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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy