Magnesium in PDB 7rr4: Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Magnesium and Pyrophosphate

The structure of Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Magnesium and Pyrophosphate, PDB code: 7rr4 was solved by L.Wang, C.Yu, P.Sliz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.34 / 1.86
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.34, 56.903, 48.564, 90, 93.6, 90
R / Rfree (%)	21.6 / 23.2

The binding sites of Magnesium atom in the Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Magnesium and Pyrophosphate (pdb code 7rr4). 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 Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Magnesium and Pyrophosphate, PDB code: 7rr4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Magnesium and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Magnesium and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:46.5 occ:1.00 O21 A:PPV303 2.6 74.3 1.0 OD2 A:ASP78 2.7 43.1 1.0 OD1 A:ASP80 2.8 59.4 1.0 O A:HOH436 3.1 45.8 1.0 OG A:SER108 3.4 50.8 1.0 O A:LEU79 3.5 39.4 1.0 CB A:SER108 3.5 42.0 1.0 CG A:ASP78 3.6 49.3 1.0 P1 A:PPV303 3.6 106.0 1.0 O11 A:PPV303 3.7 62.5 1.0 OD1 A:ASP78 3.8 56.7 1.0 CA A:GLY113 3.8 40.4 1.0 O12 A:PPV303 3.9 56.5 1.0 O32 A:PPV303 3.9 76.4 1.0 CA A:ASP80 4.0 46.7 1.0 CG A:ASP80 4.0 52.7 1.0 C A:LEU79 4.0 41.9 1.0 OPP A:PPV303 4.2 67.8 1.0 N A:LEU114 4.2 38.9 1.0 P2 A:PPV303 4.2 77.8 1.0 C A:GLY113 4.3 39.0 1.0 NE2 A:HIS115 4.3 49.5 1.0 N A:ASP80 4.3 39.7 1.0 O A:LEU114 4.4 39.6 1.0 CD2 A:HIS115 4.4 39.7 1.0 CB A:ASP80 4.6 49.2 1.0 N A:LEU79 4.7 40.2 1.0 N A:GLY113 4.7 38.5 1.0 C A:LEU114 4.9 37.4 1.0 CB A:ASP78 5.0 40.7 1.0 N A:HIS81 5.0 46.5 1.0 O31 A:PPV303 5.0 67.5 1.0 OD2 A:ASP80 5.0 58.3 1.0

Magnesium binding site 2 out of 2 in the Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Magnesium and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Deep-Sea Phage Nrs-1 Primase-Polymerase N300 in Complex with Magnesium and Pyrophosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:30.1 occ:1.00 O A:GLU142 2.6 44.0 1.0 O A:THR69 2.6 37.6 1.0 OD1 A:ASP72 2.7 41.3 1.0 O A:PHE74 2.7 38.3 1.0 O A:ASP72 2.9 37.4 1.0 CG A:ASP72 3.5 41.6 1.0 N A:PHE74 3.6 38.3 1.0 C A:GLU142 3.7 33.5 1.0 C A:ASP72 3.7 31.2 1.0 C A:THR69 3.7 41.2 1.0 C A:PHE74 3.7 31.3 1.0 CB A:GLU142 4.0 39.8 1.0 OD2 A:ASP72 4.0 40.8 1.0 CA A:GLU142 4.1 36.9 1.0 CA A:PHE74 4.2 33.0 1.0 C A:PRO73 4.2 38.4 1.0 O A:LYS70 4.4 49.2 1.0 N A:THR69 4.4 43.0 1.0 CA A:LYS70 4.4 48.5 1.0 C A:LYS70 4.4 44.2 1.0 CA A:ASP72 4.5 37.1 1.0 N A:ASP72 4.5 40.0 1.0 N A:LYS70 4.5 41.6 1.0 N A:PRO73 4.5 33.5 1.0 O A:HOH434 4.5 40.8 1.0 CB A:ASP72 4.6 41.6 1.0 CA A:PRO73 4.7 42.0 1.0 CA A:THR69 4.7 42.2 1.0 CB A:PHE74 4.8 31.3 1.0 CB A:LEU68 4.8 40.1 1.0 N A:SER143 4.9 37.4 1.0 O A:PRO73 4.9 40.0 1.0 CD2 A:LEU68 4.9 43.9 1.0 N A:VAL75 4.9 32.6 1.0

F.Huang, X.Lu, C.Yu, P.Sliz, L.Wang, B.Zhu. Molecular Dissection of the Primase and Polymerase Activities of Deep-Sea Phage Nrs-1 Primase-Polymerase Frontiers in Microbiology V. 12 66612 2021.
DOI: 10.3389/FMICB.2021.766612