Magnesium in PDB 4yor: Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 1.52A Resolution.

The structure of Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 1.52A Resolution., PDB code: 4yor 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)	19.70 / 1.52
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	112.065, 112.065, 202.282, 90.00, 90.00, 120.00
R / Rfree (%)	16 / 18

The binding sites of Magnesium atom in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 1.52A Resolution. (pdb code 4yor). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 1.52A Resolution., PDB code: 4yor:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 1.52A 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 1.52A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:22.1 occ:1.00 OD2 A:ASP80 2.0 24.0 1.0 OD1 A:ASP7 2.0 20.8 1.0 O A:HOH590 2.0 41.2 1.0 O A:HOH587 2.1 28.8 1.0 O A:HOH588 2.2 32.8 1.0 O A:HOH589 2.4 37.9 1.0 CG A:ASP7 3.0 25.5 1.0 CG A:ASP80 3.1 25.6 1.0 OD2 A:ASP7 3.3 25.5 1.0 CB A:ASP80 3.8 23.1 1.0 OE2 A:GLU61 4.1 25.7 1.0 OD1 A:ASP80 4.1 24.2 1.0 O A:HOH575 4.2 41.2 1.0 NZ A:LYS136 4.2 43.9 0.6 O A:THR8 4.3 22.4 1.0 CB A:ASP7 4.4 19.0 1.0 N A:THR8 4.4 20.6 1.0 OE1 A:GLU61 4.5 24.1 1.0 O A:ASP80 4.6 25.0 1.0 CD A:GLU61 4.7 24.5 1.0 CA A:ASP7 4.7 15.9 1.0 O A:HOH562 4.9 42.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 at 1.52A 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 1.52A Resolution. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:23.6 occ:1.00 OD2 B:ASP80 2.0 28.2 1.0 O B:HOH568 2.0 30.6 1.0 OD1 B:ASP7 2.1 21.7 1.0 O B:HOH566 2.1 26.7 1.0 O B:HOH565 2.2 32.5 1.0 O B:HOH567 2.2 32.9 1.0 CG B:ASP7 3.0 24.7 1.0 CG B:ASP80 3.2 29.0 1.0 OD2 B:ASP7 3.4 25.5 1.0 CB B:ASP80 3.9 23.8 1.0 O B:HOH551 3.9 39.4 1.0 NZ B:LYS136 4.0 36.1 0.5 O B:HOH553 4.1 54.7 1.0 OD1 B:ASP80 4.2 25.4 1.0 OE2 B:GLU61 4.2 27.1 1.0 O B:THR8 4.3 22.8 1.0 N B:THR8 4.3 20.1 1.0 O B:HOH548 4.4 52.0 1.0 CB B:ASP7 4.4 19.2 1.0 OE1 B:GLU61 4.7 26.4 1.0 CA B:ASP7 4.7 18.0 1.0 O B:ASP80 4.8 29.1 1.0 CD B:GLU61 4.8 26.1 1.0 O B:HOH550 4.8 58.2 1.0 O B:HOH435 4.9 42.6 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