Magnesium in PDB 8jmk: Structure of Helicobacter Pylori Soj Mutant, D41A Bound to Dna

The structure of Structure of Helicobacter Pylori Soj Mutant, D41A Bound to Dna, PDB code: 8jmk was solved by C.T.Wu, 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)	27.88 / 2.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	75.2, 75.198, 81.124, 71.25, 71.38, 67.7
R / Rfree (%)	22.4 / 30.3

The binding sites of Magnesium atom in the Structure of Helicobacter Pylori Soj Mutant, D41A Bound to Dna (pdb code 8jmk). 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 Mutant, D41A Bound to Dna, PDB code: 8jmk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Helicobacter Pylori Soj Mutant, D41A 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 Mutant, D41A Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:30.7 occ:1.00 O1B A:ATP501 2.2 29.1 1.0 O1G A:ATP501 2.3 23.4 1.0 OG1 A:THR18 2.7 24.2 1.0 PG A:ATP501 3.2 26.9 1.0 PB A:ATP501 3.3 22.3 1.0 O3B A:ATP501 3.4 22.3 1.0 CB A:THR18 3.4 34.9 1.0 O2G A:ATP501 3.6 23.0 1.0 O2A A:ATP501 4.0 21.6 1.0 ND2 A:ASN45 4.1 23.4 1.0 N A:THR18 4.2 30.2 1.0 O2B A:ATP501 4.3 25.8 1.0 CB A:ASN45 4.3 24.1 1.0 CA A:THR18 4.4 23.8 1.0 O3A A:ATP501 4.4 28.9 1.0 OD2 A:ASP130 4.4 25.6 1.0 CG2 A:THR18 4.5 23.8 1.0 O3G A:ATP501 4.6 22.9 1.0 PA A:ATP501 4.6 30.4 1.0 CG A:ASN45 4.7 24.0 1.0 OD1 A:ASP130 4.7 35.5 1.0 O1A A:ATP501 4.8 39.8 1.0 NZ A:LYS17 5.0 24.3 1.0

Magnesium binding site 2 out of 4 in the Structure of Helicobacter Pylori Soj Mutant, D41A 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 Mutant, D41A Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:40.7 occ:1.00 O1B B:ATP301 2.2 34.3 1.0 OG1 B:THR18 2.2 38.2 1.0 O1G B:ATP301 2.2 34.9 1.0 CB B:THR18 3.2 24.9 1.0 PG B:ATP301 3.2 30.3 1.0 PB B:ATP301 3.4 47.0 1.0 O2G B:ATP301 3.6 23.4 1.0 O3B B:ATP301 3.7 37.1 1.0 ND2 B:ASN45 3.8 39.0 1.0 OD2 B:ASP130 4.1 43.6 1.0 O2A B:ATP301 4.1 22.9 1.0 N B:THR18 4.1 48.1 1.0 CA B:THR18 4.2 25.0 1.0 CG2 B:THR18 4.2 25.4 1.0 CB B:ASN45 4.3 31.6 1.0 O2B B:ATP301 4.5 23.0 1.0 O3A B:ATP301 4.5 52.3 1.0 O3G B:ATP301 4.6 27.7 1.0 CG B:ASN45 4.6 37.1 1.0 PA B:ATP301 4.6 22.6 1.0 OD1 B:ASP130 4.7 26.2 1.0 CG B:ASP130 4.8 36.1 1.0 NZ A:LYS12 4.8 24.9 1.0 CE B:LYS17 4.9 24.3 1.0 CB B:LYS17 4.9 24.5 1.0 O1A B:ATP301 4.9 29.3 1.0

Magnesium binding site 3 out of 4 in the Structure of Helicobacter Pylori Soj Mutant, D41A 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 Mutant, D41A Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg302 b:37.8 occ:1.00 OG1 C:THR18 2.2 38.3 1.0 O1G C:ATP301 2.4 29.5 1.0 O1B C:ATP301 2.4 34.5 1.0 CB C:THR18 3.2 30.9 1.0 PG C:ATP301 3.4 29.2 1.0 PB C:ATP301 3.5 23.2 1.0 O3B C:ATP301 3.6 23.2 1.0 O2G C:ATP301 3.8 24.0 1.0 OD2 C:ASP130 4.0 26.7 1.0 N C:THR18 4.2 31.6 1.0 CG2 C:THR18 4.2 28.3 1.0 ND2 C:ASN45 4.2 24.9 1.0 CA C:THR18 4.2 24.8 1.0 CB C:ASN45 4.3 25.2 1.0 O2A C:ATP301 4.4 22.5 1.0 O2B C:ATP301 4.5 23.4 1.0 OD1 C:ASP130 4.5 39.3 1.0 CG C:LYS17 4.7 36.2 1.0 CG C:ASP130 4.7 36.6 1.0 O3A C:ATP301 4.7 22.5 1.0 O3G C:ATP301 4.7 23.9 1.0 CG C:ASN45 4.8 25.0 1.0 PA C:ATP301 4.8 34.7 1.0 O C:SER131 4.8 63.5 1.0 O1A C:ATP301 4.9 25.5 1.0

Magnesium binding site 4 out of 4 in the Structure of Helicobacter Pylori Soj Mutant, D41A 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 Mutant, D41A Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg302 b:49.7 occ:1.00 O1G D:ATP301 2.0 30.6 1.0 OG1 D:THR18 2.1 37.4 1.0 O1B D:ATP301 2.4 44.9 1.0 CB D:THR18 3.1 25.6 1.0 PG D:ATP301 3.3 30.4 1.0 PB D:ATP301 3.5 41.9 1.0 O3B D:ATP301 3.7 23.7 1.0 ND2 D:ASN45 3.7 54.0 1.0 OD2 D:ASP130 4.0 47.3 1.0 O2G D:ATP301 4.0 24.2 1.0 N D:THR18 4.0 29.6 1.0 CG2 D:THR18 4.1 26.2 1.0 O2A D:ATP301 4.1 23.5 1.0 CB D:ASN45 4.1 26.4 1.0 CA D:THR18 4.1 25.8 1.0 CG D:ASN45 4.4 49.6 1.0 O3G D:ATP301 4.5 30.3 1.0 O2B D:ATP301 4.6 23.8 1.0 O3A D:ATP301 4.6 47.2 1.0 PA D:ATP301 4.7 24.9 1.0 OD1 D:ASP130 4.7 28.2 1.0 CG D:ASP130 4.7 34.7 1.0 NZ C:LYS12 4.9 39.1 1.0 O1A D:ATP301 4.9 27.4 1.0 CB D:LYS17 4.9 25.3 1.0 CE D:LYS17 5.0 25.2 1.0

C.H.Chu, C.T.Wu, M.G.Lin, C.Y.Yen, Y.Z.Wu, C.D.Hsiao, Y.J.Sun. Insights Into the Molecular Mechanism of Parabs System in Chromosome Partition By Hppara and Hpparb Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAE450