401 2.4 40.1 1.0
C15 B:EZA401 2.4 41.8 1.0
CD2 B:TYR70 3.0 34.9 1.0
CE2 B:TYR70 3.2 37.2 1.0
CG2 B:VAL100 3.4 29.3 1.0
CD1 C:LEU56 3.6 17.5 1.0
C12 B:EZA401 3.6 40.7 1.0
C10 B:EZA401 3.6 41.0 1.0
CG B:TYR70 3.8 31.0 1.0
CZ B:TYR70 4.0 35.5 1.0
CG1 C:VAL52 4.1 12.1 1.0
C11 B:EZA401 4.1 41.2 1.0
CD2 C:LEU56 4.5 18.3 1.0
CD1 B:TYR70 4.5 34.3 1.0
CB B:TYR70 4.5 21.1 1.0
CG2 B:ILE98 4.5 12.4 1.0
CG C:LEU56 4.5 18.4 1.0
CE1 B:TYR70 4.6 35.9 1.0
CB B:VAL100 4.6 25.0 1.0
OG1 C:THR87 4.7 15.4 1.0
CG1 B:VAL100 4.7 27.9 1.0
CD1 B:LEU122 4.7 21.6 1.0
OH B:TYR70 4.7 31.6 1.0
F1 B:EZA401 4.7 41.5 1.0
C9 B:EZA401 4.9 40.8 1.0

Fluorine binding site 5 out of 14 in 7dfu

Go back to Fluorine Binding Sites List in 7dfu
Fluorine binding site 5 out of 14 in the Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.


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 Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:29.5
occ:1.00
F1 C:EZA401 0.0 29.5 1.0
C12 C:EZA401 1.3 28.4 1.0
C13 C:EZA401 2.4 25.6 1.0
C11 C:EZA401 2.4 30.2 1.0
CB D:TYR90 3.2 17.9 1.0
CA D:THR87 3.3 11.3 1.0
CD1 C:LEU122 3.3 15.6 1.0
O D:ASP86 3.6 6.4 1.0
C14 C:EZA401 3.6 28.1 1.0
C10 C:EZA401 3.6 30.7 1.0
CG D:TYR90 3.7 22.7 1.0
OG1 D:THR87 3.8 9.8 1.0
N D:THR87 3.8 7.6 1.0
CD2 D:TYR90 3.9 25.3 1.0
CB D:THR87 3.9 11.0 1.0
C D:ASP86 3.9 8.7 1.0
CG C:LEU122 4.0 16.8 1.0
C15 C:EZA401 4.1 29.2 1.0
CG2 D:THR87 4.1 7.2 1.0
O D:THR87 4.1 16.0 1.0
C D:THR87 4.2 15.4 1.0
CD2 C:LEU122 4.5 17.3 1.0
CA D:TYR90 4.5 16.3 1.0
CD1 D:TYR90 4.7 27.1 1.0
F2 C:EZA401 4.7 27.1 1.0
N D:TYR90 4.8 14.6 1.0
C9 C:EZA401 4.9 32.8 1.0
CG2 D:ILE91 5.0 10.0 1.0
N D:ILE91 5.0 14.3 1.0

Fluorine binding site 6 out of 14 in 7dfu

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Fluorine binding site 6 out of 14 in the Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.


