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Chlorine 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:

Magnesium (Mg) 4 atoms
Potassium (K) 8 atoms
Fluorine (F) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 9gef

Go back to Chlorine Binding Sites List in 9gef
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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
A:Cl1507

b:75.3
occ:1.00
 N A:GLU609 3.2 77.8 1.0
N A:ASP610 3.5 79.1 1.0
CB A:SER1008 3.6 70.0 1.0
O A:ASP610 3.7 74.1 1.0
N A:GLU1010 3.7 65.2 1.0
CB A:ALA614 3.8 66.3 1.0
CB A:GLU1010 3.8 67.5 1.0
CA A:ILE608 3.9 72.8 1.0
C A:ILE608 4.0 76.1 1.0
N A:LEU1009 4.0 65.9 1.0
CA A:GLU609 4.0 81.0 1.0
CB A:GLU609 4.1 81.8 1.0
CG2 A:ILE608 4.2 72.3 1.0
C A:GLU609 4.3 81.4 1.0
C A:ASP610 4.3 75.6 1.0
O A:THR607 4.3 67.4 1.0
CA A:ASP610 4.3 78.6 1.0
CA A:SER1008 4.3 69.3 1.0
OG A:SER1008 4.4 68.5 1.0
CA A:GLU1010 4.4 64.6 1.0
C A:SER1008 4.4 66.6 1.0
CB A:LEU1009 4.5 65.0 1.0
CA A:ALA614 4.5 65.3 1.0
CA A:LEU1009 4.6 64.3 1.0
N A:ALA614 4.6 67.1 1.0
CB A:ILE608 4.6 72.5 1.0
C A:LEU1009 4.7 63.5 1.0
CB A:ASP610 4.7 79.4 1.0
OE1 A:GLU1010 4.9 70.6 1.0
N A:ILE608 4.9 71.9 1.0

Chlorine binding site 2 out of 4 in 9gef

Go back to Chlorine Binding Sites List in 9gef
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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
B:Cl1509

b:76.8
occ:1.00
 N B:GLU609 3.3 82.4 1.0
CB B:SER1008 3.5 70.4 1.0
N B:GLU1010 3.6 66.6 1.0
CB B:GLU1010 3.7 69.2 1.0
N B:ASP610 3.7 81.8 1.0
CB B:ALA614 3.8 70.6 1.0
O B:ASP610 3.8 75.6 1.0
N B:LEU1009 3.9 65.7 1.0
CA B:ILE608 4.0 77.9 1.0
C B:ILE608 4.1 80.9 1.0
CA B:GLU609 4.2 84.5 1.0
CB B:GLU609 4.2 84.2 1.0
CA B:SER1008 4.3 69.1 1.0
CA B:GLU1010 4.3 66.2 1.0
OE1 B:GLU1010 4.3 74.0 1.0
OG B:SER1008 4.3 70.0 1.0
O B:THR607 4.3 73.1 1.0
C B:SER1008 4.3 66.3 1.0
CG2 B:ILE608 4.4 77.9 1.0
CB B:LEU1009 4.4 64.8 1.0
C B:GLU609 4.4 84.3 1.0
C B:ASP610 4.4 77.8 1.0
CA B:ALA614 4.5 69.4 1.0
CA B:LEU1009 4.5 64.3 1.0
CA B:ASP610 4.5 80.6 1.0
C B:LEU1009 4.6 64.3 1.0
N B:ALA614 4.6 71.0 1.0
CB B:ILE608 4.7 78.0 1.0
CB B:ASP610 4.8 80.1 1.0
CG B:GLU609 4.9 85.4 1.0
CG B:GLU1010 4.9 69.5 1.0
N B:ILE608 5.0 77.1 1.0

Chlorine binding site 3 out of 4 in 9gef

Go back to Chlorine Binding Sites List in 9gef
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl 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:Cl101

b:87.8
occ:1.00
 CL1 F:TE9101 0.0 87.8 1.0
C14 F:TE9101 1.7 43.5 1.0
N2 F:TE9101 2.4 37.6 1.0
C2 F:TE9101 2.6 37.9 1.0
C10 F:TE9101 2.6 37.2 1.0
C13 F:TE9101 2.6 38.9 1.0
C15 F:TE9101 2.7 37.8 1.0
N4 F:TE9101 2.9 37.6 1.0
N3 F:TE9101 3.0 36.9 1.0
C1 F:TE9101 3.0 34.8 1.0
C16 F:TE9101 3.4 38.9 1.0
N1 F:TE9101 3.6 32.1 1.0
C18 F:TE9101 3.7 36.2 1.0
CB A:ARG456 3.8 51.2 1.0
C12 F:TE9101 3.8 38.7 1.0
C17 F:TE9101 3.9 37.0 1.0
C9 F:TE9101 3.9 36.1 1.0
C2 F:DA5 4.0 42.8 1.0
C7 F:TE9101 4.0 36.5 1.0
N3 F:DA5 4.0 44.1 1.0
C11 F:TE9101 4.2 37.7 1.0
F2 F:TE9101 4.3 49.1 1.0
N1 F:DA5 4.3 42.5 1.0
C3 F:TE9101 4.4 38.6 1.0
C4 F:DA5 4.4 45.7 1.0
O A:ARG456 4.4 50.2 1.0
C8 F:TE9101 4.5 35.4 1.0
N3 H:DA1 4.5 66.7 1.0
C A:ARG456 4.5 50.1 1.0
CG A:ARG456 4.6 53.1 1.0
CD A:ARG456 4.6 54.4 1.0
CA A:ARG456 4.6 50.2 1.0
C2 H:DA1 4.7 67.2 1.0
C6 F:DA5 4.8 44.0 1.0
F3 F:TE9101 4.8 38.7 1.0
O4 F:TE9101 4.8 41.5 1.0
C5 F:DA5 4.8 45.7 1.0
C4 H:DA1 4.9 65.0 1.0
F1 F:TE9101 5.0 40.1 1.0

Chlorine binding site 4 out of 4 in 9gef

Go back to Chlorine Binding Sites List in 9gef
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl 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:Cl101

b:83.5
occ:1.00
 CL1 H:TE9101 0.0 83.5 1.0
C14 H:TE9101 1.7 42.0 1.0
N2 H:TE9101 2.3 34.1 1.0
C2 H:TE9101 2.6 34.6 1.0
C10 H:TE9101 2.6 36.0 1.0
C13 H:TE9101 2.7 37.1 1.0
C15 H:TE9101 2.7 37.6 1.0
N4 H:TE9101 2.9 35.1 1.0
C1 H:TE9101 2.9 32.0 1.0
N3 H:TE9101 3.0 35.3 1.0
C16 H:TE9101 3.4 35.4 1.0
N1 H:TE9101 3.5 31.4 1.0
C18 H:TE9101 3.7 34.2 1.0
CB B:ARG456 3.9 54.2 1.0
C17 H:TE9101 3.9 35.4 1.0
C2 H:DG5 3.9 42.6 1.0
C12 H:TE9101 3.9 40.6 1.0
C9 H:TE9101 3.9 36.1 1.0
C7 H:TE9101 4.0 36.0 1.0
N3 H:DG5 4.1 44.2 1.0
N2 H:DG5 4.1 41.9 1.0
C11 H:TE9101 4.2 37.5 1.0
N1 H:DG5 4.3 41.7 1.0
F2 H:TE9101 4.3 38.9 1.0
C3 H:TE9101 4.4 34.4 1.0
C8 H:TE9101 4.5 35.5 1.0
O B:ARG456 4.5 51.4 1.0
C4 H:DG5 4.5 45.1 1.0
N3 F:DG1 4.5 68.9 1.0
CD B:ARG456 4.6 59.9 1.0
C B:ARG456 4.6 50.9 1.0
C2 F:DG1 4.6 69.6 1.0
CG B:ARG456 4.6 57.6 1.0
CA B:ARG456 4.6 52.6 1.0
F3 H:TE9101 4.8 35.6 1.0
N2 F:DG1 4.8 72.1 1.0
C6 H:DG5 4.8 42.6 1.0
C5 H:DG5 4.9 44.5 1.0
C4 F:DG1 4.9 66.3 1.0
F1 H:TE9101 5.0 37.9 1.0
O4 H:TE9101 5.0 49.0 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 18:12:31 2024

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