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Magnesium in PDB 5j5q: Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II

Enzymatic activity of Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II

All present enzymatic activity of Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II:
5.99.1.3;

Protein crystallography data

The structure of Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II, PDB code: 5j5q was solved by I.Laponogov, X.-S.Pan, G.Skamrova, T.Umrekar, 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) 60.76 / 2.83
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.950, 72.740, 222.960, 90.00, 91.89, 90.00
R / Rfree (%) 18.4 / 26.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II (pdb code 5j5q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II, PDB code: 5j5q:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5j5q

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Magnesium binding site 1 out of 4 in the Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:36.6
occ:1.00
 O3G A:ANP501 1.8 34.1 1.0
OD1 A:ASN51 1.8 43.1 1.0
O2B A:ANP501 2.0 38.8 1.0
O2A A:ANP501 2.3 38.6 1.0
CG A:ASN51 3.0 41.2 1.0
PB A:ANP501 3.0 41.8 1.0
PA A:ANP501 3.2 43.0 1.0
PG A:ANP501 3.3 35.3 1.0
O3A A:ANP501 3.4 42.9 1.0
ND2 A:ASN51 3.5 41.2 1.0
N3B A:ANP501 3.6 37.6 1.0
OE2 A:GLU47 3.6 58.3 1.0
O2G A:ANP501 3.8 35.4 1.0
O5' A:ANP501 4.0 43.6 1.0
O A:GLU47 4.0 53.6 1.0
NZ A:LYS107 4.1 36.1 1.0
HNB1 A:ANP501 4.3 34.3 1.0
CA A:GLY118 4.3 39.0 1.0
CB A:ASN51 4.3 39.3 1.0
O1A A:ANP501 4.5 41.3 1.0
O1G A:ANP501 4.5 32.9 1.0
O1B A:ANP501 4.5 39.3 1.0
CA A:GLY123 4.6 35.0 1.0
CA A:ASN51 4.6 38.9 1.0
N A:GLY123 4.7 34.9 1.0
N A:ASN51 4.7 38.4 1.0
OD1 A:ASP54 4.8 47.7 1.0
CD A:GLU47 4.9 58.8 1.0
N A:SER124 4.9 42.2 1.0
H3' A:ANP501 5.0 40.3 1.0
H5'2 A:ANP501 5.0 48.0 1.0

Magnesium binding site 2 out of 4 in 5j5q

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Magnesium binding site 2 out of 4 in the Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:49.9
occ:1.00
 O3G B:ANP501 2.0 44.0 1.0
OD1 B:ASN51 2.1 44.8 1.0
O2A B:ANP501 2.2 41.2 1.0
O1B B:ANP501 2.4 47.0 1.0
PB B:ANP501 3.1 45.9 1.0
CG B:ASN51 3.2 42.4 1.0
PA B:ANP501 3.3 43.2 1.0
O3A B:ANP501 3.4 43.6 1.0
PG B:ANP501 3.4 43.8 1.0
N3B B:ANP501 3.6 47.4 1.0
ND2 B:ASN51 3.6 41.0 1.0
O5' B:ANP501 3.8 47.7 1.0
HNB1 B:ANP501 3.8 95.2 1.0
O1G B:ANP501 4.0 41.0 1.0
NZ B:LYS107 4.0 45.8 1.0
OE2 B:GLU47 4.2 51.3 1.0
CA B:GLY118 4.2 48.2 1.0
O2B B:ANP501 4.4 47.5 1.0
O B:GLU47 4.5 48.0 1.0
CB B:ASN51 4.5 41.8 1.0
O1A B:ANP501 4.5 39.6 1.0
O2G B:ANP501 4.6 44.2 1.0
H3' B:ANP501 4.6 56.5 1.0
CA B:ASN51 4.7 43.5 1.0
CA B:GLY123 4.7 41.4 1.0
N B:ASN51 4.7 43.3 1.0
N B:GLY118 4.9 48.1 1.0
OD1 B:ASP54 4.9 50.4 1.0

Magnesium binding site 3 out of 4 in 5j5q

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Magnesium binding site 3 out of 4 in the Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:64.9
occ:1.00
 OD1 C:ASN51 1.8 76.9 1.0
O2A C:ANP501 2.1 67.3 1.0
O1B C:ANP501 2.1 72.0 1.0
O3G C:ANP501 2.2 66.5 1.0
CG C:ASN51 2.8 75.8 1.0
PA C:ANP501 3.1 68.5 1.0
PB C:ANP501 3.2 69.1 1.0
ND2 C:ASN51 3.2 73.7 1.0
PG C:ANP501 3.4 63.9 1.0
O3A C:ANP501 3.4 68.1 1.0
OE2 C:GLU47 3.5 64.8 1.0
N3B C:ANP501 3.7 69.5 1.0
NZ C:LYS107 3.8 61.2 1.0
O5' C:ANP501 3.9 71.3 1.0
O1G C:ANP501 4.2 63.8 1.0
CB C:ASN51 4.2 77.2 1.0
O C:GLU47 4.2 65.0 1.0
O1A C:ANP501 4.3 68.7 1.0
O2B C:ANP501 4.4 69.7 1.0
O2G C:ANP501 4.4 61.8 1.0
CA C:GLY118 4.4 65.9 1.0
H3' C:ANP501 4.5 0.9 1.0
CA C:ASN51 4.5 79.3 1.0
N C:ASN51 4.6 78.5 1.0
HNB1 C:ANP501 4.6 0.3 1.0
CA C:GLY123 4.7 75.5 1.0
CD C:GLU47 4.8 64.6 1.0
N C:GLY123 4.8 76.5 1.0
N C:SER124 4.9 76.5 1.0

Magnesium binding site 4 out of 4 in 5j5q

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Magnesium binding site 4 out of 4 in the Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type II within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:71.4
occ:1.00
 OD1 D:ASN51 2.1 75.2 1.0
O3G D:ANP501 2.1 83.2 1.0
O1B D:ANP501 2.4 86.8 1.0
O1A D:ANP501 2.5 84.0 1.0
CG D:ASN51 3.2 74.0 1.0
PG D:ANP501 3.3 79.4 1.0
PB D:ANP501 3.4 84.3 1.0
PA D:ANP501 3.5 85.0 1.0
O3A D:ANP501 3.7 84.0 1.0
N3B D:ANP501 3.7 83.8 1.0
ND2 D:ASN51 3.7 71.8 1.0
OE2 D:GLU47 3.9 83.1 1.0
O5' D:ANP501 3.9 88.4 1.0
NZ D:LYS107 4.1 90.1 1.0
O D:GLU47 4.1 83.0 1.0
O1G D:ANP501 4.2 76.2 1.0
O2G D:ANP501 4.3 76.8 1.0
CA D:GLY123 4.4 64.5 1.0
CB D:ASN51 4.5 75.6 1.0
N D:ASN51 4.5 76.6 1.0
CA D:GLY118 4.5 86.2 1.0
HNB1 D:ANP501 4.6 0.3 1.0
CA D:ASN51 4.6 78.1 1.0
H3' D:ANP501 4.8 0.9 1.0
N D:GLY123 4.8 64.2 1.0
O2B D:ANP501 4.8 82.8 1.0
O2A D:ANP501 4.9 84.5 1.0
CD D:GLU47 5.0 80.2 1.0

Reference:

I.Laponogov, X.S.Pan, D.A.Veselkov, G.B.Skamrova, T.R.Umrekar, L.M.Fisher, M.R.Sanderson. Trapping of the Transport-Segment Dna By the Atpase Domains of A Type II Topoisomerase. Nat Commun V. 9 2579 2018.
ISSN: ESSN 2041-1723
PubMed: 29968711
DOI: 10.1038/S41467-018-05005-X
Page generated: Tue Aug 12 12:06:03 2025

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