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

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 9gef

Go back to Magnesium Binding Sites List in 9gef
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1502

b:45.2
occ:1.00
 O3 F:TE9101 1.9 40.8 1.0
O F:HOH203 2.1 40.0 1.0
O F:HOH202 2.2 30.6 1.0
O A:HOH1643 2.3 42.8 1.0
O2 F:TE9101 2.5 45.6 1.0
C6 F:TE9101 3.0 38.4 1.0
C5 F:TE9101 3.4 44.3 1.0
C4 F:TE9101 3.6 40.0 1.0
OG A:SER1079 4.0 38.5 1.0
N6 H:DA1 4.1 64.8 1.0
C7 F:TE9101 4.2 36.5 1.0
O4 F:DT4 4.4 59.0 1.0
C8 F:TE9101 4.5 35.4 1.0
O1 F:TE9101 4.6 44.4 1.0

Magnesium binding site 2 out of 4 in 9gef

Go back to Magnesium Binding Sites List in 9gef
Magnesium 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 Magnesium with other atoms in the Mg 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
A:Mg1503

b:21.5
occ:1.00
 O A:HOH1616 2.0 19.2 1.0
OD2 A:ASP506 2.0 43.6 1.0
O A:HOH1617 2.1 19.5 1.0
OD2 A:ASP508 2.1 43.1 1.0
O A:HOH1603 2.2 17.0 1.0
O E:HOH101 2.3 21.9 1.0
CG A:ASP508 3.0 42.0 1.0
OD1 A:ASP508 3.2 42.5 1.0
CG A:ASP506 3.2 43.2 1.0
CB A:ASP506 3.7 42.6 1.0
O A:HOH1624 3.8 29.2 1.0
OE2 A:GLU433 4.1 40.0 1.0
O A:LYS581 4.2 48.9 1.0
OD1 A:ASP506 4.3 44.3 1.0
CB A:ASP508 4.4 41.5 1.0
OP1 E:DT15 4.4 46.9 1.0
O A:HOH1632 4.6 31.9 1.0
C5' E:DT15 4.7 41.8 1.0
CD A:GLU433 4.8 41.5 1.0
OE1 A:GLU433 4.8 42.3 1.0
O H:HOH205 4.8 21.4 1.0

Magnesium binding site 3 out of 4 in 9gef

Go back to Magnesium Binding Sites List in 9gef
Magnesium 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 Magnesium with other atoms in the Mg 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
B:Mg1503

b:23.0
occ:1.00
 OD2 B:ASP506 2.0 46.9 1.0
O B:HOH1630 2.1 20.4 1.0
O B:HOH1614 2.1 21.1 1.0
OD2 B:ASP508 2.2 45.7 1.0
O B:HOH1609 2.2 25.2 1.0
O G:HOH101 2.3 25.9 1.0
CG B:ASP508 3.1 44.5 1.0
CG B:ASP506 3.2 46.9 1.0
OD1 B:ASP508 3.3 44.3 1.0
O B:HOH1635 3.4 27.4 1.0
CB B:ASP506 3.7 46.1 1.0
O B:LYS581 4.1 47.0 1.0
OE2 B:GLU433 4.2 39.2 1.0
O B:HOH1608 4.2 30.0 1.0
OD1 B:ASP506 4.3 48.8 1.0
OP1 G:DC15 4.4 42.8 1.0
CB B:ASP508 4.4 44.0 1.0
C5' G:DC15 4.7 39.8 1.0
CD B:GLU433 4.9 39.7 1.0
OE1 B:GLU433 4.9 40.1 1.0

Magnesium binding site 4 out of 4 in 9gef

Go back to Magnesium Binding Sites List in 9gef
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg102

b:54.8
occ:1.00
 O H:HOH201 1.4 52.8 1.0
O H:HOH203 1.8 50.9 1.0
O3 H:TE9101 2.3 37.5 1.0
O H:HOH202 2.7 35.7 1.0
O1 H:TE9101 2.8 38.9 1.0
C6 H:TE9101 3.4 36.2 1.0
C5 H:TE9101 3.8 38.3 1.0
C4 H:TE9101 4.0 35.7 1.0
N4 G:DC15 4.4 42.3 1.0
OG B:SER1079 4.5 36.0 1.0
C7 H:TE9101 4.5 36.0 1.0
O6 H:DG5 4.6 41.9 1.0
C8 H:TE9101 4.7 35.5 1.0
N4 H:DC4 4.8 56.0 1.0
O2 H:TE9101 5.0 41.3 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 22:33:32 2024

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