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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

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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

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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

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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

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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: Thu Aug 1 22:10:58 2024

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