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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy