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: Sun Dec 13 12:57:43 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy