Atomistry » Magnesium » PDB 3r11-3ren » 3rad
Atomistry »
  Magnesium »
    PDB 3r11-3ren »
      3rad »

Magnesium in PDB 3rad: Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae

Protein crystallography data

The structure of Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 3rad was solved by I.Laponogov, X.-S.Pan, D.A.Veselkov, K.E.Mcauley, 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) 41.67 / 3.35
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 157.128, 157.128, 211.091, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 22.8

Other elements in 3rad:

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

Fluorine (F) 2 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae (pdb code 3rad). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae, PDB code: 3rad:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3rad

Go back to Magnesium Binding Sites List in 3rad
Magnesium binding site 1 out of 6 in the Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase 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(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:87.4
occ:1.00
 O A:GLN322 2.0 82.2 1.0
O A:THR319 2.0 0.0 1.0
O A:PHE316 2.9 85.1 1.0
O A:LYS317 3.3 81.7 1.0
C A:GLN322 3.3 68.0 1.0
C A:THR319 3.3 87.3 1.0
C A:LYS317 3.9 75.2 1.0
C A:PHE316 4.0 63.4 1.0
N A:THR319 4.1 77.5 1.0
CG A:GLN322 4.1 97.6 1.0
N A:ILE323 4.2 70.4 1.0
N A:ASP320 4.2 98.7 1.0
CA A:GLN322 4.2 65.6 1.0
CA A:ILE323 4.3 70.5 1.0
CA A:ASP320 4.3 0.4 1.0
N A:GLN322 4.3 75.5 1.0
CA A:THR319 4.3 73.6 1.0
CA A:LYS317 4.4 91.5 1.0
OD1 A:ASP320 4.5 92.2 1.0
CB A:GLN322 4.6 83.7 1.0
N A:TYR318 4.6 71.7 1.0
N A:LYS317 4.7 73.8 1.0
CG2 A:ILE323 4.8 70.6 1.0
C A:TYR318 4.8 83.2 1.0
C A:ASP320 4.9 90.7 1.0
O A:LEU315 4.9 87.0 1.0

Magnesium binding site 2 out of 6 in 3rad

Go back to Magnesium Binding Sites List in 3rad
Magnesium binding site 2 out of 6 in the Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase 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(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:0.7
occ:1.00
 O03 F:NFX101 2.0 0.4 1.0
O02 F:NFX101 2.0 0.3 1.0
C19 F:NFX101 2.9 0.9 1.0
C20 F:NFX101 2.9 1.0 1.0
C18 F:NFX101 3.3 0.2 1.0
O4 E:DT15 3.7 0.9 1.0
O F:NFX101 4.2 0.2 1.0
C14 F:NFX101 4.3 0.9 1.0
H17 F:NFX101 4.4 0.9 1.0
N6 F:DA5 4.4 0.9 1.0
CB A:SER79 4.5 76.5 1.0
O6 H:DG1 4.5 0.5 1.0
C16 F:NFX101 4.6 0.5 1.0
OG A:SER79 4.6 0.4 1.0
OD2 A:ASP83 4.7 86.6 1.0
N6 E:DA14 4.7 0.4 1.0
C17 F:NFX101 4.8 0.3 1.0
C4 E:DT15 4.8 0.3 1.0

Magnesium binding site 3 out of 6 in 3rad

Go back to Magnesium Binding Sites List in 3rad
Magnesium binding site 3 out of 6 in the Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase 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(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:0.5
occ:1.00
 O B:GLN322 2.0 99.0 1.0
O B:THR319 2.0 0.9 1.0
O B:PHE316 2.9 91.5 1.0
C B:GLN322 3.3 80.6 1.0
C B:THR319 3.3 90.7 1.0
O B:LYS317 3.3 77.3 1.0
C B:LYS317 4.0 76.9 1.0
C B:PHE316 4.0 76.9 1.0
CA B:ASP320 4.1 96.1 1.0
N B:ASP320 4.1 97.6 1.0
N B:GLN322 4.2 82.8 1.0
N B:THR319 4.2 76.6 1.0
N B:ILE323 4.2 68.7 1.0
CA B:GLN322 4.2 67.5 1.0
CA B:ILE323 4.3 63.8 1.0
CA B:THR319 4.3 76.4 1.0
CA B:LYS317 4.6 92.4 1.0
CB B:GLN322 4.6 86.0 1.0
C B:ASP320 4.7 85.6 1.0
N B:TYR318 4.7 92.3 1.0
OD1 B:ASP320 4.7 96.8 1.0
N B:LEU321 4.8 70.9 1.0
CG2 B:ILE323 4.8 74.5 1.0
N B:LYS317 4.8 77.8 1.0
C B:TYR318 4.9 82.7 1.0
NE2 B:GLN322 4.9 92.7 1.0
O B:LEU315 4.9 96.9 1.0

Magnesium binding site 4 out of 6 in 3rad

Go back to Magnesium Binding Sites List in 3rad
Magnesium binding site 4 out of 6 in the Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase 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(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:0.1
occ:1.00
 O02 H:NFX101 2.0 0.5 1.0
O03 H:NFX101 2.2 0.8 1.0
C19 H:NFX101 3.0 0.8 1.0
C20 H:NFX101 3.1 0.2 1.0
C18 H:NFX101 3.4 0.1 1.0
O H:NFX101 4.3 0.9 1.0
CB B:SER79 4.3 81.9 1.0
H17 H:NFX101 4.3 0.2 1.0
C14 H:NFX101 4.4 0.1 1.0
O4 G:DT15 4.4 75.1 1.0
OG B:SER79 4.7 0.1 1.0
N6 F:DA1 4.7 0.9 1.0
OD2 B:ASP83 4.7 83.8 1.0
C16 H:NFX101 4.8 0.8 1.0
C17 H:NFX101 4.8 0.6 1.0

Magnesium binding site 5 out of 6 in 3rad

Go back to Magnesium Binding Sites List in 3rad
Magnesium binding site 5 out of 6 in the Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg701

b:87.9
occ:1.00
 OD2 C:ASP508 2.0 0.9 1.0
OD2 C:ASP506 2.6 0.9 1.0
CG C:ASP508 3.2 0.3 1.0
OD1 C:ASP508 3.6 0.8 1.0
CG C:ASP506 3.6 0.6 1.0
OP1 E:DT15 4.0 89.6 1.0
OE1 C:GLU433 4.1 0.4 1.0
CB C:ASP506 4.1 0.9 1.0
CB C:ASP508 4.4 0.3 1.0
C5' E:DT15 4.5 99.9 1.0
OD1 C:ASP506 4.7 0.0 1.0
O C:LYS581 4.7 0.7 1.0

Magnesium binding site 6 out of 6 in 3rad

Go back to Magnesium Binding Sites List in 3rad
Magnesium binding site 6 out of 6 in the Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Quinolone(Clinafloxacin)-Dna Cleavage Complex of Type IV Topoisomerase From S. Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg701

b:78.4
occ:1.00
 OD2 D:ASP508 2.0 0.5 1.0
OD2 D:ASP506 2.9 0.7 1.0
CG D:ASP508 3.1 0.3 1.0
OD1 D:ASP508 3.5 0.7 1.0
OP1 G:DT15 3.8 85.7 1.0
CG D:ASP506 3.9 0.3 1.0
O D:LYS581 4.2 0.5 1.0
CB D:ASP506 4.2 0.3 1.0
CB D:ASP508 4.4 0.9 1.0
C5' G:DT15 4.4 94.7 1.0
OE1 D:GLU433 4.5 0.2 1.0
OD1 D:ASP506 4.9 0.1 1.0

Reference:

I.Laponogov, X.S.Pan, D.A.Veselkov, R.T.Cirz, A.Wagman, H.E.Moser, L.M.Fisher, M.R.Sanderson. Exploring the Active Site of the Streptococcus Pneumoniae Topoisomerase IV-Dna Cleavage Complex with Novel 7,8-Bridged Fluoroquinolones. Open Biol V. 6 2016.
ISSN: ESSN 2046-2441
PubMed: 27655731
DOI: 10.1098/RSOB.160157
Page generated: Thu Aug 15 10:21:53 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy