Magnesium in PDB 1nui: Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein

The structure of Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein, PDB code: 1nui was solved by M.Kato, T.Ito, G.Wagner, C.C.Richardson, T.Ellenberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.459, 136.460, 85.445, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 27.7

The structure of Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein (pdb code 1nui). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein, PDB code: 1nui:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:87.2 occ:1.00 OD1 A:ASP207 2.2 28.1 1.0 OE2 A:GLU157 2.5 21.5 1.0 CG A:ASP207 3.3 25.6 1.0 CD A:GLU157 3.7 21.5 1.0 CB A:ASP207 4.1 22.8 1.0 OD2 A:ASP207 4.3 30.6 1.0 OE1 A:GLU157 4.5 22.8 1.0 CG A:GLU157 4.6 16.7 1.0 OD2 A:ASP209 4.7 22.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:88.8 occ:1.00 OD2 A:ASP237 2.5 29.1 1.0 O A:HOH807 2.8 31.6 1.0 NH2 A:ARG84 3.3 32.8 1.0 CG A:ASP237 3.4 24.1 1.0 OD1 A:ASP237 3.5 28.0 1.0 OD2 A:ASP161 4.2 30.5 1.0 CZ A:ARG84 4.4 30.4 1.0 NH1 A:ARG84 4.7 30.2 1.0 CB A:ASP237 4.7 20.6 1.0 CB A:ASN239 4.8 12.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:38.9 occ:1.00 OD1 B:ASP207 2.0 23.0 1.0 OE2 B:GLU157 2.1 16.4 1.0 O B:HOH805 2.3 26.5 1.0 CG B:ASP207 3.0 19.6 1.0 CD B:GLU157 3.1 17.9 1.0 OE1 B:GLU157 3.3 14.5 1.0 OD2 B:ASP209 3.4 24.1 1.0 CB B:ASP207 3.5 18.4 1.0 OD1 B:ASP209 3.9 26.8 1.0 NZ B:LYS236 3.9 21.8 1.0 OD2 B:ASP207 4.0 21.9 1.0 CG B:ASP209 4.1 19.6 1.0 CB B:ALA211 4.4 13.7 1.0 CG B:GLU157 4.5 17.7 1.0 CE B:LYS236 4.7 20.2 1.0 N B:GLY212 4.8 15.0 1.0 CA B:ASP207 4.9 16.7 1.0 CB B:ALA182 4.9 20.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Primase Fragment of Bacteriophage T7 Primase- Helicase Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:45.0 occ:1.00 OD2 B:ASP237 2.3 34.2 1.0 O B:HOH804 3.1 20.8 1.0 CG B:ASP237 3.3 24.2 1.0 OD1 B:ASP237 3.6 28.7 1.0 OD2 B:ASP161 4.1 27.3 1.0 NH1 B:ARG84 4.3 19.1 1.0 NZ B:LYS236 4.5 21.8 1.0 CB B:ASP237 4.6 18.4 1.0 OD1 B:ASP161 4.8 36.1 1.0 O B:HOH801 4.9 24.6 1.0 CG B:ASP161 4.9 26.4 1.0

M.Kato, T.Ito, G.Wagner, C.C.Richardson, T.Ellenberger. Modular Architecture of the Bacteriophage T7 Primase Couples Rna Primer Synthesis to Dna Synthesis Mol.Cell V. 11 1349 2003.
ISSN: ISSN 1097-2765
PubMed: 12769857
DOI: 10.1016/S1097-2765(03)00195-3