Magnesium in PDB 4flu: Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode

All present enzymatic activity of Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode:
2.7.7.7;

The structure of Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode, PDB code: 4flu was solved by J.Gouge, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.00 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.970, 114.420, 128.630, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 21.7

The binding sites of Magnesium atom in the Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode (pdb code 4flu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode, PDB code: 4flu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:32.2 occ:1.00 O A:HOH919 1.9 28.4 1.0 O A:HOH921 2.0 45.5 1.0 O A:HOH920 2.7 10.6 1.0 OE1 A:GLU251 3.6 54.7 1.0 OD2 A:ASP343 4.1 27.4 1.0 O A:ALA5 4.1 13.1 1.0 OD1 A:ASP4 4.1 24.1 1.0 O A:HOH941 4.3 20.4 1.0 OD2 A:ASP4 4.3 41.8 1.0 OD1 A:ASP343 4.4 28.8 1.0 CD A:GLU251 4.4 61.7 1.0 O1S A:MES803 4.4 77.3 1.0 CE3 A:TRP342 4.5 17.8 1.0 CG A:ASP343 4.7 27.1 1.0 CG A:ASP4 4.7 28.0 1.0 OE2 A:GLU251 4.7 58.9 1.0 CZ3 A:TRP342 4.8 19.3 1.0

Magnesium binding site 2 out of 2 in the Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:3.0 occ:1.00 OE2 A:GLU143 1.9 27.7 1.0 OD2 A:ASP315 1.9 40.4 1.0 OD2 A:ASP141 1.9 47.2 1.0 OP1 P:DG11 1.9 31.4 1.0 CG A:ASP315 2.8 36.8 1.0 CG A:ASP141 2.9 40.5 1.0 CD A:GLU143 3.0 51.5 1.0 CB A:ASP315 3.2 22.4 1.0 OD1 A:ASP141 3.2 43.0 1.0 P P:DG11 3.2 32.2 1.0 OE1 A:GLU143 3.5 68.6 1.0 O A:ILE142 3.7 28.1 1.0 OP2 P:DG11 3.8 32.0 1.0 OD1 A:ASP315 4.0 38.8 1.0 CE2 A:TYR311 4.1 17.2 1.0 O5' P:DG11 4.2 33.9 1.0 CG A:GLU143 4.2 33.3 1.0 CB A:ASP141 4.2 20.3 1.0 O3' P:DG10 4.3 29.5 1.0 C A:ILE142 4.5 25.4 1.0 C5' P:DG11 4.5 34.4 1.0 CD2 A:TYR311 4.7 15.6 1.0 CA A:ASP315 4.7 20.3 1.0 CA A:SER312 4.7 15.6 1.0 N A:ILE142 4.7 16.5 1.0 CZ A:TYR311 4.8 31.7 1.0 OH A:TYR311 4.8 41.6 1.0 O A:SER312 5.0 20.6 1.0

J.Gouge, C.Ralec, G.Henneke, M.Delarue. Molecular Recognition of Canonical and Deaminated Bases By P. Abyssi Family B Dna Polymerase. J.Mol.Biol. V. 423 315 2012.
ISSN: ISSN 0022-2836
PubMed: 22902479
DOI: 10.1016/J.JMB.2012.07.025