Atomistry » Fluorine » PDB 6lub-6mii » 6m1s
Atomistry »
  Fluorine »
    PDB 6lub-6mii »
      6m1s »

Fluorine in PDB 6m1s: The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O

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

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

Protein crystallography data

The structure of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O, PDB code: 6m1s 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) 31.07 / 2.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.694, 46.928, 89.862, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 26.2

Other elements in 6m1s:

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

Chlorine (Cl) 3 atoms

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 12O (pdb code 6m1s). 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 12O, PDB code: 6m1s:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6m1s

Go back to Fluorine Binding Sites List in 6m1s
Fluorine binding site 1 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O


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 12O within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:30.6
occ:1.00
 F37 A:EZ9301 0.0 30.6 1.0
C36 A:EZ9301 1.4 37.0 1.0
F38 A:EZ9301 2.1 39.1 1.0
F39 A:EZ9301 2.1 36.3 1.0
C34 A:EZ9301 2.4 29.4 1.0
N35 A:EZ9301 3.1 34.1 1.0
CG1 A:ILE96 3.3 63.2 1.0
C33 A:EZ9301 3.4 32.1 1.0
CD1 A:ILE96 3.6 65.8 1.0
CG2 A:ILE80 3.7 37.0 1.0
CD A:PRO81 3.8 28.5 1.0
N31 A:EZ9301 4.2 30.5 1.0
CG A:PRO81 4.4 40.3 1.0
C32 A:EZ9301 4.4 35.4 1.0
CB A:ILE96 4.5 55.5 1.0
O A:ALA92 4.6 40.7 1.0
CB A:ALA92 4.6 33.1 1.0
N A:PRO81 4.7 35.3 1.0
CB A:ILE80 4.9 31.2 1.0
C A:ALA92 4.9 38.7 1.0
CG2 A:ILE96 4.9 55.2 1.0

Fluorine binding site 2 out of 8 in 6m1s

Go back to Fluorine Binding Sites List in 6m1s
Fluorine binding site 2 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O


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 12O within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:39.1
occ:1.00
 F38 A:EZ9301 0.0 39.1 1.0
C36 A:EZ9301 1.4 37.0 1.0
F39 A:EZ9301 2.1 36.3 1.0
F37 A:EZ9301 2.1 30.6 1.0
C34 A:EZ9301 2.4 29.4 1.0
C33 A:EZ9301 2.9 32.1 1.0
CD1 A:ILE96 3.2 65.8 1.0
N35 A:EZ9301 3.7 34.1 1.0
CG1 A:ILE96 3.9 63.2 1.0
C32 A:EZ9301 4.2 35.4 1.0
N31 A:EZ9301 4.6 30.5 1.0

Fluorine binding site 3 out of 8 in 6m1s

Go back to Fluorine Binding Sites List in 6m1s
Fluorine binding site 3 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O


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 12O within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:36.3
occ:1.00
 F39 A:EZ9301 0.0 36.3 1.0
C36 A:EZ9301 1.4 37.0 1.0
F38 A:EZ9301 2.1 39.1 1.0
F37 A:EZ9301 2.1 30.6 1.0
C34 A:EZ9301 2.4 29.4 1.0
N35 A:EZ9301 3.0 34.1 1.0
CD A:PRO81 3.6 28.5 1.0
C33 A:EZ9301 3.6 32.1 1.0
CG A:PRO81 3.6 40.3 1.0
N31 A:EZ9301 4.2 30.5 1.0
N19 A:EZ9301 4.2 46.4 1.0
C18 A:EZ9301 4.4 36.7 1.0
C20 A:EZ9301 4.5 42.0 1.0
C32 A:EZ9301 4.5 35.4 1.0
CB A:PRO81 4.6 31.8 1.0
C17 A:EZ9301 4.8 26.1 1.0
N21 A:EZ9301 4.9 34.8 1.0
N A:PRO81 4.9 35.3 1.0
O23 A:EZ9301 4.9 58.4 1.0
C22 A:EZ9301 5.0 29.4 1.0

Fluorine binding site 4 out of 8 in 6m1s

Go back to Fluorine Binding Sites List in 6m1s
Fluorine binding site 4 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O


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 12O within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:33.0
occ:1.00
 F40 A:EZ9301 0.0 33.0 1.0
C06 A:EZ9301 1.4 33.2 1.0
C05 A:EZ9301 2.4 29.8 1.0
C07 A:EZ9301 2.4 26.7 1.0
CG A:ASN48 3.5 31.3 1.0
ND2 A:ASN48 3.5 30.1 1.0
C08 A:EZ9301 3.6 23.0 1.0
C04 A:EZ9301 3.6 26.8 1.0
CG1 A:VAL122 3.7 30.7 1.0
OD1 A:ASN48 3.9 48.8 1.0
CB A:ASN48 3.9 27.3 1.0
CB A:VAL122 3.9 33.6 1.0
C09 A:EZ9301 4.1 26.3 1.0
CG2 A:VAL122 4.1 32.2 1.0
O A:HOH422 4.2 48.8 1.0
CG2 A:ILE96 4.2 55.2 1.0
CD1 A:ILE80 4.2 30.1 1.0
N03 A:EZ9301 4.7 31.3 1.0
C12 A:EZ9301 4.9 23.3 1.0

Fluorine binding site 5 out of 8 in 6m1s

Go back to Fluorine Binding Sites List in 6m1s
Fluorine binding site 5 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O


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 12O within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:37.1
occ:1.00
 F37 B:EZ9304 0.0 37.1 1.0
C36 B:EZ9304 1.4 32.4 1.0
F39 B:EZ9304 2.1 34.4 1.0
F38 B:EZ9304 2.1 34.2 1.0
C34 B:EZ9304 2.4 28.6 1.0
CG2 B:ILE80 3.1 32.8 1.0
N35 B:EZ9304 3.1 36.9 1.0
CD1 B:ILE96 3.2 39.2 1.0
CG2 B:ILE96 3.2 53.5 1.0
C33 B:EZ9304 3.5 25.9 1.0
CG1 B:ILE96 3.7 35.4 1.0
O B:ALA92 3.8 28.5 1.0
C B:ALA92 4.0 33.7 1.0
CB B:ILE96 4.1 40.5 1.0
CB B:ALA92 4.1 36.3 1.0
N31 B:EZ9304 4.2 32.2 1.0
N B:ALA93 4.3 32.5 1.0
CB B:ILE80 4.4 33.5 1.0
CD B:PRO81 4.5 28.1 1.0
C32 B:EZ9304 4.5 31.4 1.0
CA B:ALA93 4.6 42.3 1.0
CA B:ALA92 4.7 36.9 1.0
CG1 B:ILE80 4.8 29.6 1.0

Fluorine binding site 6 out of 8 in 6m1s

Go back to Fluorine Binding Sites List in 6m1s
Fluorine binding site 6 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O


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 12O within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:34.2
occ:1.00
 F38 B:EZ9304 0.0 34.2 1.0
C36 B:EZ9304 1.4 32.4 1.0
F37 B:EZ9304 2.1 37.1 1.0
F39 B:EZ9304 2.1 34.4 1.0
C34 B:EZ9304 2.4 28.6 1.0
C33 B:EZ9304 2.9 25.9 1.0
CG2 B:ILE96 3.1 53.5 1.0
N35 B:EZ9304 3.7 36.9 1.0
C32 B:EZ9304 4.3 31.4 1.0
CD1 B:ILE96 4.3 39.2 1.0
CB B:ILE96 4.4 40.5 1.0
N31 B:EZ9304 4.5 32.2 1.0
CB B:ALA92 4.6 36.3 1.0
CG1 B:ILE96 4.7 35.4 1.0
O B:ALA92 4.8 28.5 1.0

Fluorine binding site 7 out of 8 in 6m1s

Go back to Fluorine Binding Sites List in 6m1s
Fluorine binding site 7 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O


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 12O within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:34.4
occ:1.00
 F39 B:EZ9304 0.0 34.4 1.0
C36 B:EZ9304 1.3 32.4 1.0
F37 B:EZ9304 2.1 37.1 1.0
F38 B:EZ9304 2.1 34.2 1.0
C34 B:EZ9304 2.3 28.6 1.0
N35 B:EZ9304 2.9 36.9 1.0
CD B:PRO81 3.4 28.1 1.0
C33 B:EZ9304 3.5 25.9 1.0
CG2 B:ILE80 4.0 32.8 1.0
CG B:PRO81 4.1 29.4 1.0
N31 B:EZ9304 4.1 32.2 1.0
C32 B:EZ9304 4.5 31.4 1.0
CB B:ALA92 4.6 36.3 1.0
C18 B:EZ9304 4.6 38.9 1.0
N B:PRO81 4.6 35.6 1.0
N19 B:EZ9304 4.7 38.4 1.0
CG2 B:ILE96 4.8 53.5 1.0
C17 B:EZ9304 4.9 29.1 1.0
CB B:PRO81 4.9 30.5 1.0
C20 B:EZ9304 5.0 37.3 1.0
CD1 B:ILE96 5.0 39.2 1.0

Fluorine binding site 8 out of 8 in 6m1s

Go back to Fluorine Binding Sites List in 6m1s
Fluorine binding site 8 out of 8 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12O


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 12O within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F304

b:24.9
occ:1.00
 F40 B:EZ9304 0.0 24.9 1.0
C06 B:EZ9304 1.3 21.1 1.0
C07 B:EZ9304 2.3 19.6 1.0
C05 B:EZ9304 2.4 20.1 1.0
CG B:ASN48 3.4 32.8 1.0
ND2 B:ASN48 3.4 21.6 1.0
OD1 B:ASN48 3.6 39.5 1.0
C04 B:EZ9304 3.6 19.2 1.0
C08 B:EZ9304 3.6 21.1 1.0
CD1 B:ILE96 3.7 39.2 1.0
CB B:ASN48 3.9 21.4 1.0
CE B:MET97 3.9 53.3 1.0
C09 B:EZ9304 4.1 17.6 1.0
CA B:GLY121 4.1 35.6 1.0
C B:GLY121 4.2 35.8 1.0
CG1 B:ILE96 4.4 35.4 1.0
O B:GLY121 4.4 34.1 1.0
CB B:VAL122 4.4 30.1 1.0
N B:GLY121 4.5 23.7 1.0
CD1 B:ILE80 4.5 24.4 1.0
N B:VAL122 4.5 32.6 1.0
CG1 B:VAL122 4.6 28.9 1.0
N03 B:EZ9304 4.8 19.6 1.0
O B:ILE96 4.9 31.4 1.0
CB B:ILE96 4.9 40.5 1.0
C12 B:EZ9304 5.0 24.9 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 13:04:20 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy