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Fluorine in PDB 6m1j: The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X

Enzymatic activity of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X

All present enzymatic activity of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X:
5.6.2.2;

Protein crystallography data

The structure of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X, PDB code: 6m1j was solved by Z.H.Xu, Z.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.92 / 1.70
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 145.216, 160.743, 41.421, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.1

Other elements in 6m1j:

The structure of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X (pdb code 6m1j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X, PDB code: 6m1j:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6m1j

Go back to Fluorine Binding Sites List in 6m1j
Fluorine binding site 1 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F305

b:22.2
occ:1.00
 F34 A:EZ6305 0.0 22.2 1.0
C33 A:EZ6305 1.3 26.1 1.0
F35 A:EZ6305 2.1 22.8 1.0
F36 A:EZ6305 2.1 22.3 1.0
C31 A:EZ6305 2.3 18.0 1.0
C30 A:EZ6305 2.9 17.3 1.0
CG2 A:ILE96 3.2 39.6 1.0
CE2 B:PHE197 3.4 29.2 1.0
N32 A:EZ6305 3.6 15.1 1.0
CZ B:PHE197 3.6 34.3 1.0
C29 A:EZ6305 4.2 15.9 1.0
CB A:ILE96 4.3 22.9 1.0
O B:HOH478 4.4 45.4 1.0
N28 A:EZ6305 4.4 12.3 1.0
CD2 B:PHE197 4.5 27.3 1.0
CD1 A:ILE96 4.6 26.9 1.0
CE1 B:PHE197 4.9 28.7 1.0
CG1 A:ILE96 5.0 23.4 1.0

Fluorine binding site 2 out of 8 in 6m1j

Go back to Fluorine Binding Sites List in 6m1j
Fluorine binding site 2 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F305

b:22.8
occ:1.00
 F35 A:EZ6305 0.0 22.8 1.0
C33 A:EZ6305 1.4 26.1 1.0
F36 A:EZ6305 2.1 22.3 1.0
F34 A:EZ6305 2.1 22.2 1.0
C31 A:EZ6305 2.3 18.0 1.0
N32 A:EZ6305 2.8 15.1 1.0
CZ B:PHE197 3.3 34.3 1.0
CD A:PRO81 3.5 11.4 1.0
C30 A:EZ6305 3.6 17.3 1.0
CG A:PRO81 3.6 24.0 1.0
N18 A:EZ6305 3.7 15.6 1.0
C24 A:EZ6305 3.9 19.6 1.0
CE2 B:PHE197 3.9 29.2 1.0
C17 A:EZ6305 3.9 17.2 1.0
C19 A:EZ6305 4.0 14.5 1.0
N28 A:EZ6305 4.0 12.3 1.0
CE1 B:PHE197 4.3 28.7 1.0
C16 A:EZ6305 4.4 15.9 1.0
C29 A:EZ6305 4.4 15.9 1.0
N20 A:EZ6305 4.5 17.5 1.0
C22 A:EZ6305 4.5 19.7 1.0
O A:HOH476 4.6 31.9 1.0
C21 A:EZ6305 4.6 15.6 1.0
CG2 A:ILE96 4.7 39.6 1.0
CB A:PRO81 4.7 22.1 1.0
N A:PRO81 4.8 16.4 1.0
C23 A:EZ6305 4.9 20.3 1.0
O B:HOH478 5.0 45.4 1.0

Fluorine binding site 3 out of 8 in 6m1j

Go back to Fluorine Binding Sites List in 6m1j
Fluorine binding site 3 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F305

b:22.3
occ:1.00
 F36 A:EZ6305 0.0 22.3 1.0
C33 A:EZ6305 1.3 26.1 1.0
F35 A:EZ6305 2.1 22.8 1.0
F34 A:EZ6305 2.1 22.2 1.0
C31 A:EZ6305 2.4 18.0 1.0
N32 A:EZ6305 3.0 15.1 1.0
CG2 A:ILE96 3.0 39.6 1.0
CZ B:PHE197 3.2 34.3 1.0
CE2 B:PHE197 3.4 29.2 1.0
C30 A:EZ6305 3.5 17.3 1.0
CG2 A:ILE80 3.6 12.1 1.0
CD1 A:ILE96 3.6 26.9 1.0
CD A:PRO81 3.8 11.4 1.0
CB A:ILE96 4.0 22.9 1.0
CG1 A:ILE96 4.1 23.4 1.0
N28 A:EZ6305 4.1 12.3 1.0
CG A:PRO81 4.4 24.0 1.0
O A:ALA92 4.4 18.6 1.0
C29 A:EZ6305 4.5 15.9 1.0
CE1 B:PHE197 4.6 28.7 1.0
N A:PRO81 4.7 16.4 1.0
CB A:ILE80 4.7 11.9 1.0
CD2 B:PHE197 4.7 27.3 1.0
C A:ALA92 4.8 17.0 1.0
CB A:ALA92 4.8 23.1 1.0

Fluorine binding site 4 out of 8 in 6m1j

Go back to Fluorine Binding Sites List in 6m1j
Fluorine binding site 4 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F305

b:15.7
occ:1.00
 F37 A:EZ6305 0.0 15.7 1.0
C05 A:EZ6305 1.3 13.1 1.0
C04 A:EZ6305 2.4 14.4 1.0
C06 A:EZ6305 2.4 10.2 1.0
ND2 A:ASN48 3.5 17.8 1.0
C07 A:EZ6305 3.6 11.1 1.0
CG2 A:VAL122 3.6 19.5 1.0
C03 A:EZ6305 3.7 10.0 1.0
CG A:ASN48 3.7 17.6 1.0
CG1 A:VAL122 3.7 16.0 1.0
CB A:VAL122 3.8 15.8 1.0
CB A:ASN48 4.1 15.5 1.0
C08 A:EZ6305 4.1 13.7 1.0
CD1 A:ILE80 4.1 15.1 1.0
OD1 A:ASN48 4.1 17.2 1.0
CD1 A:ILE96 4.2 26.9 1.0
SD A:MET97 4.3 28.0 1.0
CG2 A:VAL169 4.8 12.7 1.0
N02 A:EZ6305 4.8 11.7 1.0
C11 A:EZ6305 4.9 13.0 1.0
O A:HOH499 5.0 37.6 1.0

Fluorine binding site 5 out of 8 in 6m1j

Go back to Fluorine Binding Sites List in 6m1j
Fluorine binding site 5 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:27.8
occ:1.00
 F34 B:EZ6302 0.0 27.8 1.0
C33 B:EZ6302 1.3 28.0 1.0
F35 B:EZ6302 2.1 24.6 1.0
F36 B:EZ6302 2.2 29.6 1.0
C31 B:EZ6302 2.3 26.6 1.0
C30 B:EZ6302 2.8 24.6 1.0
CG2 B:ILE96 3.4 26.4 1.0
N32 B:EZ6302 3.6 22.6 1.0
C29 B:EZ6302 4.2 22.2 1.0
O B:HOH525 4.2 49.2 1.0
N28 B:EZ6302 4.4 19.3 1.0
O B:HOH494 4.7 47.7 1.0
CB B:ILE96 4.8 25.3 1.0
CD1 B:ILE96 5.0 25.4 1.0

Fluorine binding site 6 out of 8 in 6m1j

Go back to Fluorine Binding Sites List in 6m1j
Fluorine binding site 6 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:24.6
occ:1.00
 F35 B:EZ6302 0.0 24.6 1.0
C33 B:EZ6302 1.3 28.0 1.0
F34 B:EZ6302 2.1 27.8 1.0
F36 B:EZ6302 2.1 29.6 1.0
C31 B:EZ6302 2.3 26.6 1.0
N32 B:EZ6302 2.8 22.6 1.0
CD B:PRO81 3.5 19.8 1.0
C30 B:EZ6302 3.5 24.6 1.0
CG B:PRO81 3.7 28.3 1.0
N18 B:EZ6302 3.9 27.2 1.0
N28 B:EZ6302 4.0 19.3 1.0
C17 B:EZ6302 4.0 28.2 1.0
C24 B:EZ6302 4.3 26.2 1.0
C19 B:EZ6302 4.3 25.7 1.0
C29 B:EZ6302 4.4 22.2 1.0
C16 B:EZ6302 4.6 24.7 1.0
CG2 B:ILE80 4.6 23.6 1.0
CB B:ALA92 4.6 29.5 1.0
N20 B:EZ6302 4.8 27.9 1.0
N B:PRO81 4.8 19.4 1.0
CB B:PRO81 4.8 26.8 1.0
C22 B:EZ6302 4.8 32.1 1.0
O B:HOH494 4.9 47.7 1.0
C21 B:EZ6302 4.9 26.1 1.0

Fluorine binding site 7 out of 8 in 6m1j

Go back to Fluorine Binding Sites List in 6m1j
Fluorine binding site 7 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:29.6
occ:1.00
 F36 B:EZ6302 0.0 29.6 1.0
C33 B:EZ6302 1.3 28.0 1.0
F35 B:EZ6302 2.1 24.6 1.0
F34 B:EZ6302 2.2 27.8 1.0
C31 B:EZ6302 2.3 26.6 1.0
N32 B:EZ6302 3.0 22.6 1.0
C30 B:EZ6302 3.4 24.6 1.0
CG2 B:ILE96 3.5 26.4 1.0
CG2 B:ILE80 3.5 23.6 1.0
CB B:ALA92 3.7 29.5 1.0
O B:ALA92 3.7 23.8 1.0
C B:ALA92 4.0 22.7 1.0
N28 B:EZ6302 4.1 19.3 1.0
CD1 B:ILE96 4.2 25.4 1.0
CD B:PRO81 4.2 19.8 1.0
C29 B:EZ6302 4.4 22.2 1.0
CA B:ALA92 4.4 24.6 1.0
CG1 B:ILE96 4.5 26.5 1.0
N B:ALA93 4.5 23.2 1.0
CB B:ILE96 4.6 25.3 1.0
CB B:ILE80 4.7 18.8 1.0
CA B:ALA93 4.8 19.9 1.0
CG B:PRO81 4.9 28.3 1.0
CG1 B:ILE80 4.9 19.3 1.0

Fluorine binding site 8 out of 8 in 6m1j

Go back to Fluorine Binding Sites List in 6m1j
Fluorine binding site 8 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:23.0
occ:1.00
 F37 B:EZ6302 0.0 23.0 1.0
C05 B:EZ6302 1.3 20.6 1.0
C04 B:EZ6302 2.3 16.8 1.0
C06 B:EZ6302 2.4 19.6 1.0
C03 B:EZ6302 3.6 17.1 1.0
C07 B:EZ6302 3.6 19.6 1.0
CD1 B:ILE96 3.6 25.4 1.0
CG1 B:VAL122 3.6 29.3 1.0
ND2 B:ASN48 3.6 27.4 1.0
CG2 B:VAL122 3.8 25.9 1.0
CG B:ASN48 3.8 24.8 1.0
CE B:MET97 4.0 27.2 1.0
C08 B:EZ6302 4.0 21.6 1.0
CB B:VAL122 4.1 26.5 1.0
CB B:ASN48 4.2 20.2 1.0
OD1 B:ASN48 4.3 27.3 1.0
CD1 B:ILE80 4.3 19.2 1.0
CG2 B:VAL169 4.6 18.0 1.0
N02 B:EZ6302 4.7 18.7 1.0
CG1 B:ILE96 4.7 26.5 1.0
C11 B:EZ6302 4.9 18.2 1.0
O B:HOH449 5.0 36.3 1.0

Reference:

Y.Hu, H.Shi, M.Zhou, Q.Ren, W.Zhu, W.Zhang, Z.Zhang, C.Zhou, Y.Liu, X.Ding, H.C.Shen, S.F.Yan, F.Dey, W.Wu, G.Zhai, Z.Zhou, Z.Xu, Y.Ji, H.Lv, T.Jiang, W.Wang, Y.Xu, M.Vercruysse, X.Yao, Y.Mao, X.Yu, K.Bradley, X.Tan. Discovery of Pyrido[2,3-B]Indole Derivatives with Gram-Negative Activity Targeting Both Dna Gyrase and Topoisomerase IV. J.Med.Chem. V. 63 9623 2020.
ISSN: ISSN 0022-2623
PubMed: 32787097
DOI: 10.1021/ACS.JMEDCHEM.0C00768
Page generated: Tue Jul 15 13:04:15 2025

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