Manganese in PDB 4fm1: 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: 4fm1 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)	44.01 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.070, 114.220, 128.190, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 22.6

The binding sites of Manganese atom in the Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode (pdb code 4fm1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Pyrococcus Abyssi B Family Dna Polymerase Bound to A Dsdna, in Edition Mode, PDB code: 4fm1:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn803 b:60.4 occ:1.00 O A:HOH1099 2.5 20.2 1.0 O A:HOH1100 2.5 29.1 1.0 OE1 A:GLU251 3.6 58.8 1.0 O A:ALA5 4.1 22.0 1.0 OD1 A:ASP4 4.1 54.6 1.0 OD2 A:ASP4 4.2 56.8 1.0 O A:HOH1031 4.3 18.6 1.0 OD2 A:ASP343 4.4 23.1 1.0 O1S A:MES802 4.4 37.0 1.0 CD A:GLU251 4.5 79.6 1.0 CG A:ASP4 4.6 51.4 1.0 O A:HOH1015 4.7 17.1 1.0 OE2 A:GLU251 4.8 87.9 1.0 OD1 A:ASP343 4.9 30.2 1.0 CE3 A:TRP342 4.9 22.0 1.0 CB A:ASP6 4.9 19.5 1.0 O A:HOH955 5.0 24.9 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn804 b:71.6 occ:1.00 OE2 A:GLU143 2.3 62.1 1.0 OD2 A:ASP315 2.4 42.4 1.0 OD2 A:ASP141 2.6 41.8 1.0 CD A:GLU143 3.1 62.0 1.0 OE1 A:GLU143 3.1 53.3 1.0 O A:HOH1138 3.2 30.2 1.0 CG A:ASP141 3.4 46.6 1.0 OD1 A:ASP141 3.4 51.8 1.0 CG A:ASP315 3.5 28.9 1.0 O A:ILE142 3.8 39.5 1.0 OH A:TYR311 4.0 41.0 1.0 CB A:ASP315 4.2 19.7 1.0 CE2 A:TYR311 4.3 34.0 1.0 OD1 A:ASP315 4.3 24.8 1.0 O A:HOH1108 4.4 35.0 1.0 CZ A:TYR311 4.5 41.6 1.0 CG A:GLU143 4.5 45.3 1.0 C A:ILE142 4.8 37.1 1.0 CB A:ASP141 4.8 31.0 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