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Magnesium in PDB 4fm2: Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant) Bound to A Dsdna, in Edition Mode

Enzymatic activity of Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant) Bound to A Dsdna, in Edition Mode

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

Protein crystallography data

The structure of Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant) Bound to A Dsdna, in Edition Mode, PDB code: 4fm2 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) 44.11 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.730, 115.020, 127.260, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 22.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant) Bound to A Dsdna, in Edition Mode (pdb code 4fm2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant) Bound to A Dsdna, in Edition Mode, PDB code: 4fm2:

Magnesium binding site 1 out of 1 in 4fm2

Go back to Magnesium Binding Sites List in 4fm2
Magnesium binding site 1 out of 1 in the Pyrococcus Abyssi B Family Dna Polymerase (Triple Mutant) 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 (Triple Mutant) Bound to A Dsdna, in Edition Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:57.5
occ:1.00
 OD2 A:ASP315 2.2 76.3 1.0
OE2 A:GLU143 2.4 96.5 1.0
OD2 A:ASP141 2.4 92.9 1.0
CG A:ASP315 3.2 67.1 1.0
CG A:ASP141 3.2 84.8 1.0
CD A:GLU143 3.2 96.5 1.0
OD1 A:ASP141 3.3 86.3 1.0
OE1 A:GLU143 3.4 75.9 1.0
O A:ILE142 3.9 62.1 1.0
CB A:ASP315 3.9 58.6 1.0
OH A:TYR311 4.1 79.0 1.0
OD1 A:ASP315 4.1 68.8 1.0
CE2 A:TYR311 4.4 71.0 1.0
CZ A:TYR311 4.5 78.3 1.0
CG A:GLU143 4.7 80.1 1.0
CB A:ASP141 4.7 64.8 1.0
C A:ILE142 4.8 62.4 1.0

Reference:

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
Page generated: Fri Aug 16 15:11:33 2024

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