Magnesium in PDB 9f28: Crystal Structure of the Heterodimeric Primase From Pyrococcus Abyssi (Deletion of the Pril-Ctd Domain)

The structure of Crystal Structure of the Heterodimeric Primase From Pyrococcus Abyssi (Deletion of the Pril-Ctd Domain), PDB code: 9f28 was solved by C.Madru, L.Sauguet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.51 / 1.85
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	116.574, 116.574, 121.084, 90, 90, 90
R / Rfree (%)	19.9 / 22.4

The structure of Crystal Structure of the Heterodimeric Primase From Pyrococcus Abyssi (Deletion of the Pril-Ctd Domain) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Heterodimeric Primase From Pyrococcus Abyssi (Deletion of the Pril-Ctd Domain) (pdb code 9f28). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Heterodimeric Primase From Pyrococcus Abyssi (Deletion of the Pril-Ctd Domain), PDB code: 9f28:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Heterodimeric Primase From Pyrococcus Abyssi (Deletion of the Pril-Ctd Domain)


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 Heterodimeric Primase From Pyrococcus Abyssi (Deletion of the Pril-Ctd Domain) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:40.4 occ:1.00 OD1 A:ASP95 2.5 37.7 1.0 OG A:SER146 2.6 28.3 1.0 O A:HOH768 2.9 57.5 1.0 O A:ILE96 3.5 27.9 1.0 O A:HOH583 3.5 45.2 1.0 CB A:SER146 3.6 25.4 1.0 CG A:ASP95 3.7 36.9 1.0 NE2 A:HIS151 3.7 23.6 1.0 N A:TYR150 3.7 23.8 1.0 CA A:GLY149 3.7 27.9 1.0 O A:HOH644 3.8 41.7 1.0 CD2 A:HIS151 3.8 22.8 1.0 C A:GLY149 3.8 25.3 1.0 CA A:ASP97 3.9 32.6 1.0 C A:ILE96 4.0 29.6 1.0 N A:GLY149 4.0 29.0 1.0 OD2 A:ASP95 4.1 41.8 1.0 CB A:ASP97 4.1 35.5 1.0 N A:ASP97 4.2 30.7 1.0 O A:TYR150 4.2 22.3 1.0 C A:ARG148 4.4 30.6 1.0 C A:TYR150 4.4 21.5 1.0 O A:ARG148 4.5 30.5 1.0 O A:GLY149 4.5 24.6 1.0 N A:ILE96 4.5 26.8 1.0 CG A:ASP97 4.5 41.4 1.0 CA A:TYR150 4.6 22.8 1.0 CE1 A:HIS151 4.8 24.2 1.0 OD1 A:ASP97 4.8 40.7 1.0 CB A:ASP95 4.9 29.2 1.0 CG A:HIS151 4.9 22.7 1.0 CA A:SER146 5.0 24.4 1.0 CA A:ILE96 5.0 28.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Heterodimeric Primase From Pyrococcus Abyssi (Deletion of the Pril-Ctd Domain)


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 Heterodimeric Primase From Pyrococcus Abyssi (Deletion of the Pril-Ctd Domain) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:35.7 occ:1.00 N A:ARG292 2.9 21.5 1.0 O A:HOH517 3.0 38.4 1.0 O A:HOH583 3.1 45.2 1.0 CE1 A:HIS151 3.3 24.2 1.0 O A:HOH610 3.4 34.7 1.0 CA A:LEU291 3.6 23.6 1.0 CB A:ARG292 3.6 20.9 1.0 C A:LEU291 3.7 22.2 1.0 NE2 A:HIS151 3.7 23.6 1.0 CA A:ARG292 3.8 20.5 1.0 CD2 A:LEU291 4.0 25.9 1.0 CE2 A:TYR72 4.1 25.8 1.0 CB A:LEU291 4.3 23.8 1.0 CD2 A:TYR72 4.3 25.2 1.0 O A:HOH664 4.4 53.1 1.0 O A:ILE290 4.5 26.2 1.0 ND1 A:HIS151 4.5 24.3 1.0 O A:HOH641 4.5 57.4 1.0 CG A:LEU291 4.8 25.1 1.0 N A:LEU291 4.8 24.6 1.0 NE A:ARG292 4.8 25.4 1.0 O A:LEU291 4.9 21.9 1.0 CG A:ARG292 5.0 20.8 1.0

M.Martinez-Carranza, L.Vialle, C.Madru, F.Cordier, A.Diskirici Tekpinar, A.Haouz, P.Legrand, R.A.Le Meur, P.England, R.Dulermo, I.Guijarro, G.Henneke, L.Sauguet. Communication Between Dna Polymerases and Replication Protein A Within the Archaeal Replisome To Be Published.