Magnesium in PDB 6iud: Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna

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

Resolution Low / High (Å)	29.96 / 2.51
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	74.773, 74.690, 80.749, 71.54, 71.59, 67.73
R / Rfree (%)	20.5 / 25.8

The binding sites of Magnesium atom in the Structure of Helicobacter Pylori Soj-Adp Complex Bound to Dna (pdb code 6iud). 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-Adp Complex Bound to Dna, PDB code: 6iud:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Helicobacter Pylori Soj-Adp 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-Adp Complex Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:56.7 occ:1.00 OG1 A:THR18 2.3 44.3 1.0 O1B A:ADP500 2.4 38.6 1.0 O3B A:ADP500 3.4 37.0 1.0 PB A:ADP500 3.4 37.5 1.0 OD1 A:ASP41 3.5 39.8 1.0 CB A:THR18 3.6 44.3 1.0 NE2 A:GLN43 3.8 41.9 1.0 ND2 A:ASN45 4.0 39.0 1.0 O2A A:ADP500 4.2 40.6 1.0 NZ B:LYS12 4.3 68.5 1.0 N A:THR18 4.4 52.4 1.0 OD2 A:ASP130 4.4 50.7 1.0 CG2 A:THR18 4.5 36.3 1.0 OD1 A:ASP130 4.5 57.5 1.0 O2B A:ADP500 4.5 36.1 1.0 CA A:THR18 4.5 35.2 1.0 O3A A:ADP500 4.5 38.3 1.0 CB A:ASN45 4.6 38.0 1.0 O A:SER131 4.6 49.8 1.0 CG A:ASP41 4.6 62.3 1.0 CG A:ASN45 4.6 38.3 1.0 CE A:LYS17 4.7 36.2 1.0 CD A:GLN43 4.8 85.6 1.0 PA A:ADP500 4.8 40.1 1.0 CG A:ASP130 4.9 56.4 1.0 NZ A:LYS17 4.9 35.8 1.0 CB A:ASP41 5.0 62.1 1.0

Magnesium binding site 2 out of 4 in the Structure of Helicobacter Pylori Soj-Adp 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-Adp Complex Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:64.6 occ:1.00 OG1 B:THR18 2.0 55.6 1.0 O2B B:ADP500 2.3 55.5 1.0 OD1 B:ASP41 3.3 41.4 1.0 CB B:THR18 3.3 42.1 1.0 PB B:ADP500 3.6 49.1 1.0 O3B B:ADP500 3.9 52.5 1.0 OD1 B:ASP130 3.9 38.3 1.0 OD2 B:ASP130 3.9 53.9 1.0 N B:THR18 4.1 36.4 1.0 CG2 B:THR18 4.1 38.6 1.0 CA B:THR18 4.2 37.1 1.0 NZ B:LYS17 4.2 52.4 1.0 CG B:ASP130 4.4 60.8 1.0 CG B:ASP41 4.5 52.0 1.0 O B:SER131 4.5 51.1 1.0 O2A B:ADP500 4.5 46.8 1.0 O1B B:ADP500 4.5 51.5 1.0 OD1 B:ASN45 4.6 56.4 1.0 O3A B:ADP500 4.6 48.5 1.0 CB B:LYS17 4.6 36.2 1.0 CB B:ASN45 4.7 40.6 1.0 CB B:ASP41 4.8 42.4 1.0 NZ A:LYS12 4.9 34.5 1.0 C B:LYS17 5.0 37.1 1.0

Magnesium binding site 3 out of 4 in the Structure of Helicobacter Pylori Soj-Adp 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-Adp Complex Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:50.9 occ:1.00 OG1 C:THR18 2.3 66.9 1.0 O2B C:ADP500 2.8 42.6 1.0 OD1 C:ASP41 3.3 50.8 1.0 CB C:THR18 3.5 45.0 1.0 O3B C:ADP500 3.8 42.8 1.0 PB C:ADP500 3.9 43.1 1.0 ND2 C:ASN45 3.9 41.3 1.0 OD1 C:ASP130 4.0 44.7 1.0 CB C:ASN45 4.3 38.4 1.0 CG C:ASP41 4.3 46.4 1.0 CG2 C:THR18 4.4 36.4 1.0 OD2 C:ASP130 4.4 49.8 1.0 O C:SER131 4.5 50.2 1.0 N C:THR18 4.5 42.0 1.0 CG C:ASN45 4.5 45.3 1.0 O1A C:ADP500 4.5 39.0 1.0 CA C:THR18 4.5 34.5 1.0 CG C:ASP130 4.6 58.3 1.0 CB C:ASP41 4.7 85.0 1.0 O1B C:ADP500 5.0 41.6 1.0 O3A C:ADP500 5.0 40.1 1.0

Magnesium binding site 4 out of 4 in the Structure of Helicobacter Pylori Soj-Adp 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-Adp Complex Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:60.0 occ:1.00 OG1 D:THR18 2.2 40.7 1.0 O1B D:ADP500 2.2 42.4 1.0 PB D:ADP500 3.4 41.6 1.0 OD2 D:ASP41 3.4 71.6 1.0 CB D:THR18 3.4 36.9 1.0 O3B D:ADP500 3.5 43.2 1.0 NZ D:LYS17 3.9 55.3 1.0 N D:THR18 4.1 35.1 1.0 OD1 D:ASN45 4.2 39.6 1.0 OD1 D:ASP130 4.3 36.5 1.0 CA D:THR18 4.3 36.0 1.0 OD2 D:ASP130 4.3 38.7 1.0 O2B D:ADP500 4.4 41.5 1.0 CG2 D:THR18 4.4 37.8 1.0 O1A D:ADP500 4.5 39.8 1.0 O3A D:ADP500 4.5 38.8 1.0 O D:SER131 4.5 64.3 1.0 CG D:ASP41 4.6 56.8 1.0 CG D:ASP130 4.7 55.4 1.0 CB D:ASN45 4.7 40.4 1.0 CB D:LYS17 4.7 34.5 1.0 CG D:ASN45 4.8 40.6 1.0 PA D:ADP500 4.9 38.4 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