Magnesium in PDB 4flz: 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: 4flz 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)	47.04 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.050, 115.150, 128.520, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.4

The binding sites of Magnesium atom in the Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode (pdb code 4flz). 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: 4flz:
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:40.1 occ:1.00 O A:HOH961 1.9 51.7 1.0 OD2 A:ASP315 2.0 78.1 1.0 OD2 A:ASP141 2.1 77.5 1.0 OE2 A:GLU143 2.2 73.2 1.0 O A:HOH959 3.0 41.8 1.0 CG A:ASP141 3.0 71.8 1.0 CG A:ASP315 3.1 68.7 1.0 CD A:GLU143 3.1 85.4 1.0 OD1 A:ASP141 3.2 72.7 1.0 OE1 A:GLU143 3.3 82.7 1.0 CB A:ASP315 3.7 57.1 1.0 O A:ILE142 3.8 64.7 1.0 OD1 A:ASP315 4.0 70.2 1.0 OH A:TYR311 4.2 74.6 1.0 CE2 A:TYR311 4.3 69.4 1.0 CB A:ASP141 4.5 56.2 1.0 CG A:GLU143 4.5 70.5 1.0 CZ A:TYR311 4.5 77.8 1.0 C A:ILE142 4.8 62.8 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:26.5 occ:1.00 OE2 A:GLU251 3.1 0.4 1.0 OP1 T:DG3 3.3 0.2 1.0 OD2 A:ASP343 3.7 64.4 1.0 OD1 A:ASP4 3.7 59.1 1.0 CD A:GLU251 3.7 0.8 1.0 OE1 A:GLU251 3.8 0.9 1.0 O A:ALA5 4.0 54.0 1.0 OD2 A:ASP4 4.1 73.7 1.0 OD1 A:ASP343 4.2 68.6 1.0 CG A:ASP4 4.4 62.0 1.0 CG A:ASP343 4.4 63.6 1.0 CE3 A:TRP342 4.6 44.3 1.0 O T:HOH102 4.7 49.0 1.0 P T:DG3 4.8 0.4 1.0 CG A:GLU251 4.9 75.0 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