Atomistry » Magnesium » PDB 5j2n-5jc8 » 5j5p
Atomistry »
  Magnesium »
    PDB 5j2n-5jc8 »
      5j5p »

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: Sun Sep 29 17:36:46 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy