Magnesium in PDB 8xif: The Crystal Structure of the Aep Domain of Vacv D5

The structure of The Crystal Structure of the Aep Domain of Vacv D5, PDB code: 8xif was solved by J.Gan, W.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.31 / 1.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.47, 56.62, 74.16, 90, 90, 90
R / Rfree (%)	17.9 / 19.7

The binding sites of Magnesium atom in the The Crystal Structure of the Aep Domain of Vacv D5 (pdb code 8xif). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Crystal Structure of the Aep Domain of Vacv D5, PDB code: 8xif:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Crystal Structure of the Aep Domain of Vacv D5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the Aep Domain of Vacv D5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:15.1 occ:1.00 OD2 A:ASP170 2.1 22.9 1.0 OD2 A:ASP70 2.1 19.0 1.0 OD2 A:ASP72 2.1 18.9 1.0 O A:HOH532 2.1 26.0 1.0 O A:HOH443 2.1 19.4 1.0 O A:HOH533 2.2 24.4 1.0 CG A:ASP170 3.1 23.1 1.0 CG A:ASP72 3.2 17.6 1.0 CG A:ASP70 3.2 18.3 1.0 CB A:ASP170 3.5 18.4 1.0 OD1 A:ASP72 3.5 15.6 1.0 MG A:MG303 3.6 13.7 1.0 OD1 A:ASP70 3.7 15.2 1.0 O A:HOH501 3.9 29.4 1.0 O A:HOH480 3.9 32.1 1.0 O A:HOH545 4.1 28.2 1.0 O A:HOH556 4.2 31.1 1.0 OD1 A:ASP170 4.3 22.4 1.0 CB A:ASP70 4.4 16.9 1.0 CB A:ASP72 4.5 17.8 1.0 O11 A:PPV301 4.5 18.1 1.0 O31 A:PPV301 4.6 14.8 1.0 CG1 A:VAL173 4.7 21.1 1.0 O22 A:PPV301 4.8 16.6 1.0 O A:HOH568 4.9 35.5 1.0

Magnesium binding site 2 out of 2 in the The Crystal Structure of the Aep Domain of Vacv D5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the Aep Domain of Vacv D5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:13.7 occ:1.00 OD1 A:ASP72 2.0 15.6 1.0 O22 A:PPV301 2.1 16.6 1.0 OD1 A:ASP70 2.1 15.2 1.0 O31 A:PPV301 2.1 14.8 1.0 O A:HOH424 2.1 16.6 1.0 O A:HOH443 2.2 19.4 1.0 CG A:ASP70 3.0 18.3 1.0 CG A:ASP72 3.1 17.6 1.0 P1 A:PPV301 3.2 16.9 1.0 OD2 A:ASP70 3.3 19.0 1.0 P2 A:PPV301 3.3 16.9 1.0 OD2 A:ASP72 3.5 18.9 1.0 OPP A:PPV301 3.6 16.8 1.0 O11 A:PPV301 3.6 18.1 1.0 MG A:MG302 3.6 15.1 1.0 NE2 A:HIS134 3.9 14.7 1.0 O A:HOH545 4.0 28.2 1.0 OG A:SER132 4.1 18.3 1.0 O32 A:PPV301 4.1 18.4 1.0 O A:HOH492 4.1 23.0 1.0 O A:VAL71 4.3 16.2 1.0 CD2 A:HIS134 4.3 14.9 1.0 CB A:ASP72 4.4 17.8 1.0 CB A:ASP70 4.4 16.9 1.0 O12 A:PPV301 4.5 20.2 1.0 O21 A:PPV301 4.5 17.2 1.0 C A:VAL71 4.6 16.2 1.0 O A:HOH556 4.7 31.1 1.0 CA A:ASP72 4.7 16.7 1.0 N A:VAL71 4.7 14.6 1.0 O A:HOH532 4.8 26.0 1.0 C A:ASP70 4.8 15.3 1.0 CA A:ASP70 4.9 15.3 1.0 O A:HOH533 4.9 24.4 1.0 N A:ASP72 4.9 15.8 1.0

J.Gan, W.Zhang. Structural and Functional Insights Into the Helicase Protein E5 of Mpox Virus. Cell Discov 2024.
ISSN: ESSN 2056-5968