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Magnesium in PDB 4z4q: Quinazolinedione(Pd 0305970)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae

Enzymatic activity of Quinazolinedione(Pd 0305970)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae

All present enzymatic activity of Quinazolinedione(Pd 0305970)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae:
5.99.1.3;

Protein crystallography data

The structure of Quinazolinedione(Pd 0305970)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae, PDB code: 4z4q 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) 44.59 / 3.04
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.020, 158.020, 211.220, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 20.5

Other elements in 4z4q:

The structure of Quinazolinedione(Pd 0305970)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Quinazolinedione(Pd 0305970)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae (pdb code 4z4q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Quinazolinedione(Pd 0305970)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae, PDB code: 4z4q:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4z4q

Go back to Magnesium Binding Sites List in 4z4q
Magnesium binding site 1 out of 4 in the Quinazolinedione(Pd 0305970)-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 Quinazolinedione(Pd 0305970)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1501

b:96.9
occ:1.00
 O A:GLN1322 2.0 62.3 1.0
O A:THR1319 2.6 62.4 1.0
O A:PHE1316 2.8 55.9 1.0
C A:GLN1322 3.3 55.6 1.0
C A:THR1319 3.5 48.6 1.0
O A:LYS1317 3.6 58.1 1.0
C A:PHE1316 3.9 54.1 1.0
C A:LYS1317 3.9 55.8 1.0
CA A:ASP1320 4.1 50.4 1.0
N A:ILE1323 4.2 49.1 1.0
N A:ASP1320 4.2 47.9 1.0
N A:GLN1322 4.2 50.6 1.0
CA A:GLN1322 4.2 51.0 1.0
N A:THR1319 4.3 45.4 1.0
CA A:ILE1323 4.3 51.0 1.0
OD1 A:ASP1320 4.3 79.9 1.0
CA A:LYS1317 4.4 54.6 1.0
CA A:THR1319 4.5 46.1 1.0
N A:TYR1318 4.6 49.5 1.0
N A:LYS1317 4.6 47.5 1.0
CB A:GLN1322 4.6 47.1 1.0
C A:ASP1320 4.7 63.5 1.0
CG2 A:ILE1323 4.8 49.2 1.0
C A:TYR1318 4.9 56.5 1.0
N A:LEU1321 5.0 58.7 1.0

Magnesium binding site 2 out of 4 in 4z4q

Go back to Magnesium Binding Sites List in 4z4q
Magnesium binding site 2 out of 4 in the Quinazolinedione(Pd 0305970)-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 Quinazolinedione(Pd 0305970)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1502

b:94.0
occ:1.00
 OD2 A:ASP506 1.8 0.5 1.0
OD2 A:ASP508 2.0 96.5 1.0
CG A:ASP506 2.9 91.2 1.0
CG A:ASP508 3.1 85.8 1.0
OD1 A:ASP508 3.4 75.3 1.0
CB A:ASP506 3.5 79.7 1.0
OE1 A:GLU433 3.9 81.4 1.0
OD1 A:ASP506 4.0 87.2 1.0
CB A:ASP508 4.4 56.6 1.0
O A:LYS581 4.5 80.8 1.0
OP1 E:DC15 4.5 72.9 1.0
CD A:GLU433 4.7 85.6 1.0
OE2 A:GLU433 4.9 89.0 1.0
C5' E:DC15 4.9 63.5 1.0

Magnesium binding site 3 out of 4 in 4z4q

Go back to Magnesium Binding Sites List in 4z4q
Magnesium binding site 3 out of 4 in the Quinazolinedione(Pd 0305970)-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 Quinazolinedione(Pd 0305970)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1501

b:0.9
occ:1.00
 O B:GLN1322 2.0 73.0 1.0
O B:THR1319 2.4 70.6 1.0
O B:PHE1316 3.0 71.3 1.0
C B:GLN1322 3.2 69.0 1.0
C B:THR1319 3.4 61.9 1.0
O B:LYS1317 3.9 62.9 1.0
CA B:ASP1320 4.1 62.3 1.0
N B:ASP1320 4.1 62.6 1.0
N B:ILE1323 4.1 56.8 1.0
N B:GLN1322 4.2 65.0 1.0
CA B:GLN1322 4.2 68.6 1.0
OD1 B:ASP1320 4.2 83.1 1.0
C B:PHE1316 4.2 66.5 1.0
CA B:ILE1323 4.2 61.2 1.0
C B:LYS1317 4.3 61.6 1.0
N B:THR1319 4.3 60.3 1.0
CA B:THR1319 4.4 56.1 1.0
CB B:GLN1322 4.5 75.5 1.0
C B:ASP1320 4.7 66.3 1.0
CG2 B:ILE1323 4.8 56.1 1.0
N B:TYR1318 4.8 58.8 1.0
CA B:LYS1317 4.8 59.0 1.0
C B:TYR1318 4.8 62.2 1.0
N B:LYS1317 5.0 55.4 1.0
N B:LEU1321 5.0 60.9 1.0

Magnesium binding site 4 out of 4 in 4z4q

Go back to Magnesium Binding Sites List in 4z4q
Magnesium binding site 4 out of 4 in the Quinazolinedione(Pd 0305970)-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 Quinazolinedione(Pd 0305970)-Dna Cleavage Complex of Topoisomerase IV From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1502

b:79.0
occ:1.00
 OD2 B:ASP506 1.8 0.6 1.0
OD2 B:ASP508 2.0 90.3 1.0
CG B:ASP506 2.9 0.1 1.0
CG B:ASP508 3.1 86.2 1.0
OD1 B:ASP508 3.5 83.4 1.0
CB B:ASP506 3.6 91.3 1.0
OE1 B:GLU433 3.7 98.4 1.0
OD1 B:ASP506 4.0 92.5 1.0
CB B:ASP508 4.5 53.7 1.0
O B:LYS581 4.5 77.9 1.0
CD B:GLU433 4.5 91.2 1.0
OP1 G:DT15 4.8 64.1 1.0
OE2 B:GLU433 4.8 91.7 1.0
C5' G:DT15 5.0 57.9 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: Mon Dec 14 19:56:33 2020

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