Magnesium in PDB 4i3h: A Three-Gate Structure of Topoisomerase IV From Streptococcus Pneumoniae

All present enzymatic activity of A Three-Gate Structure of Topoisomerase IV From Streptococcus Pneumoniae:
5.99.1.3;

The structure of A Three-Gate Structure of Topoisomerase IV From Streptococcus Pneumoniae, PDB code: 4i3h was solved by I.Laponogov, D.A.Veselkov, X.-S.Pan, I.Crevel, 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)	71.82 / 3.70
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	160.600, 160.600, 280.560, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 24.8

The binding sites of Magnesium atom in the A Three-Gate Structure of Topoisomerase IV From Streptococcus Pneumoniae (pdb code 4i3h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the A Three-Gate Structure of Topoisomerase IV From Streptococcus Pneumoniae, PDB code: 4i3h:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the A Three-Gate Structure of Topoisomerase IV From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A Three-Gate Structure of Topoisomerase IV From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1700 b:94.2 occ:1.00 O A:GLN1322 2.0 72.2 1.0 O A:THR1319 2.8 92.5 1.0 O A:PHE1316 2.9 73.2 1.0 C A:GLN1322 3.3 68.5 1.0 O A:LYS1317 3.5 80.6 1.0 C A:PHE1316 4.1 75.3 1.0 C A:THR1319 4.1 90.5 1.0 C A:LYS1317 4.1 81.5 1.0 N A:ILE1323 4.2 71.9 1.0 CA A:GLN1322 4.2 71.5 1.0 CA A:ILE1323 4.3 73.3 1.0 CG A:GLN1322 4.3 90.6 1.0 N A:GLN1322 4.3 74.1 1.0 CB A:GLN1322 4.4 80.8 1.0 CA A:LYS1317 4.6 79.1 1.0 OD1 A:ASP1320 4.7 96.1 1.0 CA A:ASP1320 4.7 85.5 1.0 N A:THR1319 4.7 88.0 1.0 N A:LYS1317 4.8 78.9 1.0 N A:TYR1318 4.9 83.1 1.0 N A:ASP1320 4.9 88.7 1.0 CG2 A:ILE1323 4.9 69.2 1.0

Magnesium binding site 2 out of 3 in the A Three-Gate Structure of Topoisomerase IV From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A Three-Gate Structure of Topoisomerase IV From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1700 b:0.3 occ:1.00 O B:THR1319 2.0 91.0 1.0 O B:GLN1322 2.0 79.0 1.0 O B:PHE1316 3.0 77.3 1.0 C B:GLN1322 3.3 72.0 1.0 C B:THR1319 3.3 85.8 1.0 N B:THR1319 4.0 85.0 1.0 CA B:ASP1320 4.0 78.3 1.0 N B:GLN1322 4.1 67.9 1.0 N B:ASP1320 4.1 83.6 1.0 C B:PHE1316 4.1 78.3 1.0 CA B:GLN1322 4.2 71.8 1.0 N B:ILE1323 4.2 66.5 1.0 CA B:THR1319 4.3 80.1 1.0 C B:LYS1317 4.3 88.4 1.0 CA B:ILE1323 4.3 59.2 1.0 O B:LYS1317 4.3 95.8 1.0 OD1 B:ASP1320 4.5 88.0 1.0 CB B:GLN1322 4.5 74.6 1.0 N B:TYR1318 4.5 85.4 1.0 C B:ASP1320 4.5 62.6 1.0 N B:LEU1321 4.6 64.3 1.0 CG2 B:ILE1323 4.7 55.6 1.0 CA B:LYS1317 4.7 81.7 1.0 C B:TYR1318 4.8 85.2 1.0 O B:LEU1315 4.9 91.2 1.0 N B:LYS1317 4.9 83.4 1.0

Magnesium binding site 3 out of 3 in the A Three-Gate Structure of Topoisomerase IV From Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A Three-Gate Structure of Topoisomerase IV From Streptococcus Pneumoniae within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg1901 b:72.8 occ:1.00 C2 G:DA26 4.1 0.7 1.0 N3 G:DA26 4.3 0.2 1.0 O2 H:DT9 4.3 0.2 1.0 O4' H:DG10 4.5 0.3 1.0 N3 H:DG10 4.8 0.2 1.0

I.Laponogov, D.A.Veselkov, I.M.Crevel, X.S.Pan, L.M.Fisher, M.R.Sanderson. Structure of An 'Open' Clamp Type II Topoisomerase-Dna Complex Provides A Mechanism For Dna Capture and Transport. Nucleic Acids Res. V. 41 9911 2013.
ISSN: ISSN 0305-1048
PubMed: 23965305
DOI: 10.1093/NAR/GKT749