Fluorine in PDB 9gef: Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex

Enzymatic activity of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex

All present enzymatic activity of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex:
5.6.2.2;

Protein crystallography data

The structure of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex, PDB code: 9gef was solved by B.Wang, S.Najmudin, X.-S.Pan, V.Mykhaylyk, C.Orr, A.Wagner, L.Govada, N.E.Chayen, L.M.Fisher, M.R.Sanderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 79.39 / 2.62
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.533, 158.533, 210.82, 90, 90, 120
R / Rfree (%) 18 / 20.9

Other elements in 9gef:

The structure of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Magnesium (Mg) 4 atoms
Potassium (K) 8 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex (pdb code 9gef). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex, PDB code: 9gef:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 9gef

Go back to Fluorine Binding Sites List in 9gef
Fluorine binding site 1 out of 6 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:40.1
occ:1.00
 F1 F:TE9101 0.0 40.1 1.0
C9 F:TE9101 1.3 36.1 1.0
C10 F:TE9101 2.3 37.2 1.0
C8 F:TE9101 2.4 35.4 1.0
N4 F:TE9101 2.7 37.6 1.0
C11 F:TE9101 2.9 37.7 1.0
C2 F:DT4 2.9 61.2 1.0
N1 F:DT4 3.0 62.3 1.0
N3 F:DT4 3.0 59.9 1.0
C8 F:DA5 3.1 48.7 1.0
N7 F:DA5 3.1 47.7 1.0
C6 F:DT4 3.2 62.9 1.0
C4 F:DT4 3.3 60.4 1.0
C5 F:DT4 3.4 62.1 1.0
O2 F:DT4 3.5 61.2 1.0
C14 F:TE9101 3.6 43.5 1.0
C7 F:TE9101 3.6 36.5 1.0
C2' F:DT4 3.7 62.3 1.0
N9 F:DA5 3.7 47.7 1.0
C5 F:DA5 3.7 45.7 1.0
C1' F:DT4 3.8 63.1 1.0
O4 F:DT4 4.1 59.0 1.0
C15 F:TE9101 4.1 37.8 1.0
C4 F:DA5 4.1 45.7 1.0
C13 F:TE9101 4.2 38.9 1.0
N1 H:DA1 4.2 66.8 1.0
C12 F:TE9101 4.3 38.7 1.0
O4' F:DA5 4.4 51.1 1.0
C7 F:DT4 4.4 63.1 1.0
C1' F:DA5 4.6 48.6 1.0
C6 F:DA5 4.6 44.0 1.0
C2 H:DA1 4.7 67.2 1.0
C6 F:TE9101 4.8 38.4 1.0
CL1 F:TE9101 5.0 87.8 1.0
C6 H:DA1 5.0 64.9 1.0
N6 F:DA5 5.0 43.8 1.0
C3' F:DT4 5.0 64.8 1.0

Fluorine binding site 2 out of 6 in 9gef

Go back to Fluorine Binding Sites List in 9gef
Fluorine binding site 2 out of 6 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:49.1
occ:1.00
 F2 F:TE9101 0.0 49.1 1.0
C16 F:TE9101 1.3 38.9 1.0
C2 F:TE9101 2.4 37.9 1.0
C17 F:TE9101 2.4 37.0 1.0
N3 F:TE9101 2.8 36.9 1.0
C3 F:TE9101 3.0 38.6 1.0
C2 E:DT15 3.0 42.3 1.0
N3 E:DT15 3.2 43.0 1.0
N1 E:DT15 3.2 42.1 1.0
O2 E:DT15 3.4 42.2 1.0
C2' E:DT15 3.5 46.5 1.0
N2 F:TE9101 3.6 37.6 1.0
C18 F:TE9101 3.6 36.2 1.0
C6 E:DT15 3.6 43.1 1.0
C4 E:DT15 3.7 43.4 1.0
C1' E:DT15 3.8 42.0 1.0
C5 E:DT15 3.9 43.5 1.0
C15 F:TE9101 4.0 37.8 1.0
C1 F:TE9101 4.1 34.8 1.0
CA A:GLY457 4.1 48.5 1.0
C4 F:TE9101 4.2 40.0 1.0
N1 F:DA5 4.3 42.5 1.0
CL1 F:TE9101 4.3 87.8 1.0
O4 E:DT15 4.4 44.1 1.0
N A:GLY457 4.5 49.5 1.0
C14 F:TE9101 4.6 43.5 1.0
C2 F:DA5 4.6 42.8 1.0
O1 F:TE9101 4.6 44.4 1.0
F3 F:TE9101 4.7 38.7 1.0
C5 F:TE9101 4.9 44.3 1.0
C7 F:TE9101 4.9 36.5 1.0
C7 E:DT15 5.0 44.7 1.0
C A:ARG456 5.0 50.1 1.0
OP1 H:DA1 5.0 72.8 1.0
C3' E:DT15 5.0 45.9 1.0