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 Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:27.1
occ:1.00
F2 C:EZA401 0.0 27.1 1.0
C14 C:EZA401 1.3 28.1 1.0
C13 C:EZA401 2.4 25.6 1.0
C15 C:EZA401 2.4 29.2 1.0
CD2 C:TYR70 3.0 31.0 1.0
CE2 C:TYR70 3.2 33.9 1.0
CG2 C:VAL100 3.4 24.5 1.0
C12 C:EZA401 3.6 28.4 1.0
C10 C:EZA401 3.6 30.7 1.0
CD1 D:LEU56 3.7 10.5 1.0
CG C:TYR70 3.8 26.8 1.0
CG1 D:VAL52 4.0 10.0 1.0
CZ C:TYR70 4.0 32.8 1.0
C11 C:EZA401 4.1 30.2 1.0
CB C:TYR70 4.4 19.0 1.0
CD1 C:TYR70 4.5 29.8 1.0
CG2 C:ILE98 4.5 13.3 1.0
CB C:VAL100 4.5 20.2 1.0
CD2 D:LEU56 4.6 13.4 1.0
CG1 C:VAL100 4.6 21.6 1.0
CE1 C:TYR70 4.6 31.5 1.0
CG D:LEU56 4.6 12.2 1.0
OG1 D:THR87 4.7 9.8 1.0
F1 C:EZA401 4.7 29.5 1.0
OH C:TYR70 4.8 32.3 1.0
C9 C:EZA401 4.9 32.8 1.0

Fluorine binding site 7 out of 14 in 7dfu

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Fluorine binding site 7 out of 14 in the Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.


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 Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:30.4
occ:1.00
F1 D:EZA401 0.0 30.4 1.0
C12 D:EZA401 1.3 31.3 1.0
C13 D:EZA401 2.4 29.1 1.0
C11 D:EZA401 2.4 31.6 1.0
CB E:TYR90 3.1 24.0 1.0
CA E:THR87 3.2 18.3 1.0
O E:ASP86 3.3 17.0 1.0
CD2 D:LEU122 3.4 26.2 1.0
CD1 D:LEU122 3.4 28.0 1.0
C14 D:EZA401 3.6 29.3 1.0
C10 D:EZA401 3.6 31.1 1.0
N E:THR87 3.7 15.2 1.0
C E:ASP86 3.7 17.2 1.0
CG E:TYR90 3.8 30.4 1.0
OG1 E:THR87 3.9 16.7 1.0
CB E:THR87 4.0 16.5 1.0
CG D:LEU122 4.0 24.8 1.0
CD2 E:TYR90 4.1 34.1 1.0
C15 D:EZA401 4.1 30.3 1.0
O E:THR87 4.2 19.5 1.0
C E:THR87 4.2 20.1 1.0
CG2 E:THR87 4.3 18.1 1.0
CA E:TYR90 4.4 22.1 1.0
N E:TYR90 4.7 16.9 1.0
O E:HOH545 4.7 15.4 1.0
F2 D:EZA401 4.7 28.8 1.0
CD1 E:TYR90 4.8 35.0 1.0
CB E:ASP86 4.8 14.4 1.0
C9 D:EZA401 4.9 32.3 1.0
CA E:ASP86 4.9 14.5 1.0

Fluorine binding site 8 out of 14 in 7dfu

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Fluorine binding site 8 out of 14 in the Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.


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 Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:28.8
occ:1.00
F2 D:EZA401 0.0 28.8 1.0
C14 D:EZA401 1.3 29.3 1.0
C13 D:EZA401 2.4 29.1 1.0
C15 D:EZA401 2.4 30.3 1.0
CD2 D:TYR70 3.1 33.7 1.0
CE2 D:TYR70 3.1 36.9 1.0
CD1 E:LEU56 3.5 19.3 1.0
CG2 D:VAL100 3.6 24.0 1.0
C12 D:EZA401 3.6 31.3 1.0
C10 D:EZA401 3.6 31.1 1.0
CG1 E:VAL52 3.9 10.3 1.0
CG D:TYR70 3.9 31.1 1.0
CZ D:TYR70 4.0 39.0 1.0
C11 D:EZA401 4.1 31.6 1.0
CD2 E:LEU56 4.3 19.1 1.0
CG E:LEU56 4.4 18.6 1.0
OG1 E:THR87 4.5 16.7 1.0
CB D:TYR70 4.6 21.6 1.0
CD1 D:TYR70 4.6 37.2 1.0
CE1 D:TYR70 4.7 40.0 1.0
CB D:VAL100 4.7 22.6 1.0
CG1 D:VAL100 4.7 24.4 1.0
F1 D:EZA401 4.7 30.4 1.0
OH D:TYR70 4.7 37.8 1.0
CD1 D:LEU122 4.8 28.0 1.0
CG2 D:ILE98 4.9 16.6 1.0
C9 D:EZA401 4.9 32.3 1.0

Fluorine binding site 9 out of 14 in 7dfu

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Fluorine binding site 9 out of 14 in the Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.


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 Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F401

b:41.8
occ:1.00
F1 E:EZA401 0.0 41.8 1.0
C12 E:EZA401 1.3 41.0 1.0
C13 E:EZA401 2.4 39.1 1.0
C11 E:EZA401 2.4 41.8 1.0
CB F:TYR90 3.2 29.3 1.0
CA F:THR87 3.3 14.9 1.0
CD2 E:LEU122 3.5 24.1 1.0
CD1 E:LEU122 3.6 27.7 1.0
O F:ASP86 3.6 13.6 1.0
C14 E:EZA401 3.6 38.4 1.0
C10 E:EZA401 3.6 41.5 1.0
CG F:TYR90 3.7 31.9 1.0
N F:THR87 3.8 14.2 1.0
OG1 F:THR87 3.8 15.2 1.0
CB F:THR87 3.9 15.1 1.0
CD2 F:TYR90 3.9 33.4 1.0
C F:ASP86 3.9 17.0 1.0
CG2 F:THR87 4.1 15.9 1.0
C15 E:EZA401 4.1 39.5 1.0
CG E:LEU122 4.1 23.1 1.0
O F:THR87 4.2 20.4 1.0
C F:THR87 4.2 17.1 1.0
CA F:TYR90 4.5 26.0 1.0
F2 E:EZA401 4.7 36.8 1.0
CD1 F:TYR90 4.7 35.6 1.0
N F:TYR90 4.8 23.5 1.0
C9 E:EZA401 4.9 43.8 1.0

Fluorine binding site 10 out of 14 in 7dfu

Go back to Fluorine Binding Sites List in 7dfu
Fluorine binding site 10 out of 14 in the Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4.


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 Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F401

b:36.8
occ:1.00
F2 E:EZA401 0.0 36.8 1.0
C14 E:EZA401 1.3 38.4 1.0
C13 E:EZA401 2.4 39.1 1.0
C15 E:EZA401 2.4 39.5 1.0
CD2 E:TYR70 3.0 36.7 1.0
CE2 E:TYR70 3.0 38.5 1.0
CG2 E:VAL100 3.5 25.9 1.0
CD1 F:LEU56 3.6 21.2 1.0
C12 E:EZA401 3.6 41.0 1.0
C10 E:EZA401 3.6 41.5 1.0
CG E:TYR70 3.8 32.6 1.0
CZ E:TYR70 3.8 38.4 1.0
C11 E:EZA401 4.1 41.8 1.0
CG1 F:VAL52 4.1 11.6 1.0
CD2 F:LEU56 4.4 18.8 1.0
CD1 E:TYR70 4.4 36.0 1.0
CG2 E:ILE98 4.5 15.0 1.0
CE1 E:TYR70 4.5 38.5 1.0
CG F:LEU56 4.5 17.8 1.0
CB E:TYR70 4.5 21.6 1.0
OH E:TYR70 4.6 34.1 1.0
F1 E:EZA401 4.7 41.8 1.0
CB E:VAL100 4.7 20.5 1.0
CD1 E:LEU122 4.7 27.7 1.0
OG1 F:THR87 4.8 15.2 1.0
CG1 E:VAL100 4.8 23.5 1.0
C9 E:EZA401 4.9 43.8 1.0

Reference:

C.-G.Yang, T.Yang. Crystal Structure of Xanthomonas Oryzae Clpp S68Y in Complex with ADEP4. To Be Published.
Page generated: Sat Jul 10 14:06:47 2021

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