Magnesium in PDB 4you: Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.20A Resolution.

The structure of Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.20A Resolution., PDB code: 4you was solved by K.Miyazono, K.Tsutsumi, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.940, 88.980, 93.950, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.3

The binding sites of Magnesium atom in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.20A Resolution. (pdb code 4you). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.20A Resolution., PDB code: 4you:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.20A Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.20A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:46.4 occ:1.00 OD1 A:ASP80 1.9 47.9 1.0 O A:HOH434 2.0 43.6 1.0 O A:HOH432 2.0 50.0 1.0 O A:HOH433 2.0 47.3 1.0 O A:HOH438 2.1 46.4 1.0 OD1 A:ASP7 2.1 38.7 1.0 CG A:ASP7 3.0 35.2 1.0 CG A:ASP80 3.0 36.5 1.0 OD2 A:ASP7 3.3 38.2 1.0 CB A:ASP80 3.5 31.4 1.0 NZ A:LYS136 3.8 68.3 1.0 OE2 A:GLU61 3.9 36.2 1.0 OD2 A:ASP80 4.1 37.7 1.0 O A:ASP80 4.2 43.1 1.0 CB A:ASP7 4.3 26.6 1.0 O A:THR8 4.3 40.1 1.0 N A:THR8 4.4 27.8 1.0 OE1 A:GLU61 4.5 41.6 1.0 CD A:GLU61 4.5 32.7 1.0 CA A:ASP7 4.7 32.9 1.0 CA A:ASP80 4.9 27.9 1.0 CE A:LYS136 4.9 66.7 1.0 C A:ASP80 5.0 35.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.20A Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.20A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:59.0 occ:1.00 O B:HOH427 2.1 50.3 1.0 OD1 B:ASP80 2.2 59.9 1.0 OD1 B:ASP7 2.2 38.5 1.0 O B:HOH426 2.6 45.5 1.0 CG B:ASP7 3.3 42.1 1.0 CG B:ASP80 3.3 53.0 1.0 OD2 B:ASP7 3.6 51.6 1.0 OE2 B:GLU61 3.7 64.1 1.0 CB B:ASP80 4.0 54.1 1.0 O B:THR8 4.3 49.1 1.0 N B:THR8 4.3 44.5 1.0 OD2 B:ASP80 4.4 44.9 1.0 CD B:GLU61 4.6 63.4 1.0 CB B:ASP7 4.6 42.2 1.0 OE1 B:GLU61 4.6 74.0 1.0 CA B:ASP7 4.8 41.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.20A Resolution.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 2.20A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:47.2 occ:1.00 OD1 C:ASP80 1.9 47.6 1.0 OD1 C:ASP7 2.0 42.2 1.0 O C:HOH423 2.0 45.6 1.0 O C:HOH419 2.0 46.9 1.0 O C:HOH418 2.0 44.1 1.0 O C:HOH417 2.1 35.5 1.0 CG C:ASP7 2.9 41.1 1.0 CG C:ASP80 3.0 39.5 1.0 OD2 C:ASP7 3.1 43.6 1.0 CB C:ASP80 3.5 34.5 1.0 OE2 C:GLU61 3.6 44.6 1.0 OD2 C:ASP80 4.1 37.5 1.0 O C:THR8 4.2 48.1 1.0 CB C:ASP7 4.3 32.7 1.0 N C:THR8 4.3 27.8 1.0 OE1 C:GLU61 4.3 44.3 1.0 CD C:GLU61 4.3 41.8 1.0 O C:ASP80 4.4 38.0 1.0 NZ C:LYS136 4.5 56.7 1.0 CA C:ASP7 4.6 35.3 1.0 CA C:ASP80 4.9 38.0 1.0

K.Miyazono, S.Ishino, K.Tsutsumi, T.Ito, Y.Ishino, M.Tanokura. Structural Basis For Substrate Recognition and Processive Cleavage Mechanisms of the Trimeric Exonuclease Phoexo I Nucleic Acids Res. V. 43 7122 2015.
ISSN: ESSN 1362-4962
PubMed: 26138487
DOI: 10.1093/NAR/GKV654