Magnesium in PDB 6iub: Structure of Helicobacter Pylori Soj Protein

The structure of Structure of Helicobacter Pylori Soj Protein, PDB code: 6iub was solved by C.H.Chu, C.Y.Yen, Y.J.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.142, 93.322, 110.892, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 21.3

The binding sites of Magnesium atom in the Structure of Helicobacter Pylori Soj Protein (pdb code 6iub). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Helicobacter Pylori Soj Protein, PDB code: 6iub:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Helicobacter Pylori Soj Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Helicobacter Pylori Soj Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:10.4 occ:1.00 OG1 A:THR18 2.1 8.4 1.0 O1G A:ATP500 2.1 15.9 1.0 O1B A:ATP500 2.1 9.2 1.0 O A:HOH633 2.1 12.5 1.0 O A:HOH645 2.1 13.6 1.0 O A:HOH726 2.2 9.4 1.0 CB A:THR18 3.2 10.6 1.0 PB A:ATP500 3.3 10.9 1.0 PG A:ATP500 3.3 32.1 1.0 O3B A:ATP500 3.5 12.1 1.0 N A:THR18 3.8 9.2 1.0 CA A:THR18 4.0 9.7 1.0 OD2 A:ASP41 4.1 15.1 1.0 OD2 A:ASP130 4.1 10.3 1.0 O2A A:ATP500 4.1 11.4 1.0 O2G A:ATP500 4.2 32.2 1.0 OD1 A:ASP130 4.2 10.0 1.0 OD1 A:ASN45 4.2 17.9 1.0 O A:HOH660 4.2 10.5 1.0 O2B A:ATP500 4.3 10.9 1.0 O3A A:ATP500 4.3 10.9 1.0 CG2 A:THR18 4.3 9.0 1.0 O3G A:ATP500 4.3 25.3 1.0 O A:HOH667 4.4 21.2 1.0 CB A:ASN45 4.5 10.7 1.0 CB A:LYS17 4.6 11.2 1.0 CG A:ASP130 4.6 11.1 1.0 PA A:ATP500 4.6 12.2 1.0 O A:SER131 4.6 9.8 1.0 CE A:LYS17 4.7 13.5 1.0 O1A A:ATP500 4.8 10.8 1.0 CG A:ASN45 4.8 17.6 1.0 C A:LYS17 4.8 9.6 1.0

Magnesium binding site 2 out of 2 in the Structure of Helicobacter Pylori Soj Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Helicobacter Pylori Soj Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:12.3 occ:1.00 O2B B:ATP500 2.1 9.3 1.0 O B:HOH643 2.1 15.1 1.0 O B:HOH646 2.2 12.8 1.0 OG1 B:THR18 2.2 11.4 1.0 O B:HOH657 2.2 11.1 1.0 O3G B:ATP500 2.2 18.2 1.0 CB B:THR18 3.2 10.8 1.0 PB B:ATP500 3.3 11.8 1.0 PG B:ATP500 3.4 17.3 1.0 O3B B:ATP500 3.5 11.7 1.0 N B:THR18 3.8 13.1 1.0 OD2 B:ASP41 3.9 21.6 1.0 CA B:THR18 4.0 11.7 1.0 OD2 B:ASP130 4.1 11.5 1.0 O1A B:ATP500 4.2 13.3 1.0 O1G B:ATP500 4.2 18.8 1.0 OD1 B:ASP130 4.2 14.1 1.0 O B:HOH697 4.2 20.2 1.0 O1B B:ATP500 4.3 12.2 1.0 ND2 B:ASN45 4.3 10.6 1.0 CG2 B:THR18 4.4 10.2 1.0 O B:HOH638 4.4 11.5 1.0 O3A B:ATP500 4.4 12.1 1.0 O2G B:ATP500 4.5 18.8 1.0 CB B:LYS17 4.5 13.6 1.0 CG B:ASP130 4.6 16.7 1.0 CB B:ASN45 4.6 12.2 1.0 O B:SER131 4.7 14.2 1.0 CE B:LYS17 4.7 11.8 1.0 PA B:ATP500 4.7 12.6 1.0 C B:LYS17 4.8 13.8 1.0 O2A B:ATP500 4.9 13.0 1.0 CG B:ASP41 4.9 18.0 1.0 CG B:ASN45 5.0 13.8 1.0

C.H.Chu, C.Y.Yen, B.W.Chen, M.G.Lin, L.H.Wang, K.Z.Tang, C.D.Hsiao, Y.J.Sun. Crystal Structures of Hpsoj-Dna Complexes and the Nucleoid-Adaptor Complex Formation in Chromosome Segregation. Nucleic Acids Res. V. 47 2113 2019.
ISSN: ESSN 1362-4962
PubMed: 30544248
DOI: 10.1093/NAR/GKY1251