Atomistry » Magnesium » PDB 5j2n-5jc8 » 5j5q
Atomistry »
  Magnesium »
    PDB 5j2n-5jc8 »
      5j5q »

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

Go back to Magnesium Binding Sites List in 5j5q
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

Go back to Magnesium Binding Sites List in 5j5q
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

Go back to Magnesium Binding Sites List in 5j5q
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

Go back to Magnesium Binding Sites List in 5j5q
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: Mon Dec 14 20:32:49 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy