Magnesium in PDB 4flw: 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: 4flw 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 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.029, 114.492, 127.796, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 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 4flw). 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: 4flw:
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:34.1 occ:1.00 O A:HOH906 2.0 34.9 1.0 O A:HOH901 2.0 26.9 1.0 O A:HOH903 2.0 32.1 1.0 O A:HOH902 2.1 25.6 1.0 O A:HOH904 2.1 30.4 1.0 O A:HOH905 2.1 25.3 1.0 OE1 A:GLU251 3.6 45.2 1.0 O A:HOH1032 3.9 37.1 1.0 O A:HOH963 4.0 24.7 1.0 O A:HOH924 4.0 43.4 1.0 OD2 A:ASP343 4.1 33.7 1.0 OD1 A:ASP4 4.2 34.5 1.0 O A:ALA5 4.2 30.3 1.0 OD1 A:ASP343 4.3 37.5 1.0 CE3 A:TRP342 4.3 25.1 1.0 OD2 A:ASP4 4.3 41.2 1.0 O A:HOH1027 4.4 34.5 1.0 O1S A:MES803 4.4 47.8 1.0 CD A:GLU251 4.4 65.2 1.0 O A:HOH1451 4.6 62.5 1.0 CG A:ASP343 4.6 36.9 1.0 CZ3 A:TRP342 4.6 26.8 1.0 OE2 A:GLU251 4.7 51.1 1.0 CG A:ASP4 4.7 38.8 1.0 CD2 A:TRP342 4.8 23.5 1.0 O A:HOH1195 5.0 40.6 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:15.4 occ:1.00 OE2 A:GLU143 1.9 40.2 1.0 OP1 P:DG11 1.9 38.6 1.0 OD2 A:ASP315 1.9 35.6 1.0 OD2 A:ASP141 1.9 41.3 1.0 CD A:GLU143 2.9 47.7 1.0 CG A:ASP315 2.9 36.5 1.0 CG A:ASP141 2.9 35.3 1.0 P P:DG11 3.2 40.7 1.0 OD1 A:ASP141 3.3 35.0 1.0 CB A:ASP315 3.3 30.0 1.0 OE1 A:GLU143 3.4 36.6 1.0 O A:ILE142 3.6 30.6 1.0 O A:HOH958 3.7 48.2 1.0 O A:HOH965 3.8 40.5 1.0 OP2 P:DG11 3.8 38.7 1.0 O A:HOH953 4.0 38.6 1.0 O5' P:DG11 4.0 42.2 1.0 OD1 A:ASP315 4.0 37.2 1.0 CG A:GLU143 4.1 39.3 1.0 CE2 A:TYR311 4.2 32.3 1.0 O3' P:DG10 4.3 39.1 1.0 CB A:ASP141 4.3 26.5 1.0 C A:ILE142 4.4 29.2 1.0 O A:HOH925 4.4 35.7 1.0 N A:ILE142 4.6 25.6 1.0 CD2 A:TYR311 4.7 32.5 1.0 CZ A:TYR311 4.8 41.0 1.0 CA A:SER312 4.8 29.9 1.0 CA A:ASP315 4.9 28.5 1.0 OH A:TYR311 4.9 44.2 1.0 C5' P:DG11 5.0 45.0 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