Sodium in PDB 5j5p: 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;

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

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

Magnesium

(Mg)

4 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Amp-Pnp-Stabilized Atpase Domain of Topoisomerase IV From Streptococcus Pneumoniae, Complex Type I, PDB code: 5j5p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na502 b:9.4 occ:1.00 O A:GLY121 2.8 17.8 1.0 O A:ILE98 2.8 15.9 1.0 O1A A:ANP501 2.9 16.9 1.0 O A:ILE101 2.9 18.5 1.0 O A:ALA104 2.9 17.8 1.0 OG A:SER125 3.1 18.4 1.0 H5'1 A:ANP501 3.4 21.9 1.0 C A:GLY121 3.6 16.9 1.0 CB A:SER125 3.8 16.7 1.0 C A:ILE98 3.8 19.0 1.0 C A:ALA104 4.0 19.4 1.0 H5'2 A:ANP501 4.0 21.9 1.0 N A:ALA104 4.1 14.8 1.0 C A:ILE101 4.1 20.6 1.0 C5' A:ANP501 4.1 18.2 1.0 CB A:ALA104 4.2 21.8 1.0 CA A:ILE98 4.2 18.3 1.0 CA A:VAL122 4.2 16.7 1.0 N A:VAL122 4.2 14.7 1.0 PA A:ANP501 4.2 15.2 1.0 O A:VAL97 4.3 19.8 1.0 N A:SER125 4.3 11.7 1.0 CA A:ALA104 4.3 21.1 1.0 CA A:GLY121 4.4 15.5 1.0 C A:VAL122 4.5 14.7 1.0 O5' A:ANP501 4.6 18.2 1.0 O A:VAL122 4.6 17.6 1.0 O3A A:ANP501 4.7 13.7 1.0 CA A:SER125 4.7 16.6 1.0 CA A:LEU102 4.7 17.8 1.0 N A:HIS103 4.7 17.3 1.0 N A:LEU102 4.9 19.8 1.0 N A:ILE101 4.9 18.2 1.0 N A:PHE99 5.0 18.9 1.0 C A:LEU102 5.0 19.3 1.0

Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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 B:Na502 b:7.3 occ:1.00 O B:GLY121 2.7 15.1 1.0 O2A B:ANP501 2.8 18.6 1.0 O B:ILE98 2.8 16.7 1.0 O B:ILE101 2.9 15.5 1.0 OG B:SER125 3.0 18.2 1.0 O B:ALA104 3.0 14.0 1.0 H5'1 B:ANP501 3.5 20.1 1.0 C B:GLY121 3.6 15.0 1.0 CB B:SER125 3.8 15.5 1.0 C B:ILE98 3.8 16.3 1.0 H5'2 B:ANP501 3.9 20.1 1.0 C B:ILE101 4.0 16.1 1.0 C B:ALA104 4.0 17.5 1.0 N B:ALA104 4.1 12.8 1.0 C5' B:ANP501 4.1 16.8 1.0 CA B:VAL122 4.2 14.8 1.0 CA B:ILE98 4.2 13.8 1.0 PA B:ANP501 4.2 14.3 1.0 N B:VAL122 4.2 12.3 1.0 N B:SER125 4.2 11.6 1.0 CB B:ALA104 4.3 17.7 1.0 O B:VAL97 4.4 17.5 1.0 CA B:ALA104 4.4 18.7 1.0 C B:VAL122 4.5 13.7 1.0 CA B:GLY121 4.5 12.5 1.0 O5' B:ANP501 4.6 16.6 1.0 O3A B:ANP501 4.6 13.2 1.0 O B:VAL122 4.6 14.0 1.0 CA B:SER125 4.7 12.0 1.0 CA B:LEU102 4.7 18.5 1.0 N B:HIS103 4.7 14.7 1.0 N B:LEU102 4.8 16.5 1.0 N B:ILE101 4.9 18.2 1.0 C B:LEU102 4.9 17.3 1.0

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