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Magnesium in PDB 5j5p: Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type I

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

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

Protein crystallography data

The structure of Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type I, PDB code: 5j5p 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) 45.18 / 1.97
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 134.440, 136.460, 136.270, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17.4

Other elements in 5j5p:

The structure of Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type I also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type I (pdb code 5j5p). 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 I, PDB code: 5j5p:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5j5p

Go back to Magnesium Binding Sites List in 5j5p
Magnesium binding site 1 out of 4 in the Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:26.9
occ:1.00
 OD1 A:ASN51 2.0 15.9 1.0
O3G A:ANP501 2.1 22.2 1.0
O A:HOH650 2.1 20.2 1.0
O A:HOH818 2.1 22.1 1.0
O2B A:ANP501 2.3 26.0 1.0
O2A A:ANP501 2.5 18.1 1.0
CG A:ASN51 3.0 20.9 1.0
PB A:ANP501 3.1 17.2 1.0
PG A:ANP501 3.4 16.7 1.0
ND2 A:ASN51 3.4 18.8 1.0
PA A:ANP501 3.5 15.2 1.0
O3A A:ANP501 3.5 13.7 1.0
N3B A:ANP501 3.7 22.6 1.0
NZ A:LYS107 3.9 16.1 1.0
O A:HOH801 3.9 26.7 1.0
HNB1 A:ANP501 4.0 27.2 1.0
O5' A:ANP501 4.2 18.2 1.0
O2G A:ANP501 4.3 15.0 1.0
O A:GLU47 4.3 15.2 1.0
CA A:GLY118 4.3 13.1 1.0
OE2 A:GLU47 4.3 24.7 1.0
CB A:ASN51 4.3 13.7 1.0
O1G A:ANP501 4.4 14.6 1.0
O1B A:ANP501 4.4 23.4 1.0
CA A:GLY123 4.6 13.7 1.0
H3' A:ANP501 4.6 18.5 1.0
CA A:ASN51 4.6 15.2 1.0
N A:ASN51 4.6 16.1 1.0
N A:GLY123 4.8 14.4 1.0
O1A A:ANP501 4.8 16.9 1.0
OD1 A:ASP54 4.8 19.7 1.0
N A:SER124 4.9 16.4 1.0

Magnesium binding site 2 out of 4 in 5j5p

Go back to Magnesium Binding Sites List in 5j5p
Magnesium binding site 2 out of 4 in the Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:74.3
occ:1.00
 O A:HOH736 2.2 54.2 1.0
O A:HOH892 2.2 50.6 1.0
OD1 A:ASP345 3.1 30.8 1.0
O A:HOH944 3.3 46.9 1.0
NZ A:LYS281 3.4 44.0 1.0
OD2 A:ASP345 3.8 34.1 1.0
CG A:ASP345 3.8 34.4 1.0
CE A:LYS281 4.1 38.9 1.0
O A:HOH966 4.1 39.5 1.0
CD A:LYS281 4.3 37.2 1.0
O A:HOH719 4.5 21.6 1.0
O A:HOH722 4.6 24.2 1.0
O A:THR343 4.7 20.6 1.0
CB A:THR343 4.7 27.6 1.0
O B:HOH916 4.9 48.5 1.0
O A:HOH717 4.9 22.6 1.0

Magnesium binding site 3 out of 4 in 5j5p

Go back to Magnesium Binding Sites List in 5j5p
Magnesium binding site 3 out of 4 in the Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:25.5
occ:1.00
 OD1 B:ASN51 2.0 17.1 1.0
O B:HOH641 2.1 19.1 1.0
O B:HOH813 2.1 18.9 1.0
O1G B:ANP501 2.2 20.1 1.0
O1B B:ANP501 2.3 22.3 1.0
O1A B:ANP501 2.5 17.4 1.0
CG B:ASN51 2.9 18.0 1.0
PB B:ANP501 3.1 17.6 1.0
ND2 B:ASN51 3.3 16.1 1.0
PG B:ANP501 3.4 17.1 1.0
PA B:ANP501 3.5 14.3 1.0
O3A B:ANP501 3.6 13.2 1.0
N3B B:ANP501 3.7 22.7 1.0
NZ B:LYS107 3.9 13.4 1.0
O B:HOH780 4.0 30.2 1.0
HNB1 B:ANP501 4.0 27.2 1.0
O5' B:ANP501 4.2 16.6 1.0
OE2 B:GLU47 4.2 20.6 1.0
O3G B:ANP501 4.2 15.4 1.0
O B:GLU47 4.2 14.0 1.0
CA B:GLY118 4.3 14.9 1.0
CB B:ASN51 4.3 15.7 1.0
O2G B:ANP501 4.4 15.1 1.0
O2B B:ANP501 4.5 25.0 1.0
CA B:GLY123 4.6 12.7 1.0
H3' B:ANP501 4.6 20.0 1.0
CA B:ASN51 4.6 15.6 1.0
N B:ASN51 4.7 14.2 1.0
N B:GLY123 4.7 13.8 1.0
O2A B:ANP501 4.9 18.6 1.0
OD1 B:ASP54 4.9 20.2 1.0
N B:SER124 4.9 15.8 1.0

Magnesium binding site 4 out of 4 in 5j5p

Go back to Magnesium Binding Sites List in 5j5p
Magnesium binding site 4 out of 4 in the Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:67.5
occ:1.00
 O B:HOH947 2.2 61.2 1.0
O B:HOH788 2.2 49.5 1.0
O B:HOH635 2.2 52.3 1.0
OD1 B:ASP345 3.4 28.2 1.0
OD2 B:ASP345 4.0 33.8 1.0
CG B:ASP345 4.1 30.3 1.0
O B:HOH956 4.1 33.8 1.0
O B:HOH796 4.3 24.4 1.0
NZ B:LYS281 4.4 46.6 1.0
ND1 B:HIS43 4.4 40.0 1.0
O B:THR343 4.6 21.5 1.0
CE B:LYS281 4.6 38.3 1.0
CB B:THR343 4.7 29.0 1.0
CG2 B:THR343 4.9 32.9 1.0
O B:HOH700 4.9 37.2 1.0
O B:HOH709 4.9 21.8 1.0
O B:HOH672 4.9 24.0 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: Mon Dec 14 20:32:47 2020

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