Magnesium in PDB 7tu5: Structure of the L. Blandensis Dgtpase in the Apo Form

All present enzymatic activity of Structure of the L. Blandensis Dgtpase in the Apo Form:
3.1.5.1;

The binding sites of Magnesium atom in the Structure of the L. Blandensis Dgtpase in the Apo Form (pdb code 7tu5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of the L. Blandensis Dgtpase in the Apo Form, PDB code: 7tu5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of the L. Blandensis Dgtpase in the Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the L. Blandensis Dgtpase in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:19.9 occ:1.00 NE2 A:HIS116 1.9 26.6 1.0 NE2 A:HIS68 2.0 26.6 1.0 O A:HOH701 2.2 20.0 1.0 OD1 A:ASP253 2.2 26.6 1.0 CG A:ASP253 2.7 26.6 1.0 CE1 A:HIS68 2.7 26.6 1.0 CE1 A:HIS116 2.8 26.6 1.0 OD2 A:ASP253 2.8 26.6 1.0 CD2 A:HIS116 2.9 26.6 1.0 CD2 A:HIS68 3.1 26.6 1.0 CB A:ASP253 3.9 26.6 1.0 ND1 A:HIS116 3.9 26.6 1.0 ND1 A:HIS68 3.9 26.6 1.0 CG A:HIS116 4.0 26.6 1.0 CG2 A:VAL72 4.1 26.6 1.0 CG A:HIS68 4.2 26.6 1.0 CA A:ASP253 4.5 26.6 1.0 O A:ASP253 4.6 26.6 1.0 C A:ASP253 4.9 26.6 1.0

Magnesium binding site 2 out of 6 in the Structure of the L. Blandensis Dgtpase in the Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the L. Blandensis Dgtpase in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:19.9 occ:1.00 NE2 B:HIS116 1.9 26.6 1.0 NE2 B:HIS68 2.0 26.6 1.0 O B:HOH701 2.2 20.0 1.0 OD1 B:ASP253 2.2 26.6 1.0 CG B:ASP253 2.7 26.6 1.0 CE1 B:HIS68 2.7 26.6 1.0 CE1 B:HIS116 2.8 26.6 1.0 OD2 B:ASP253 2.8 26.6 1.0 CD2 B:HIS116 2.9 26.6 1.0 CD2 B:HIS68 3.1 26.6 1.0 CB B:ASP253 3.9 26.6 1.0 ND1 B:HIS116 3.9 26.6 1.0 ND1 B:HIS68 3.9 26.6 1.0 CG B:HIS116 4.0 26.6 1.0 CG2 B:VAL72 4.1 26.6 1.0 CG B:HIS68 4.2 26.6 1.0 CA B:ASP253 4.5 26.6 1.0 O B:ASP253 4.6 26.6 1.0 C B:ASP253 4.9 26.6 1.0

Magnesium binding site 3 out of 6 in the Structure of the L. Blandensis Dgtpase in the Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the L. Blandensis Dgtpase in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:19.9 occ:1.00 NE2 C:HIS116 1.9 26.6 1.0 NE2 C:HIS68 2.0 26.6 1.0 O C:HOH701 2.2 20.0 1.0 OD1 C:ASP253 2.2 26.6 1.0 CG C:ASP253 2.7 26.6 1.0 CE1 C:HIS68 2.7 26.6 1.0 CE1 C:HIS116 2.8 26.6 1.0 OD2 C:ASP253 2.8 26.6 1.0 CD2 C:HIS116 2.9 26.6 1.0 CD2 C:HIS68 3.1 26.6 1.0 CB C:ASP253 3.9 26.6 1.0 ND1 C:HIS116 3.9 26.6 1.0 ND1 C:HIS68 3.9 26.6 1.0 CG C:HIS116 4.0 26.6 1.0 CG2 C:VAL72 4.1 26.6 1.0 CG C:HIS68 4.2 26.6 1.0 CA C:ASP253 4.5 26.6 1.0 O C:ASP253 4.6 26.6 1.0 C C:ASP253 4.9 26.6 1.0

Magnesium binding site 4 out of 6 in the Structure of the L. Blandensis Dgtpase in the Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the L. Blandensis Dgtpase in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:19.9 occ:1.00 NE2 D:HIS116 1.9 26.6 1.0 NE2 D:HIS68 2.0 26.6 1.0 O D:HOH701 2.2 20.0 1.0 OD1 D:ASP253 2.2 26.6 1.0 CG D:ASP253 2.7 26.6 1.0 CE1 D:HIS68 2.7 26.6 1.0 CE1 D:HIS116 2.8 26.6 1.0 OD2 D:ASP253 2.8 26.6 1.0 CD2 D:HIS116 2.9 26.6 1.0 CD2 D:HIS68 3.1 26.6 1.0 CB D:ASP253 3.9 26.6 1.0 ND1 D:HIS116 3.9 26.6 1.0 ND1 D:HIS68 3.9 26.6 1.0 CG D:HIS116 4.0 26.6 1.0 CG2 D:VAL72 4.1 26.6 1.0 CG D:HIS68 4.2 26.6 1.0 CA D:ASP253 4.5 26.6 1.0 O D:ASP253 4.6 26.6 1.0 C D:ASP253 4.9 26.6 1.0

Magnesium binding site 5 out of 6 in the Structure of the L. Blandensis Dgtpase in the Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the L. Blandensis Dgtpase in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:19.9 occ:1.00 NE2 E:HIS116 1.9 26.6 1.0 NE2 E:HIS68 2.0 26.6 1.0 O E:HOH701 2.2 20.0 1.0 OD1 E:ASP253 2.2 26.6 1.0 CG E:ASP253 2.7 26.6 1.0 CE1 E:HIS68 2.7 26.6 1.0 CE1 E:HIS116 2.8 26.6 1.0 OD2 E:ASP253 2.8 26.6 1.0 CD2 E:HIS116 2.9 26.6 1.0 CD2 E:HIS68 3.1 26.6 1.0 CB E:ASP253 3.9 26.6 1.0 ND1 E:HIS116 3.9 26.6 1.0 ND1 E:HIS68 3.9 26.6 1.0 CG E:HIS116 4.0 26.6 1.0 CG2 E:VAL72 4.1 26.6 1.0 CG E:HIS68 4.2 26.6 1.0 CA E:ASP253 4.5 26.6 1.0 O E:ASP253 4.6 26.6 1.0 C E:ASP253 4.9 26.6 1.0

Magnesium binding site 6 out of 6 in the Structure of the L. Blandensis Dgtpase in the Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the L. Blandensis Dgtpase in the Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:19.9 occ:1.00 NE2 F:HIS116 1.9 26.6 1.0 NE2 F:HIS68 2.0 26.6 1.0 O F:HOH701 2.2 20.0 1.0 OD1 F:ASP253 2.2 26.6 1.0 CG F:ASP253 2.7 26.6 1.0 CE1 F:HIS68 2.7 26.6 1.0 CE1 F:HIS116 2.8 26.6 1.0 OD2 F:ASP253 2.8 26.6 1.0 CD2 F:HIS116 2.9 26.6 1.0 CD2 F:HIS68 3.1 26.6 1.0 CB F:ASP253 3.9 26.6 1.0 ND1 F:HIS116 3.9 26.6 1.0 ND1 F:HIS68 3.9 26.6 1.0 CG F:HIS116 4.0 26.6 1.0 CG2 F:VAL72 4.1 26.6 1.0 CG F:HIS68 4.2 26.6 1.0 CA F:ASP253 4.5 26.6 1.0 O F:ASP253 4.6 26.6 1.0 C F:ASP253 4.9 26.6 1.0

B.P.Klemm, A.P.Sikkema, A.L.Hsu, J.C.Horng, T.M.T.Hall, M.J.Borgnia, R.M.Schaaper. High-Resolution Structures of the SAMHD1 Dgtpase Homolog From Leeuwenhoekiella Blandensis Reveal A Novel Mechanism of Allosteric Activation By Datp. J.Biol.Chem. V. 298 02073 2022.
ISSN: ESSN 1083-351X
PubMed: 35643313
DOI: 10.1016/J.JBC.2022.102073