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Magnesium in PDB 4z53: Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae

Enzymatic activity of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae

All present enzymatic activity of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae:
5.99.1.3;

Protein crystallography data

The structure of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae, PDB code: 4z53 was solved by I.Laponogov, D.A.Veselkov, X.-S.Pan, J.Selvarajah, I.M.-T.Crevel, 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) 73.90 / 3.26
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.830, 157.830, 210.580, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 20.7

Other elements in 4z53:

The structure of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae (pdb code 4z53). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae, PDB code: 4z53:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4z53

Go back to Magnesium Binding Sites List in 4z53
Magnesium binding site 1 out of 4 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1501

b:92.1
occ:1.00
 O27 F:TR6101 2.0 0.8 1.0
O29 F:TR6101 2.0 0.6 1.0
C23 F:TR6101 2.9 0.6 1.0
C26 F:TR6101 3.0 0.3 1.0
C24 F:TR6101 3.3 0.3 1.0
O28 F:TR6101 4.1 0.7 1.0
O4 E:DT15 4.2 0.3 1.0
C22 F:TR6101 4.2 99.5 1.0
H211 F:TR6101 4.2 0.5 1.0
O6 H:DG1 4.3 0.0 1.0
OG A:SER1079 4.4 0.2 1.0
C21 F:TR6101 4.6 96.3 1.0
OD2 A:ASP1083 4.6 76.6 1.0
CB A:SER1079 4.6 89.9 1.0
C25 F:TR6101 4.7 0.0 1.0
N6 F:DA5 4.8 0.1 1.0

Magnesium binding site 2 out of 4 in 4z53

Go back to Magnesium Binding Sites List in 4z53
Magnesium binding site 2 out of 4 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1502

b:90.3
occ:1.00
 OD2 A:ASP508 2.0 93.4 1.0
OD2 A:ASP506 2.1 0.2 1.0
CG A:ASP506 3.0 0.9 1.0
CG A:ASP508 3.1 88.4 1.0
CB A:ASP506 3.3 89.2 1.0
OE1 A:GLU433 3.4 85.6 1.0
OD1 A:ASP508 3.4 88.3 1.0
OD1 A:ASP506 4.1 0.1 1.0
CD A:GLU433 4.4 97.6 1.0
CB A:ASP508 4.4 79.6 1.0
O A:LYS581 4.5 95.1 1.0
OP1 E:DT15 4.7 85.2 1.0
OE2 A:GLU433 4.7 0.7 1.0
C5' E:DT15 4.8 92.6 1.0
CA A:ASP506 4.9 79.8 1.0

Magnesium binding site 3 out of 4 in 4z53

Go back to Magnesium Binding Sites List in 4z53
Magnesium binding site 3 out of 4 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1501

b:0.6
occ:1.00
 O28 H:TR6101 2.0 0.4 1.0
O29 H:TR6101 2.0 0.2 1.0
C23 H:TR6101 2.9 1.0 1.0
C26 H:TR6101 3.0 0.0 1.0
C24 H:TR6101 3.3 0.7 1.0
O4 G:DT15 4.0 79.7 1.0
O27 H:TR6101 4.1 0.5 1.0
H211 H:TR6101 4.2 0.4 1.0
C22 H:TR6101 4.2 0.0 1.0
OG B:SER1079 4.2 0.4 1.0
N6 F:DA1 4.3 1.0 1.0
CB B:SER1079 4.5 85.4 1.0
OD2 B:ASP1083 4.5 80.7 1.0
C21 H:TR6101 4.6 0.1 1.0
C25 H:TR6101 4.7 0.9 1.0
N6 H:DA5 4.9 1.0 1.0

Magnesium binding site 4 out of 4 in 4z53

Go back to Magnesium Binding Sites List in 4z53
Magnesium binding site 4 out of 4 in the Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Quinolone(Trovafloxacin)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1502

b:84.5
occ:1.00
 OD2 B:ASP506 1.9 0.8 1.0
OD2 B:ASP508 2.0 0.6 1.0
CG B:ASP506 2.9 0.0 1.0
CG B:ASP508 3.1 1.0 1.0
CB B:ASP506 3.4 0.3 1.0
OD1 B:ASP508 3.4 0.9 1.0
OE1 B:GLU433 3.5 97.8 1.0
OD1 B:ASP506 4.0 0.3 1.0
CD B:GLU433 4.3 96.7 1.0
CB B:ASP508 4.4 96.0 1.0
OP1 G:DT15 4.5 77.1 1.0
C5' G:DT15 4.6 81.0 1.0
OE2 B:GLU433 4.6 98.2 1.0
O B:LYS581 4.6 98.7 1.0
O3' G:DT15 4.8 0.7 1.0
C3' G:DT15 4.9 88.7 1.0
CA B:ASP506 4.9 98.3 1.0
O5' G:DT15 4.9 75.4 1.0

Reference:

I.Laponogov, D.A.Veselkov, X.-S.Pan, J.Selvarajah, I.M.-T.Crevel, L.M.Fisher, M.R.Sanderson. Structural Studies of the Drug-Stabilized Cleavage Complexes of Topoisomerase IV and Gyrase From Streptococcus Pneumoniae To Be Published.
Page generated: Sat Sep 28 23:55:57 2024

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