Fluorine binding site 3 out of 6 in 9gef

Go back to Fluorine Binding Sites List in 9gef
Fluorine binding site 3 out of 6 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F101

b:38.7
occ:1.00
 F3 F:TE9101 0.0 38.7 1.0
C18 F:TE9101 1.3 36.2 1.0
C1 F:TE9101 2.4 34.8 1.0
C17 F:TE9101 2.4 37.0 1.0
N1 F:TE9101 2.7 32.1 1.0
OD1 A:ASP435 3.0 40.2 1.0
O5' H:DA1 3.2 68.6 1.0
CA A:ARG456 3.3 50.2 1.0
CA A:GLY434 3.5 41.1 1.0
N2 F:TE9101 3.6 37.6 1.0
C16 F:TE9101 3.6 38.9 1.0
CG A:ARG456 3.6 53.1 1.0
N A:ASP435 3.6 40.6 1.0
CB A:ARG456 3.7 51.2 1.0
O A:LEU455 3.8 49.2 1.0
OP1 H:DA1 3.9 72.8 1.0
N A:GLY457 3.9 49.5 1.0
P H:DA1 3.9 70.1 1.0
C A:ARG456 4.0 50.1 1.0
C4' H:DA1 4.1 66.0 1.0
C2 F:TE9101 4.1 37.9 1.0
C A:GLY434 4.1 41.6 1.0
CG A:ASP435 4.2 40.8 1.0
C5' H:DA1 4.2 66.0 1.0
N A:ARG456 4.3 50.4 1.0
O4' H:DA1 4.3 65.6 1.0
C A:LEU455 4.4 49.9 1.0
OP2 H:DA1 4.5 71.0 1.0
N A:GLY434 4.5 42.0 1.0
CD A:ARG456 4.7 54.4 1.0
CB A:ASP435 4.7 40.7 1.0
F2 F:TE9101 4.7 49.1 1.0
CA A:ASP435 4.8 40.9 1.0
CL1 F:TE9101 4.8 87.8 1.0
CA A:GLY457 5.0 48.5 1.0

Fluorine binding site 4 out of 6 in 9gef

Go back to Fluorine Binding Sites List in 9gef
Fluorine binding site 4 out of 6 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:37.9
occ:1.00
 F1 H:TE9101 0.0 37.9 1.0
C9 H:TE9101 1.4 36.1 1.0
C10 H:TE9101 2.3 36.0 1.0
C8 H:TE9101 2.4 35.5 1.0
N4 H:TE9101 2.7 35.1 1.0
C2 H:DC4 2.7 59.0 1.0
C11 H:TE9101 2.8 37.5 1.0
N3 H:DC4 2.9 57.5 1.0
N1 H:DC4 3.0 60.0 1.0
N7 H:DG5 3.1 46.1 1.0
C8 H:DG5 3.2 47.6 1.0
O2 H:DC4 3.2 59.7 1.0
C4 H:DC4 3.3 57.0 1.0
C6 H:DC4 3.3 59.8 1.0
C2' H:DC4 3.5 60.3 1.0
C5 H:DC4 3.5 58.3 1.0
C14 H:TE9101 3.6 42.0 1.0
C1' H:DC4 3.6 61.3 1.0
C7 H:TE9101 3.6 36.0 1.0
C5 H:DG5 3.7 44.5 1.0
N9 H:DG5 3.8 47.2 1.0
C4 H:DG5 4.1 45.1 1.0
C15 H:TE9101 4.1 37.6 1.0
N4 H:DC4 4.2 56.0 1.0
C12 H:TE9101 4.2 40.6 1.0
C13 H:TE9101 4.2 37.1 1.0
N1 F:DG1 4.3 68.0 1.0
O4' H:DG5 4.4 51.2 1.0
C6 H:DG5 4.6 42.6 1.0
C1' H:DG5 4.6 48.8 1.0
N2 F:DG1 4.6 72.1 1.0
C3' H:DC4 4.7 61.9 1.0
C2 F:DG1 4.8 69.6 1.0
C6 H:TE9101 4.8 36.2 1.0
O6 H:DG5 4.9 41.9 1.0
O4' H:DC4 5.0 63.6 1.0
CL1 H:TE9101 5.0 83.5 1.0

Fluorine binding site 5 out of 6 in 9gef

Go back to Fluorine Binding Sites List in 9gef
Fluorine binding site 5 out of 6 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:38.9
occ:1.00
 F2 H:TE9101 0.0 38.9 1.0
C16 H:TE9101 1.3 35.4 1.0
C2 H:TE9101 2.4 34.6 1.0
C17 H:TE9101 2.4 35.4 1.0
N3 H:TE9101 2.9 35.3 1.0
C2 G:DC15 3.0 40.8 1.0
C3 H:TE9101 3.0 34.4 1.0
N3 G:DC15 3.2 41.5 1.0
N1 G:DC15 3.3 40.2 1.0
O2 G:DC15 3.3 41.0 1.0
C2' G:DC15 3.4 43.5 1.0
N2 H:TE9101 3.6 34.1 1.0
C4 G:DC15 3.6 41.5 1.0
C18 H:TE9101 3.6 34.2 1.0
C6 G:DC15 3.7 40.5 1.0
C1' G:DC15 3.8 40.0 1.0
C5 G:DC15 3.9 41.0 1.0
C15 H:TE9101 4.0 37.6 1.0
C1 H:TE9101 4.1 32.0 1.0
C4 H:TE9101 4.2 35.7 1.0
CA B:GLY457 4.2 47.8 1.0
N2 H:DG5 4.3 41.9 1.0
CL1 H:TE9101 4.3 83.5 1.0
N1 H:DG5 4.4 41.7 1.0
N4 G:DC15 4.4 42.3 1.0
N B:GLY457 4.6 49.4 1.0
C14 H:TE9101 4.7 42.0 1.0
O F:HOH205 4.7 21.0 1.0
C2 H:DG5 4.7 42.6 1.0
F3 H:TE9101 4.8 35.6 1.0
OP1 F:DG1 4.8 70.0 1.0
C3' G:DC15 4.8 43.4 1.0
O2 H:TE9101 4.9 41.3 1.0
C5 H:TE9101 5.0 38.3 1.0

Fluorine binding site 6 out of 6 in 9gef

Go back to Fluorine Binding Sites List in 9gef
Fluorine binding site 6 out of 6 in the Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in the Delafloxacin-Stabilized Streptococcus Pneumoniae Topoisomerase IV Dna Cleavage Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F101

b:35.6
occ:1.00
 F3 H:TE9101 0.0 35.6 1.0
C18 H:TE9101 1.4 34.2 1.0
C1 H:TE9101 2.4 32.0 1.0
C17 H:TE9101 2.4 35.4 1.0
N1 H:TE9101 2.7 31.4 1.0
O5' F:DG1 3.1 67.9 1.0
OD2 B:ASP435 3.1 38.9 1.0
CA B:ARG456 3.4 52.6 1.0
CA B:GLY434 3.5 39.5 1.0
N2 H:TE9101 3.6 34.1 1.0
N B:ASP435 3.6 39.3 1.0
C16 H:TE9101 3.6 35.4 1.0
O F:HOH205 3.8 21.0 1.0
OP1 F:DG1 3.8 70.0 1.0
P F:DG1 3.8 68.3 1.0
CG B:ARG456 3.8 57.6 1.0
CB B:ARG456 3.9 54.2 1.0
N B:GLY457 3.9 49.4 1.0
O B:LEU455 3.9 53.0 1.0
C4' F:DG1 4.1 66.6 1.0
C B:ARG456 4.1 50.9 1.0
C2 H:TE9101 4.1 34.6 1.0
C B:GLY434 4.1 40.0 1.0
O4' F:DG1 4.1 66.3 1.0
C5' F:DG1 4.1 65.9 1.0
CG B:ASP435 4.2 39.9 1.0
OP2 F:DG1 4.3 69.7 1.0
N B:ARG456 4.4 52.9 1.0
C B:LEU455 4.5 52.4 1.0
N B:GLY434 4.5 40.3 1.0
CB B:ASP435 4.7 39.7 1.0
CD B:ARG456 4.8 59.9 1.0
CL1 H:TE9101 4.8 83.5 1.0
F2 H:TE9101 4.8 38.9 1.0
CA B:ASP435 4.8 39.9 1.0
CA B:GLY457 4.9 47.8 1.0

Reference:

B.Wang, S.Najmudin, X.S.Pan, V.Mykhaylyk, C.Orr, A.Wagner, L.Govada, N.E.Chayen, L.M.Fisher, M.R.Sanderson. Experimental Localization of Metal-Binding Sites Reveals the Role of Metal Ions in Type II Dna Topoisomerases. Proc.Natl.Acad.Sci.Usa V. 121 57121 2024.
ISSN: ESSN 1091-6490
PubMed: 39361644
DOI: 10.1073/PNAS.2413357121
Page generated: Thu Oct 31 20:07:50 2024

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