Magnesium in PDB 4yoy: Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 in Complex with Poly-Dt and MG2+ Ion

The structure of Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 in Complex with Poly-Dt and MG2+ Ion, PDB code: 4yoy was solved by K.Miyazono, T.Ito, M.Tanokura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.878, 94.891, 106.457, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.4

The binding sites of Magnesium atom in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 in Complex with Poly-Dt and MG2+ Ion (pdb code 4yoy). 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 in Complex with Poly-Dt and MG2+ Ion, PDB code: 4yoy:
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 in Complex with Poly-Dt and MG2+ Ion


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 in Complex with Poly-Dt and MG2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:62.5 occ:1.00 OP1 D:DT6 1.9 58.0 1.0 OE2 C:GLU145 2.1 43.9 1.0 OD2 C:ASP7 2.5 45.1 1.0 O C:HOH454 2.5 38.4 1.0 P D:DT6 3.0 64.1 1.0 CD C:GLU145 3.1 39.6 1.0 OP2 D:DT6 3.2 59.8 1.0 CG C:ASP7 3.3 41.1 1.0 ND2 C:ASN80 3.4 50.6 1.0 OD1 C:ASP7 3.4 40.8 1.0 CG C:GLU145 3.6 35.4 1.0 OE1 C:GLU145 4.0 40.6 1.0 O5' D:DT6 4.0 65.3 1.0 O3' D:DT5 4.1 62.4 1.0 O D:HOH103 4.2 32.5 1.0 CB C:GLU145 4.2 35.5 1.0 O C:THR8 4.3 40.4 1.0 CG C:ASN80 4.6 52.2 1.0 C5' D:DT6 4.6 58.5 1.0 OP2 D:DT7 4.7 46.4 1.0 CB C:ASP7 4.7 38.0 1.0 O C:HOH438 4.8 46.6 1.0 O C:HOH402 4.9 41.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A Trimeric Exonuclease Phoexo I From Pyrococcus Horikoshii OT3 in Complex with Poly-Dt and MG2+ Ion


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 in Complex with Poly-Dt and MG2+ Ion within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg301 b:95.0 occ:1.00 OP1 F:DT6 1.9 71.2 1.0 OE2 E:GLU145 2.1 57.1 1.0 OD2 E:ASP7 2.3 52.1 1.0 O F:HOH103 2.4 46.3 1.0 CD E:GLU145 3.0 54.0 1.0 CG E:ASP7 3.1 52.9 1.0 P F:DT6 3.1 69.0 1.0 OD1 E:ASP7 3.2 55.7 1.0 ND2 E:ASN80 3.3 66.2 1.0 CG E:GLU145 3.5 44.1 1.0 OP2 F:DT6 3.5 59.0 1.0 CB E:GLU145 4.1 39.8 1.0 OE1 E:GLU145 4.1 52.4 1.0 O E:THR8 4.1 58.4 1.0 O3' F:DT5 4.1 64.5 1.0 O5' F:DT6 4.2 76.4 1.0 O F:HOH102 4.2 40.9 1.0 CB E:ASP7 4.5 56.5 1.0 CG E:ASN80 4.5 63.5 1.0 C5' F:DT6 4.7 72.1 1.0 OP2 F:DT7 4.8 64.2 1.0 CA E:GLU145 5.0 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