Magnesium in PDB 6iuc: Structure of Helicobacter Pylori Soj-Atp Complex Bound to Dna

The structure of Structure of Helicobacter Pylori Soj-Atp Complex Bound to Dna, PDB code: 6iuc 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)	26.79 / 3.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	74.418, 74.628, 80.351, 71.38, 71.56, 67.83
R / Rfree (%)	20.2 / 26.3

The binding sites of Magnesium atom in the Structure of Helicobacter Pylori Soj-Atp Complex Bound to Dna (pdb code 6iuc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Helicobacter Pylori Soj-Atp Complex Bound to Dna, PDB code: 6iuc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Helicobacter Pylori Soj-Atp Complex Bound to Dna


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-Atp Complex Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:75.1 occ:1.00 O1G A:ATP500 2.1 74.8 1.0 OG1 A:THR18 2.1 75.2 1.0 OD2 A:ASP41 3.0 90.3 1.0 O1B A:ATP500 3.0 74.3 1.0 PG A:ATP500 3.3 74.5 1.0 CB A:THR18 3.4 74.9 1.0 O2G A:ATP500 3.8 74.4 1.0 O3B A:ATP500 4.0 74.0 1.0 PB A:ATP500 4.0 74.1 1.0 CG2 A:THR18 4.1 75.0 1.0 CG A:ASP41 4.1 88.9 1.0 OD2 A:ASP130 4.3 76.2 1.0 OD1 A:ASP130 4.4 76.3 1.0 ND2 A:ASN45 4.5 74.5 1.0 CA A:THR18 4.5 75.1 1.0 N A:THR18 4.5 75.0 1.0 O A:SER131 4.5 76.5 1.0 CB A:ASN45 4.5 75.0 1.0 O2A A:ATP500 4.5 77.8 1.0 O3G A:ATP500 4.6 74.6 1.0 CB A:ASP41 4.6 83.1 1.0 O2B A:ATP500 4.7 76.3 1.0 CG A:ASP130 4.8 76.5 1.0 CG A:ASN45 5.0 74.8 1.0

Magnesium binding site 2 out of 4 in the Structure of Helicobacter Pylori Soj-Atp Complex Bound to Dna


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-Atp Complex Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:75.7 occ:1.00 OG1 B:THR18 2.0 75.7 1.0 O3G B:ATP500 2.1 75.1 1.0 O2B B:ATP500 3.2 74.7 1.0 OD2 B:ASP41 3.2 76.5 1.0 CB B:THR18 3.4 75.5 1.0 PG B:ATP500 3.5 74.8 1.0 ND2 B:ASN45 3.5 75.9 1.0 OD2 B:ASP130 3.7 76.7 1.0 OD1 B:ASP130 3.7 76.2 1.0 CB B:ASN45 4.0 76.4 1.0 CG B:ASP130 4.1 76.6 1.0 CG B:ASP41 4.1 76.9 1.0 O2G B:ATP500 4.1 74.9 1.0 PB B:ATP500 4.2 74.3 1.0 O3B B:ATP500 4.2 74.3 1.0 CG2 B:THR18 4.3 75.7 1.0 CG B:ASN45 4.3 76.2 1.0 CA B:THR18 4.3 75.5 1.0 CB B:ASP41 4.3 77.3 1.0 N B:THR18 4.3 75.1 1.0 O B:SER131 4.4 76.8 1.0 O1B B:ATP500 4.7 74.3 1.0 O1G B:ATP500 4.7 74.5 1.0

Magnesium binding site 3 out of 4 in the Structure of Helicobacter Pylori Soj-Atp Complex Bound to Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Helicobacter Pylori Soj-Atp Complex Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:75.8 occ:1.00 O2G C:ATP500 2.1 90.6 1.0 OG1 C:THR18 2.1 75.7 1.0 OD2 C:ASP41 2.7 76.6 1.0 O2B C:ATP500 3.2 74.9 1.0 CB C:THR18 3.2 75.3 1.0 PG C:ATP500 3.6 93.7 1.0 ND2 C:ASN45 3.6 75.5 1.0 CG C:ASP41 3.8 77.1 1.0 CG2 C:THR18 3.9 75.4 1.0 CB C:ASN45 3.9 75.8 1.0 OD2 C:ASP130 4.0 76.7 1.0 O3B C:ATP500 4.1 82.2 1.0 CB C:ASP41 4.2 78.3 1.0 PB C:ATP500 4.3 74.6 1.0 CG C:ASN45 4.3 75.7 1.0 O1G C:ATP500 4.3 97.0 1.0 CA C:THR18 4.4 75.4 1.0 O1A C:ATP500 4.5 74.2 1.0 N C:THR18 4.5 75.3 1.0 O3G C:ATP500 4.6 0.9 1.0 OD1 C:ASP130 4.6 76.6 1.0 O C:SER131 4.7 77.0 1.0 CG C:ASP130 4.7 76.9 1.0 OD1 C:ASP41 4.8 77.4 1.0

Magnesium binding site 4 out of 4 in the Structure of Helicobacter Pylori Soj-Atp Complex Bound to Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Helicobacter Pylori Soj-Atp Complex Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:76.5 occ:1.00 O1G D:ATP500 2.0 75.9 1.0 OG1 D:THR18 2.0 76.3 1.0 OD2 D:ASP41 3.0 77.3 1.0 PG D:ATP500 3.4 75.5 1.0 CB D:THR18 3.4 76.2 1.0 O1B D:ATP500 3.5 75.3 1.0 ND2 D:ASN45 3.7 76.4 1.0 CG D:ASP41 3.9 77.7 1.0 O3G D:ATP500 3.9 75.6 1.0 OD1 D:ASP130 4.0 77.2 1.0 OD2 D:ASP130 4.0 77.5 1.0 CG2 D:THR18 4.0 76.5 1.0 O D:SER131 4.1 77.2 1.0 CB D:ASN45 4.2 77.0 1.0 O3B D:ATP500 4.2 75.0 1.0 PB D:ATP500 4.3 75.0 1.0 CB D:ASP41 4.3 78.2 1.0 CG D:ASP130 4.4 77.5 1.0 CG D:ASN45 4.5 76.8 1.0 CA D:THR18 4.5 76.3 1.0 N D:THR18 4.6 76.0 1.0 O2G D:ATP500 4.6 75.3 1.0 O2B D:ATP500 4.7 75.1 1.0 OD1 D:ASP41 4.9 78.0 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