Magnesium in PDB 4flt: 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: 4flt 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)	44.02 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.930, 114.400, 128.580, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 20.6

The binding sites of Magnesium atom in the Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode (pdb code 4flt). 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: 4flt:
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:19.5 occ:1.00 O A:HOH1193 2.1 21.8 1.0 O A:HOH1191 2.4 9.9 1.0 O A:HOH1192 2.4 31.5 1.0 O A:HOH1190 2.6 6.6 1.0 OE1 A:GLU251 3.2 61.8 1.0 O A:HOH1024 3.9 32.5 1.0 CD A:GLU251 4.0 57.6 1.0 OD1 A:ASP4 4.2 25.4 1.0 OD2 A:ASP343 4.2 36.1 1.0 OD2 A:ASP4 4.2 48.6 1.0 OE2 A:GLU251 4.3 44.5 1.0 O A:ALA5 4.3 15.1 1.0 CE3 A:TRP342 4.4 8.6 1.0 O1S A:MES803 4.4 0.3 1.0 OD1 A:ASP343 4.5 37.3 1.0 CG A:ASP4 4.7 31.4 1.0 CZ3 A:TRP342 4.7 9.0 1.0 CG A:ASP343 4.8 32.7 1.0 CD2 A:TRP342 4.8 7.9 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 1.8 12.3 1.0 OP1 P:DG11 1.9 37.1 1.0 OD2 A:ASP141 1.9 22.8 1.0 OD2 A:ASP315 1.9 42.4 1.0 CG A:ASP141 2.9 23.0 1.0 CG A:ASP315 2.9 32.6 1.0 CD A:GLU143 2.9 41.8 1.0 OD1 A:ASP141 3.2 27.1 1.0 P P:DG11 3.2 35.1 1.0 CB A:ASP315 3.3 16.6 1.0 OE1 A:GLU143 3.5 46.3 1.0 O A:ILE142 3.6 18.0 1.0 OP2 P:DG11 3.8 33.4 1.0 OD1 A:ASP315 4.0 34.4 1.0 O5' P:DG11 4.1 36.4 1.0 CE2 A:TYR311 4.1 15.7 1.0 CG A:GLU143 4.2 23.9 1.0 CB A:ASP141 4.2 14.8 1.0 O3' P:DG10 4.3 33.6 1.0 C A:ILE142 4.4 17.4 1.0 N A:ILE142 4.7 14.5 1.0 CD2 A:TYR311 4.7 15.1 1.0 CZ A:TYR311 4.8 27.8 1.0 CA A:SER312 4.8 17.9 1.0 O A:HOH1171 4.8 30.7 1.0 CA A:ASP315 4.8 15.2 1.0 OH A:TYR311 4.8 31.0 1.0 C5' P:DG11 4.9 38.4 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